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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RAS-LIKE, FAMILY 12 PROTEIN IN COMPLEX WITH GDP
 
Authors :  L. Shen, Y. Tong, W. Tempel, P. Loppnau, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  31 Jan 08  (Deposition) - 12 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ras, Rasl12, Gdp, Gtpase, Structural Genomics Consortium, Sgc, Limited Proteolysis, Gtp-Binding, Nucleotide-Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Shen, Y. Tong, W. Tempel, P. Loppnau, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Ras-Like, Family 12 Protein In Complex With Gdp.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-LIKE PROTEIN 12
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-CODONPLUS(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 18-186
    GeneRASL12, RIS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAS-LIKE PROTEIN RIS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1GDP4Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG7Ligand/IonMAGNESIUM ION
3UNX3Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3UNX1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3UNX-1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3UNX1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3UNX1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:34 , GDP A:201 , HOH A:301 , HOH A:302 , HOH A:303 , HOH A:304BINDING SITE FOR RESIDUE MG A 202
02AC2SOFTWAREASP A:55 , HOH A:352 , HOH A:355 , HOH A:359BINDING SITE FOR RESIDUE MG A 203
03AC3SOFTWARESER B:34 , GDP B:201 , HOH B:301 , HOH B:302 , HOH B:303 , HOH B:304BINDING SITE FOR RESIDUE MG B 202
04AC4SOFTWAREASP B:55 , HOH B:370 , HOH B:371BINDING SITE FOR RESIDUE MG B 203
05AC5SOFTWARESER C:34 , GDP C:201 , HOH C:301 , HOH C:302 , HOH C:303 , HOH C:304BINDING SITE FOR RESIDUE MG C 202
06AC6SOFTWAREASP C:55 , HOH C:352BINDING SITE FOR RESIDUE MG C 203
07AC7SOFTWARESER D:34 , GDP D:201 , HOH D:301 , HOH D:302 , HOH D:303 , HOH D:304BINDING SITE FOR RESIDUE MG D 202
08AC8SOFTWAREARG A:29 , GLY A:30 , ALA A:31 , GLY A:32 , LYS A:33 , SER A:34 , ALA A:35 , SER A:47 , ASN A:134 , LYS A:135 , ASP A:137 , MET A:138 , SER A:164 , ALA A:165 , CYS A:166 , MG A:202 , HOH A:301 , HOH A:303 , HOH A:304 , HOH A:308 , HOH A:317 , HOH A:326 , HOH A:353 , ASN B:89BINDING SITE FOR RESIDUE GDP A 201
09AC9SOFTWAREARG A:142 , THR A:145 , LYS A:146BINDING SITE FOR RESIDUE UNX A 204
10BC1SOFTWAREARG B:28 , GLY B:30 , ALA B:31 , GLY B:32 , LYS B:33 , SER B:34 , ALA B:35 , SER B:47 , ASN B:134 , LYS B:135 , ASP B:137 , MET B:138 , SER B:164 , ALA B:165 , CYS B:166 , MG B:202 , HOH B:301 , HOH B:304 , HOH B:311 , HOH B:312 , HOH B:333 , HOH B:367BINDING SITE FOR RESIDUE GDP B 201
11BC2SOFTWAREARG C:29 , GLY C:30 , ALA C:31 , GLY C:32 , LYS C:33 , SER C:34 , ALA C:35 , SER C:47 , ASN C:134 , LYS C:135 , ASP C:137 , MET C:138 , SER C:164 , ALA C:165 , CYS C:166 , MG C:202 , HOH C:301 , HOH C:304 , HOH C:307 , HOH C:313 , HOH C:326 , HOH C:329 , HOH C:334 , ASN D:89BINDING SITE FOR RESIDUE GDP C 201
12BC3SOFTWAREARG C:44 , PHE C:45 , HOH D:340BINDING SITE FOR RESIDUE UNX C 204
13BC4SOFTWAREARG B:44 , ARG D:28 , ARG D:29 , GLY D:30 , ALA D:31 , GLY D:32 , LYS D:33 , SER D:34 , ALA D:35 , PHE D:45 , SER D:47 , ASN D:134 , LYS D:135 , ASP D:137 , MET D:138 , SER D:164 , ALA D:165 , CYS D:166 , MG D:202 , HOH D:301 , HOH D:303 , HOH D:304 , HOH D:314 , HOH D:319BINDING SITE FOR RESIDUE GDP D 201
14BC5SOFTWAREASP D:55 , PHE D:156BINDING SITE FOR RESIDUE UNX D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C5C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C5C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C5C)

(-) Exons   (5, 20)

Asymmetric Unit (5, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002200622aENSE00001937611chr15:65360450-65360071380RASLC_HUMAN1-35354A:19-35
B:19-35
C:17-35
D:19-35
17
17
19
17
1.3ENST000002200623ENSE00000693613chr15:65357611-6535755557RASLC_HUMAN35-54204A:35-54
B:35-54
C:35-54
D:35-54
20
20
20
20
1.4ENST000002200624ENSE00000693610chr15:65351756-6535168374RASLC_HUMAN54-78254A:54-77
B:54-78
C:54-78
D:54-78
24
25
25
25
1.5ENST000002200625ENSE00000693607chr15:65350955-65350765191RASLC_HUMAN79-142644A:81-142
B:79-142
C:81-142 (gaps)
D:82-142
62
64
62
61
1.6bENST000002200626bENSE00001883781chr15:65347612-653456751938RASLC_HUMAN142-2661254A:142-185
B:142-185
C:142-185
D:142-185
44
44
44
44

(-) 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:164
 aligned with RASLC_HUMAN | Q9NYN1 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:167
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       
          RASLC_HUMAN    19 LEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADLDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
               SCOP domains d3c5ca_ A: automated matches                                                                                                                                            SCOP domains
               CATH domains 3c5cA00 A:19-185 P-loop containing nucleotide triphosphate    hydrolases                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee...---...hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhh..hhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a        ------------------Exon 1.4  PDB: A:54-77   Exon 1.5  PDB: A:81-142 UniProt: 79-142 [INCOMPLETE]            ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.3            ---------------------------------------------------------------------------------------Exon 1.6b  PDB: A:142-185 UniProt: 142-266   Transcript 1 (2)
                 3c5c A  19 LEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTAD---PRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
                                    28        38        48        58        68        |-  |     88        98       108       118       128       138       148       158       168       178       
                                                                                     77  81                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with RASLC_HUMAN | Q9NYN1 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:167
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       
          RASLC_HUMAN    19 LEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADLDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
               SCOP domains d3c5cb_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains 3c5cB00 B:19-185 P-loop containing nucleotide triphosphate hydrolases                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee.........hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a        ------------------Exon 1.4  PDB: B:54-78   Exon 1.5  PDB: B:79-142 UniProt: 79-142                         ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.3            ---------------------------------------------------------------------------------------Exon 1.6b  PDB: B:142-185 UniProt: 142-266   Transcript 1 (2)
                 3c5c B  19 LEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADLDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       

Chain C from PDB  Type:PROTEIN  Length:164
 aligned with RASLC_HUMAN | Q9NYN1 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:169
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176         
          RASLC_HUMAN    17 APLEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADLDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
               SCOP domains d3c5cc_ C: automated matches                                                                                                                                              SCOP domains
               CATH domains 3c5cC00 C:17-185 P-loop containing nucleotide triphosphate hyd  rolases                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee....--...hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh---.eeeeeehhhhhhhh..hhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a          ------------------Exon 1.4  PDB: C:54-78   Exon 1.5  PDB: C:81-142 (gaps) UniProt: 79-142 [INCOMPLETE]     ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.3            ---------------------------------------------------------------------------------------Exon 1.6b  PDB: C:142-185 UniProt: 142-266   Transcript 1 (2)
                 3c5c C  17 GPLEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADL--PRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQ---PALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
                                    26        36        46        56        66        76 |  |   86        96       106       116       | - |     136       146       156       166       176         
                                                                                        78 81                                        124 128                                                         

Chain D from PDB  Type:PROTEIN  Length:164
 aligned with RASLC_HUMAN | Q9NYN1 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:167
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       
          RASLC_HUMAN    19 LEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADLDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
               SCOP domains d3c5cd_ D: automated matches                                                                                                                                            SCOP domains
               CATH domains 3c5cD00 D:19-185 P-loop containing nucleotide triphosphate h   ydrolases                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee....---..hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhh..hhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a        ------------------Exon 1.4  PDB: D:54-78   Exon 1.5  PDB: D:82-142 UniProt: 79-142 [INCOMPLETE]            ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.3            ---------------------------------------------------------------------------------------Exon 1.6b  PDB: D:142-185 UniProt: 142-266   Transcript 1 (2)
                 3c5c D  19 LEVNLAILGRRGAGKSALTVKFLTKRFISEYDPNLEDTYSSEETVDHQPVHLRVMDTADL---RNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARR 185
                                    28        38        48        58        68        78   |    88        98       108       118       128       138       148       158       168       178       
                                                                                      78  82                                                                                                       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C5C)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RASLC_HUMAN | Q9NYN1)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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.
biological process
    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.
    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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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