Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SEC7 DOMAIN FROM HUMAN CYTOHESIN1
 
Authors :  J. C. Zeeh, A. W. Thompson, J. Cherfils, V. Biou
Date :  19 Oct 11  (Deposition) - 31 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  All Alpha, Guanine-Nucleotide Releasing Factor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Zeeh, A. W. Thompson, J. Cherfils, V. Biou
Crystal Structure Of The Sec7 Domain From Human Cytohesin1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOHESIN1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: PLYSS
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: SEC7 DOMAIN, RESIDUES 63-248
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PH,SEC7 AND COILED-COIL DOMAIN-CONTAINING PROTEIN 1, SEC7 HOMOLOG B2-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:166 , PHE A:195 , HOH A:2210 , ASP B:166 , GOL B:1253 , HOH B:2166 , HOH B:2168BINDING SITE FOR RESIDUE GOL A1253
2AC2SOFTWAREASP A:166 , GOL A:1253 , ASP B:166 , TYR B:191 , PHE B:195 , HOH B:2167BINDING SITE FOR RESIDUE GOL B1253

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A4P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A4P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A4P)

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003611011bENSE00001287973chr17:76778376-7677828493CYH1_HUMAN1-880--
1.7aENST000003611017aENSE00001674390chr17:76705814-7670573283CYH1_HUMAN8-35280--
1.8ENST000003611018ENSE00000745796chr17:76704343-7670427965CYH1_HUMAN36-57220--
1.9bENST000003611019bENSE00000949392chr17:76698686-7669862067CYH1_HUMAN57-79232A:67-83
B:67-83		17
17
1.10ENST0000036110110ENSE00001731743chr17:76698322-76698204119CYH1_HUMAN80-119402A:84-123
B:84-123		40
40
1.11bENST0000036110111bENSE00000949394chr17:76697833-7669775381CYH1_HUMAN119-146282A:123-150
B:123-150		28
28
1.12cENST0000036110112cENSE00002171956chr17:76696525-76696413113CYH1_HUMAN146-184392A:150-188
B:150-188		39
39
1.13ENST0000036110113ENSE00000745793chr17:76695050-76694902149CYH1_HUMAN184-233502A:188-237
B:188-237		50
50
1.14bENST0000036110114bENSE00001662887chr17:76694462-76694350113CYH1_HUMAN234-271382A:238-252
B:238-252		15
15
1.16bENST0000036110116bENSE00001753312chr17:76688577-7668849979CYH1_HUMAN271-297270--
1.17bENST0000036110117bENSE00001287897chr17:76677124-7667705372CYH1_HUMAN298-321240--
1.18ENST0000036110118ENSE00001287887chr17:76676426-76676272155CYH1_HUMAN322-373520--
1.20eENST0000036110120eENSE00001287965chr17:76672251-766701302122CYH1_HUMAN373-398260--

(-) 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:186
 aligned with CYH1_HUMAN | Q15438 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:186
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           CYH1_HUMAN    63 NKQVAMGRKKFNMDPKKGIQFLIENDLLKNTCEDIAQFLYKGEGLNKTAIGDYLGERDEFNIQVLHAFVELHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYCQCNNGVFQSTDTCYVLSFAIIMLNTSLHNPNVKDKPTVERFIAMNRGINDGGDLPEELLRNLYESIKNEPFKIPE 248
               SCOP domains d4a4pa_ A: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.9b        Exon 1.10  PDB: A:84-123 UniProt: 80-119--------------------------Exon 1.12c  PDB: A:150-188             -------------------------------------------------Exon 1.14b      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.11b  PDB: A:123-150  -------------------------------------Exon 1.13  PDB: A:188-237 UniProt: 184-233        --------------- Transcript 1 (2)
                 4a4p A  67 NKQVAMGRKKFNMDPKKGIQFLIENDLLKNTCEDIAQFLYKGEGLNKTAIGDYLGERDEFNIQVLHAFVELHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYCQCNNGVFQSTDTCYVLSFAIIMLNTSLHNPNVKDKPTVERFIAMNRGINDGGDLPEELLRNLYESIKNEPFKIPE 252
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246      


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with CYH1_HUMAN | Q15438 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:186
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           CYH1_HUMAN    63 NKQVAMGRKKFNMDPKKGIQFLIENDLLKNTCEDIAQFLYKGEGLNKTAIGDYLGERDEFNIQVLHAFVELHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYCQCNNGVFQSTDTCYVLSFAIIMLNTSLHNPNVKDKPTVERFIAMNRGINDGGDLPEELLRNLYESIKNEPFKIPE 248
               SCOP domains d4a4pb_ B: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.9b        Exon 1.10  PDB: B:84-123 UniProt: 80-119--------------------------Exon 1.12c  PDB: B:150-188             -------------------------------------------------Exon 1.14b      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.11b  PDB: B:123-150  -------------------------------------Exon 1.13  PDB: B:188-237 UniProt: 184-233        --------------- Transcript 1 (2)
                 4a4p B  67 NKQVAMGRKKFNMDPKKGIQFLIENDLLKNTCEDIAQFLYKGEGLNKTAIGDYLGERDEFNIQVLHAFVELHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYCQCNNGVFQSTDTCYVLSFAIIMLNTSLHNPNVKDKPTVERFIAMNRGINDGGDLPEELLRNLYESIKNEPFKIPE 252
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A4P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A4P)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYH1_HUMAN | Q15438)
molecular function
    GO:0005086    ARF guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0032012    regulation of ARF protein signal transduction    Any process that modulates the frequency, rate or extent of ARF protein signal transduction.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4a4p)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4a4p
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CYH1_HUMAN | Q15438
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CYH1_HUMAN | Q15438
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CYH1_HUMAN | Q15438: 1bc9

(-) Related Entries Specified in the PDB File

1bc9 CYTOHESIN-1/B2-1 SEC7 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE