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(-) Description

Title :  RAB DOMAIN OF HUMAN RASEF IN COMPLEX WITH GDP
 
Authors :  H. Zhu, J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  16 Mar 07  (Deposition) - 27 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  G-Protein, Rab, Gdp, Structural Genomics, Sgc, Structural Genomics Consortium, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhu, J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Rab Domain Of Human Rasef In Complex With Gdp
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS AND EF-HAND DOMAIN CONTAINING
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-LIC-THROMBIN
    Expression System Strain: BL21 (DE3) CODON(+) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 533-712
    Gene: RASEF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNX3Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 2P5S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P5S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P5S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P5S)

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003764471bENSE00001391250chr9:85678043-85677352692RASEF_HUMAN1-1441440--
1.3ENST000003764473ENSE00001307793chr9:85640836-85640690147RASEF_HUMAN144-193500--
1.4ENST000003764474ENSE00001090428chr9:85637341-8563725191RASEF_HUMAN193-223310--
1.5ENST000003764475ENSE00001090425chr9:85630815-8563072096RASEF_HUMAN224-255320--
1.6ENST000003764476ENSE00001090422chr9:85627426-8562734978RASEF_HUMAN256-281260--
1.7ENST000003764477ENSE00001090432chr9:85624671-85624556116RASEF_HUMAN282-320390--
1.8ENST000003764478ENSE00001293362chr9:85622420-8562235269RASEF_HUMAN320-343240--
1.9ENST000003764479ENSE00001308048chr9:85620415-8562033185RASEF_HUMAN343-371290--
1.10ENST0000037644710ENSE00001328763chr9:85619501-8561941389RASEF_HUMAN372-401300--
1.11ENST0000037644711ENSE00001294194chr9:85616045-85615811235RASEF_HUMAN401-479790--
1.12ENST0000037644712ENSE00001313770chr9:85615485-85615348138RASEF_HUMAN480-525460--
1.13ENST0000037644713ENSE00001298797chr9:85615231-85615084148RASEF_HUMAN526-575502A:541-567
B:541-575 (gaps)		27
35
1.14ENST0000037644714ENSE00001383554chr9:85613361-8561328082RASEF_HUMAN575-602282A:578-602
B:575-602		25
28
1.15ENST0000037644715ENSE00001321082chr9:85612041-85611927115RASEF_HUMAN602-640392A:602-640
B:602-640		39
39
1.16ENST0000037644716ENSE00001299807chr9:85607940-85607821120RASEF_HUMAN641-680402A:641-680 (gaps)
B:641-680 (gaps)		40
40
1.17ENST0000037644717ENSE00001317027chr9:85605382-8560530677RASEF_HUMAN681-706262A:681-706
B:681-706		26
26
1.18ENST0000037644718ENSE00001295835chr9:85597697-855945003198RASEF_HUMAN706-740352A:706-710
B:706-711		5
6

(-) Sequences/Alignments

Asymmetric/Biological 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:157
 aligned with RASEF_HUMAN | Q8IZ41 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:170
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710
          RASEF_HUMAN   541 AYKIVLAGDAAVGKSSFLMRLCKNEFRENISATLGVDFQMKTLIVDGERTVLQLWDTAGQERFRSIAKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAAHETVPIMLVGNKADIRDTAATEGQKCVPGHFGEKLAMTYGALFCETSAKDGSNIVEAVLHLAREVKK 710
               SCOP domains d2p5sa_ A: automated matche          s                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh...----------.eeeeeee..eeeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh---..eeeeeehhhhhhhhhhh.....hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13  PDB: A:541-567          --------------------------Exon 1.15  PDB: A:602-640              Exon 1.16  PDB: A:641-680 (gaps)        Exon 1.17  PDB: A:681-706 ---- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.14  PDB: A:578-602   -------------------------------------------------------------------------------------------------------1.18  Transcript 1 (2)
                 2p5s A 541 AYKIVLAGDAAVGKSSFLMRLCKNEFR----------FQMKTLIVDGERTVLQLWDTAGQERFRSIAKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAA---VPIMLVGNKADIRDTAATEGQKCVPGHFGEKLAMTYGALFCETSAKDGSNIVEAVLHLAREVKK 710
                                   550       560      |  -       580       590       600       610       620       630       640  |   |650       660       670       680       690       700       710
                                                    567        578                                                              643 647                                                               


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with RASEF_HUMAN | Q8IZ41 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:171
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710 
          RASEF_HUMAN   541 AYKIVLAGDAAVGKSSFLMRLCKNEFRENISATLGVDFQMKTLIVDGERTVLQLWDTAGQERFRSIAKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAAHETVPIMLVGNKADIRDTAATEGQKCVPGHFGEKLAMTYGALFCETSAKDGSNIVEAVLHLAREVKKR 711
               SCOP domains d2p5sb_ B: automated matche       s                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Ras-2p5sB01 B:543-710                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) --Ras-2p5sB02 B:543-710                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh...-------...eeeeeeee..eeeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh---..eeeeeehhhhhhhhhhh.....hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13  PDB: B:541-575 (gaps)   --------------------------Exon 1.15  PDB: B:602-640              Exon 1.16  PDB: B:641-680 (gaps)        Exon 1.17  PDB: B:681-706 ----- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.14  PDB: B:575-602   -------------------------------------------------------------------------------------------------------1.18   Transcript 1 (2)
                 2p5s B 541 AYKIVLAGDAAVGKSSFLMRLCKNEFR-------GVDFQMKTLIVDGERTVLQLWDTAGQERFRSIAKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAA---VPIMLVGNKADIRDTAATEGQKCVPGHFGEKLAMTYGALFCETSAKDGSNIVEAVLHLAREVKKR 711
                                   550       560      |  -    |  580       590       600       610       620       630       640  |   |650       660       670       680       690       700       710 
                                                    567     575                                                                 643 647
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P5S)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: Ras (176)
(-)
Homo sapiens (Human) (141)
1aRas-2p5sB01B:543-710
1bRas-2p5sB02B:543-710

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RASEF_HUMAN | Q8IZ41)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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        RASEF_HUMAN | Q8IZ41: 2pmy

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