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(-) Description

Title :  CRYSTAL STRUCTURE OF ACAP1 C-PORTION MUTANT S554D FUSED WITH INTEGRIN BETA1 PEPTIDE
 
Authors :  F. Sun, X. Pang, K. Zhang, J. Ma, Q. Zhou
Date :  03 Aug 11  (Deposition) - 18 Jul 12  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Arfgap Domain, Ank Repeat, Zinc-Binding Module, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Bai, X. Pang, J. Lou, Q. Zhou, K. Zhang, J. Ma, J. Li, F. Sun, V. W. Hsu
Mechanistic Insights Into Regulated Cargo Binding By Acap1 Protein
J. Biol. Chem. V. 287 28675 2012
PubMed-ID: 22645133  |  Reference-DOI: 10.1074/JBC.M112.378810

(-) Compounds

Molecule 1 - ARF-GAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN- CONTAINING PROTEIN 1,PEPTIDE FROM INTEGRIN BETA-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneACAP1, CENTB1, KIAA0050, ITGB1, FNRB, MDF2, MSK12
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsFUSION PROTEIN OF ACAP1 C-PORTION MUTANT S554D (UNP RESIDUES 378-740 FROM Q15027), LINKER (GSSNSGSNSG), PEPTIDE FROM INTEGRIN BETA-1 (UNP RESIDUES 758-769 FROM P05556)
    SynonymCENTAURIN-BETA-1,CNT-B1,FIBRONECTIN RECEPTOR SUBUNIT BETA, GLYCOPROTEIN IIA,GPIIA,VLA-4 SUBUNIT BETA

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:420 , CYS A:423 , CYS A:440 , CYS A:443BINDING SITE FOR RESIDUE ZN A 999
2AC2SOFTWAREHOH A:116 , HIS A:570 , PRO A:571 , GLY A:572 , ALA A:573 , TRP A:600BINDING SITE FOR RESIDUE SO4 A 201
3AC3SOFTWARECYS B:420 , CYS B:423 , CYS B:440 , CYS B:443BINDING SITE FOR RESIDUE ZN B 999
4AC4SOFTWAREHOH B:83 , HIS B:570 , PRO B:571 , GLY B:572 , ALA B:573 , TRP B:600BINDING SITE FOR RESIDUE SO4 B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T9K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:581 -Pro A:582
2Gly A:705 -Gln A:706
3Thr A:711 -Tyr A:712
4His B:581 -Pro B:582

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T9K)

(-) PROSITE Motifs  (3, 8)

Asymmetric Unit (3, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFGAPPS50115 ARF GTPase-activating proteins domain profile.ACAP1_HUMAN405-527
 
  2A:405-527
B:405-525
2ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.ACAP1_HUMAN592-692
 
  2A:592-692
B:592-692
3ANK_REPEATPS50088 Ankyrin repeat profile.ACAP1_HUMAN606-638
 
639-671
 
  4A:606-638
B:606-638
A:639-671
B:639-671
Biological Unit 1 (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFGAPPS50115 ARF GTPase-activating proteins domain profile.ACAP1_HUMAN405-527
 
  1A:405-527
-
2ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.ACAP1_HUMAN592-692
 
  1A:592-692
-
3ANK_REPEATPS50088 Ankyrin repeat profile.ACAP1_HUMAN606-638
 
639-671
 
  2A:606-638
-
A:639-671
-
Biological Unit 2 (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFGAPPS50115 ARF GTPase-activating proteins domain profile.ACAP1_HUMAN405-527
 
  1-
B:405-525
2ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.ACAP1_HUMAN592-692
 
  1-
B:592-692
3ANK_REPEATPS50088 Ankyrin repeat profile.ACAP1_HUMAN606-638
 
639-671
 
  2-
B:606-638
-
B:639-671

(-) Exons   (0, 0)

(no "Exon" information available for 3T9K)

(-) 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:281
 aligned with ACAP1_HUMAN | Q15027 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:321
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724 
          ACAP1_HUMAN   405 GHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRGRRGGRGRPRGQPPVPPKPSIRPRPGSLRSKPEPPSEDLGSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAEAAQGQAGDETYLDIFRDFSLMASD 725
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh................eee....eeehhhhhhhhhh.......eee......hhhhhhhhhhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhh.............---------------------------------------..hhhhhhhhhhh...hhhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh-... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ARFGAP  PDB: A:405-527 UniProt: 405-527                                                                                    ----------------------------------------------------------------ANK_REP_REGION  PDB: A:592-692 UniProt: 592-692                                                      --------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ANK_REPEAT  PDB: A:606-638       ANK_REPEAT  PDB: A:639-671       ------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t9k A 405 GHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRG---------------------------------------SLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAEAAQGQAGDETYLDIFRDFSL-ASD 725
                                   414       424       434       444       454       464       474       484       494       504       514       524   |     -         -         -         -   |   574       584       594       604       614       624       634       644       654       664       674       684       694       704       714      |724 
                                                                                                                                                     528                                     568                                                                                                                                                      721 |  
                                                                                                                                                                                                                                                                                                                                                        723  

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with ACAP1_HUMAN | Q15027 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:317
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       
          ACAP1_HUMAN   405 GHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRGRRGGRGRPRGQPPVPPKPSIRPRPGSLRSKPEPPSEDLGSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAEAAQGQAGDETYLDIFRDFSL 721
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh................eee....eeehhhhhhhhhhh......eee......hhhhhhhhhh.hhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhh..........-----------------------------------------...hhhhhhhhhhh...hhhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh---...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ARFGAP  PDB: B:405-525 UniProt: 405-527                                                                                    ----------------------------------------------------------------ANK_REP_REGION  PDB: B:592-692 UniProt: 592-692                                                      ----------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ANK_REPEAT  PDB: B:606-638       ANK_REPEAT  PDB: B:639-671       -------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t9k B 405 GHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPE-----------------------------------------GSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAEAAQ---GDETYLDIFRDFSL 721
                                   414       424       434       444       454       464       474       484       494       504       514       524|        -         -         -         -  |    574       584       594       604       614       624       634       644       654       664       674       684       694       704   |   714       
                                                                                                                                                  525                                       567                                                                                                                                      704 708             

   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  (0, 0)

(no "SCOP Domain" information available for 3T9K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T9K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T9K)

(-) Gene Ontology  (139, 144)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACAP1_HUMAN | Q15027)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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.
cellular component
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACAP1_HUMAN | Q150273jue 4ckg 4ckh 4f1p 4nsw
        ITB1_HUMAN | P055561k11 1lha 3g9w 3vi3 3vi4 4dx9 4wjk 4wk0 4wk2 4wk4

(-) Related Entries Specified in the PDB File

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