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(-) Description

Title :  CRYSTAL STRUCTURE OF OCRL1 540-678 IN COMPLEX WITH RAB8A:GPPNHP
 
Authors :  X. Hou, N. Hagemann, S. Schoebel, W. Blankenfeldt, R. S. Goody, K. S. Erd A. Itzen
Date :  14 Jan 11  (Deposition) - 23 Mar 11  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Protein Transport, Vesicular Trafficking, Gtpase, Lowe Syndrome, Immunoglobulin Fold, Rab8A, Ocrl1, Endocytosis, Clathrin, Appl1, Phosphoinositide, Ash, Rhogap, Protein Transport-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Hou, N. Hagemann, S. Schoebel, W. Blankenfeldt, R. S. Goody, K. S. Erdmann, A. Itzen
A Structural Basis For Lowe Syndrome Caused By Mutations In The Rab-Binding Domain Of Ocrl1.
Embo J. V. 30 1659 2011
PubMed-ID: 21378754  |  Reference-DOI: 10.1038/EMBOJ.2011.60

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-8A
    ChainsA, C, E, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19MOD
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 6-176
    GeneMEL, RAB8, RAB8A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainSYNTHETIC DNA
    SynonymONCOGENE C-MEL
 
Molecule 2 - INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1
    ChainsB, D, F, H
    EC Number3.1.3.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPINM
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 540-678
    GeneINPP5F, OCRL, OCRL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainSYNTHETIC DNA
    SynonymLOWE OCULOCEREBRORENAL SYNDROME PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB      
Biological Unit 2 (1x)  CD    
Biological Unit 3 (1x)    EF  
Biological Unit 4 (1x)      GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1GNP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:22 , THR A:40 , GNP A:200 , HOH A:219 , HOH A:566BINDING SITE FOR RESIDUE MG A 201
02AC2SOFTWARESER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , THR A:22 , CYS A:23 , PHE A:33 , SER A:39 , THR A:40 , GLY A:66 , ASN A:121 , LYS A:122 , ASP A:124 , VAL A:125 , SER A:151 , ALA A:152 , LYS A:153 , HOH A:180 , MG A:201 , HOH A:219 , HOH A:231 , HOH A:566BINDING SITE FOR RESIDUE GNP A 200
03AC3SOFTWARETHR C:22 , THR C:40 , GNP C:200 , HOH C:211 , HOH C:252BINDING SITE FOR RESIDUE MG C 201
04AC4SOFTWARESER C:17 , GLY C:18 , VAL C:19 , GLY C:20 , LYS C:21 , THR C:22 , CYS C:23 , PHE C:33 , SER C:39 , THR C:40 , GLY C:66 , ASN C:121 , LYS C:122 , ASP C:124 , VAL C:125 , SER C:151 , ALA C:152 , LYS C:153 , HOH C:195 , MG C:201 , HOH C:202 , HOH C:211 , HOH C:252BINDING SITE FOR RESIDUE GNP C 200
05AC5SOFTWARETHR E:22 , THR E:40 , HOH E:187 , GNP E:200 , HOH E:309BINDING SITE FOR RESIDUE MG E 201
06AC6SOFTWARESER E:17 , GLY E:18 , VAL E:19 , GLY E:20 , LYS E:21 , THR E:22 , CYS E:23 , PHE E:33 , SER E:39 , THR E:40 , GLY E:66 , ASN E:121 , LYS E:122 , ASP E:124 , VAL E:125 , SER E:151 , ALA E:152 , LYS E:153 , HOH E:182 , HOH E:187 , MG E:201 , HOH E:309 , HOH E:593BINDING SITE FOR RESIDUE GNP E 200
07AC7SOFTWARETHR G:22 , THR G:40 , HOH G:192 , GNP G:200 , HOH G:302BINDING SITE FOR RESIDUE MG G 201
08AC8SOFTWARESER G:17 , GLY G:18 , VAL G:19 , GLY G:20 , LYS G:21 , THR G:22 , CYS G:23 , PHE G:33 , SER G:39 , THR G:40 , GLY G:66 , ASN G:121 , LYS G:122 , ASP G:124 , VAL G:125 , SER G:151 , ALA G:152 , LYS G:153 , HOH G:192 , HOH G:193 , MG G:201 , HOH G:302 , HOH G:369BINDING SITE FOR RESIDUE GNP G 200
09AC9SOFTWARETHR A:40 , ARG B:570 , LYS B:665 , ASP B:666 , TYR B:667BINDING SITE FOR RESIDUE SO4 B 1
10BC1SOFTWAREILE C:41 , HOH D:7 , HOH D:18 , ARG D:570 , ASP D:666 , TYR D:667BINDING SITE FOR RESIDUE SO4 D 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QBT)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu B:618 -Pro B:619
2Glu D:618 -Pro D:619
3Glu F:618 -Pro F:619
4Glu H:618 -Pro H:619

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064790N591KOCRL_HUMANDisease (OCRL)137853844B/D/F/HN591K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064790N591KOCRL_HUMANDisease (OCRL)137853844BN591K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064790N591KOCRL_HUMANDisease (OCRL)137853844DN591K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064790N591KOCRL_HUMANDisease (OCRL)137853844FN591K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064790N591KOCRL_HUMANDisease (OCRL)137853844HN591K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QBT)

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003711132aENSE00001518494X:128674252-128674455204OCRL_HUMAN1-13130--
1.3aENST000003711133aENSE00001454376X:128674721-12867480080OCRL_HUMAN14-40270--
1.4ENST000003711134ENSE00001613852X:128678935-12867901480OCRL_HUMAN40-67280--
1.5aENST000003711135aENSE00001633886X:128682540-12868257839OCRL_HUMAN67-80140--
1.7ENST000003711137ENSE00000828196X:128691302-128691412111OCRL_HUMAN80-117380--
1.8ENST000003711138ENSE00000828195X:128691838-12869192790OCRL_HUMAN117-147310--
1.9ENST000003711139ENSE00000828194X:128692610-128692730121OCRL_HUMAN147-187410--
1.10bENST0000037111310bENSE00000828193X:128692817-128692978162OCRL_HUMAN187-241550--
1.11ENST0000037111311ENSE00000828192X:128694527-128694628102OCRL_HUMAN241-275350--
1.12ENST0000037111312ENSE00000828191X:128695156-128695270115OCRL_HUMAN275-313390--
1.13ENST0000037111313ENSE00000828190X:128696361-128696477117OCRL_HUMAN314-352390--
1.14ENST0000037111314ENSE00000828189X:128696576-128696763188OCRL_HUMAN353-415630--
1.15ENST0000037111315ENSE00000828188X:128699749-128699860112OCRL_HUMAN415-452380--
1.16aENST0000037111316aENSE00000828187X:128701231-128701340110OCRL_HUMAN453-489370--
1.17ENST0000037111317ENSE00001795169X:128703241-128703376136OCRL_HUMAN489-534460--
1.18ENST0000037111318ENSE00000828185X:128709117-128709227111OCRL_HUMAN535-571374B:549-571
D:549-571
F:540-571
H:540-571
23
23
32
32
1.19ENST0000037111319ENSE00000828184X:128709874-128710039166OCRL_HUMAN572-627564B:572-627
D:572-627
F:572-627
H:572-627
56
56
56
56
1.20bENST0000037111320bENSE00000828183X:128710294-128710529236OCRL_HUMAN627-705794B:627-678
D:627-678
F:627-678
H:627-678
52
52
52
52
1.21ENST0000037111321ENSE00001454375X:128718321-12871834424OCRL_HUMAN706-71380--
1.23ENST0000037111323ENSE00000828182X:128720979-128721095117OCRL_HUMAN714-752390--
1.24ENST0000037111324ENSE00000828181X:128722156-12872224085OCRL_HUMAN753-781290--
1.25ENST0000037111325ENSE00000828180X:128722863-128722990128OCRL_HUMAN781-823430--
1.26bENST0000037111326bENSE00000828179X:128723822-128723933112OCRL_HUMAN824-861380--
1.27cENST0000037111327cENSE00001170507X:128724123-1287265382416OCRL_HUMAN861-901410--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:170
 aligned with RAB8A_HUMAN | P61006 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:170
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176
          RAB8A_HUMAN     7 YLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK 176
               SCOP domains d3qbta_ A: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeee...hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbt A   7 YLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK 176
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with OCRL_HUMAN | Q01968 from UniProtKB/Swiss-Prot  Length:901

    Alignment length:130
                                   558       568       578       588       598       608       618       628       638       648       658       668       678
           OCRL_HUMAN   549 DSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...eee...eeeeeee.....eeeeeeeee.....eeeeee............eeee..eeee....eeeeeeee..hhhhhhhhhhh.....eeeeeee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------K--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18 [INCOMPLETE] Exon 1.19  PDB: B:572-627 UniProt: 572-627              --------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------Exon 1.20b  PDB: B:627-678 UniProt: 627-705          Transcript 1 (2)
                 3qbt B 549 DSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
                                   558       568       578       588       598       608       618       628       638       648       658       668       678

Chain C from PDB  Type:PROTEIN  Length:171
 aligned with RAB8A_HUMAN | P61006 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 
          RAB8A_HUMAN     6 DYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK 176
               SCOP domains d3qbtc_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeee...hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbt C   6 DYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK 176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with OCRL_HUMAN | Q01968 from UniProtKB/Swiss-Prot  Length:901

    Alignment length:130
                                   558       568       578       588       598       608       618       628       638       648       658       668       678
           OCRL_HUMAN   549 DSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...eee...eeeeeeee....eeeeeeeee.....eeeeee............eeee..eeee....eeeeeeee..hhhhhhhhhhh.....eeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------K--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18 [INCOMPLETE] Exon 1.19  PDB: D:572-627 UniProt: 572-627              --------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------Exon 1.20b  PDB: D:627-678 UniProt: 627-705          Transcript 1 (2)
                 3qbt D 549 DSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
                                   558       568       578       588       598       608       618       628       638       648       658       668       678

Chain E from PDB  Type:PROTEIN  Length:169
 aligned with RAB8A_HUMAN | P61006 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:169
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166         
          RAB8A_HUMAN     7 YLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDK 175
               SCOP domains d3qbte_ E: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeeee..hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbt E   7 YLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDK 175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166         

Chain F from PDB  Type:PROTEIN  Length:139
 aligned with OCRL_HUMAN | Q01968 from UniProtKB/Swiss-Prot  Length:901

    Alignment length:139
                                   549       559       569       579       589       599       609       619       629       639       649       659       669         
           OCRL_HUMAN   540 ERRYRKVFEDSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee....eeeeeeeee.....eeeeee............eeee..eeee....eeeeeeee.....hhhhhh....eeeeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------K--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18  PDB: F:540-571       Exon 1.19  PDB: F:572-627 UniProt: 572-627              --------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.20b  PDB: F:627-678 UniProt: 627-705          Transcript 1 (2)
                 3qbt F 540 ERRYRKVFEDSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
                                   549       559       569       579       589       599       609       619       629       639       649       659       669         

Chain G from PDB  Type:PROTEIN  Length:169
 aligned with RAB8A_HUMAN | P61006 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:169
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166         
          RAB8A_HUMAN     7 YLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDK 175
               SCOP domains d3qbtg_ G: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Ras-3qbtG01 G:10-171                                                                                                                                              ---- Pfam domains (1)
           Pfam domains (2) ---Ras-3qbtG02 G:10-171                                                                                                                                              ---- Pfam domains (2)
           Pfam domains (3) ---Ras-3qbtG03 G:10-171                                                                                                                                              ---- Pfam domains (3)
           Pfam domains (4) ---Ras-3qbtG04 G:10-171                                                                                                                                              ---- Pfam domains (4)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qbt G   7 YLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDK 175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166         

Chain H from PDB  Type:PROTEIN  Length:139
 aligned with OCRL_HUMAN | Q01968 from UniProtKB/Swiss-Prot  Length:901

    Alignment length:139
                                   549       559       569       579       589       599       609       619       629       639       649       659       669         
           OCRL_HUMAN   540 ERRYRKVFEDSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeee.....eeeeeeeee.....eeeee.............eeee..eeee....eeeeeeee..hhhhhhhhh....eeeeeeeeee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------K--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18  PDB: H:540-571       Exon 1.19  PDB: H:572-627 UniProt: 572-627              --------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.20b  PDB: H:627-678 UniProt: 627-705          Transcript 1 (2)
                 3qbt H 540 ERRYRKVFEDSVRIMDRMENDFLPSLELSRREFVFENVKFRQLQKEKFQISNNGQVPCHFSFIPKLNDSQYCKPWLRAEPFEGYLEPNETVDISLDVYVSKDSVTILNSGEDKIEDILVLHLDRGKDYFLTISGNYLPS 678
                                   549       559       569       579       589       599       609       619       629       639       649       659       669         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QBT)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Family: Ras (176)
1aRas-3qbtG01G:10-171
1bRas-3qbtG02G:10-171
1cRas-3qbtG03G:10-171
1dRas-3qbtG04G:10-171

(-) Gene Ontology  (75, 89)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (RAB8A_HUMAN | P61006)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0031489    myosin V binding    Interacting selectively and non-covalently with a class V myosin; myosin V is a dimeric molecule involved in intracellular transport.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0048210    Golgi vesicle fusion to target membrane    The joining of the lipid bilayer membrane around a Golgi transport vesicle to the target lipid bilayer membrane.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0061024    membrane organization    A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0048169    regulation of long-term neuronal synaptic plasticity    A process that modulates long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0051223    regulation of protein transport    Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0006904    vesicle docking involved in exocytosis    The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005814    centriole    A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0036064    ciliary basal body    A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.
    GO:0097546    ciliary base    Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0030140    trans-Golgi network transport vesicle    A vesicle that mediates transport between the trans-Golgi network and other parts of the cell.

Chain B,D,F,H   (OCRL_HUMAN | Q01968)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0052745    inositol phosphate phosphatase activity    Catalysis of the reaction: inositol phosphate(n) + H2O = inositol phosphate(n-1) + phosphate. This reaction is the removal of a phosphate group from an inositol phosphate.
    GO:0052659    inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
    GO:0052658    inositol-1,4,5-trisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + H2O = 1D-myo-inositol 1,4-bisphosphate + phosphate.
    GO:0004439    phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005795    Golgi stack    The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.
    GO:0005798    Golgi-associated vesicle    Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    GO:0001750    photoreceptor outer segment    The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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        OCRL_HUMAN | Q019682kie 2qv2 3qis 4cmn
        RAB8A_HUMAN | P610063tnf 4lhv 4lhw 4lhx 4lhy 4lhz 4li0 5szi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QBT)