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(-) Description

Title :  CRYSTAL STRUCTURE OF ARFGAP AND ANK REPEAT DOMAIN OF ACAP1
 
Authors :  X. Pang, K. Zhang, J. Ma, Q. Zhou, F. Sun
Date :  15 Sep 09  (Deposition) - 22 Sep 10  (Release) - 16 Jan 13  (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, Gtpase Activation, Metal-Binding, Nitration, Phosphoprotein, Protein Transport, Transport, Zinc-Finger, Protein Transport-Endocytosis Complex (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 - ARFGAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN- CONTAINING PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentARFGAP AND ANK REPEAT DOMAIN, RESIDUES 378-740
    GeneACAP1, CENTB1, KIAA0050
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCENTAURIN-BETA-1, CNT-B1

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:420 , CYS A:423 , CYS A:440 , CYS A:443BINDING SITE FOR RESIDUE ZN A 999
2AC2SOFTWAREHIS A:570 , PRO A:571 , GLY A:572 , ALA A:573 , TRP A:600BINDING SITE FOR RESIDUE SO4 A 1133
3AC3SOFTWARETRP A:430 , ILE A:441 , SER A:444 , GLY A:445 , ARG A:448 , GLN B:412 , SER B:413BINDING SITE FOR RESIDUE SO4 A 1135
4AC4SOFTWARECYS B:420 , CYS B:423 , CYS B:440 , CYS B:443BINDING SITE FOR RESIDUE ZN B 999
5AC5SOFTWAREHIS B:570 , PRO B:571 , GLY B:572 , ALA B:573 , TRP B:600 , HOH B:1042BINDING SITE FOR RESIDUE SO4 B 1134

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:581 -Pro A:582
2His B:581 -Pro B:582

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 8)

Asymmetric Unit (3, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFGAPPS50115 ARF GTPase-activating proteins domain profile.ACAP1_HUMAN405-527
 
  2A:405-524
B:405-524
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:405-524
-
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:405-524
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 3JUE)

(-) 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:250
 aligned with ACAP1_HUMAN | Q15027 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:294
                                   413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693    
          ACAP1_HUMAN   404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRGRRGGRGRPRGQPPVPPKPSIRPRPGSLRSKPEPPSEDLGSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKM 697
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh................eee....eeehhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh.........--------------------------------------------.hhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -ARFGAP  PDB: A:405-524 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
                 3jue A 404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLP--------------------------------------------LHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKM 697
                                   413       423       433       443       453       463       473       483       493       503       513       523|        -         -         -         -     | 573       583       593       603       613       623       633       643       653       663       673       683       693    
                                                                                                                                                  524                                          569                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with ACAP1_HUMAN | Q15027 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:298
                                   413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693        
          ACAP1_HUMAN   404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLPEIRGRRGGRGRPRGQPPVPPKPSIRPRPGSLRSKPEPPSEDLGSLHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAE 701
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -ArfGap-3jueB05 B:405-523                                                                                               -------------------------------------------------------------------------------------------------------------------Ank-3jueB01 B:639-671            ------------------------------ Pfam domains (1)
           Pfam domains (2) -ArfGap-3jueB06 B:405-523                                                                                               -------------------------------------------------------------------------------------------------------------------Ank-3jueB02 B:639-671            ------------------------------ Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-3jueB03 B:639-671            ------------------------------ Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ank-3jueB04 B:639-671            ------------------------------ Pfam domains (4)
         Sec.struct. author .hhhhhhhhh................eee....eeehhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhh.........--------------------------------------------.hhhhhhhhhhh...hhhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ARFGAP  PDB: B:405-524 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
                 3jue B 404 VGHVVAQVQSVDGNAQCCDCREPAPEWASINLGVTLCIQCSGIHRSLGVHFSKVRSLTLDSWEPELVKLMCELGNVIINQIYEARVEAMAVKKPGPSCSRQEKEAWIHAKYVEKKFLTKLP--------------------------------------------LHPGALLFRASGHPPSLPTMADALAHGADVNWVNGGQDNATPLIQATAANSLLACEFLLQNGANVNQADSAGRGPLHHATILGHTGLACLFLKRGADLGARDSEGRDPLTIAMETANADIVTLLRLAKMREAE 701
                                   413       423       433       443       453       463       473       483       493       503       513       523|        -         -         -         -     | 573       583       593       603       613       623       633       643       653       663       673       683       693        
                                                                                                                                                  524                                          569                                                                                                                                    

   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 3JUE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: Ank (35)
(-)
Family: Ank (23)
1aAnk-3jueB01B:639-671
1bAnk-3jueB02B:639-671
1cAnk-3jueB03B:639-671
1dAnk-3jueB04B:639-671

(-) Gene Ontology  (9, 9)

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 | Q150273t9k 4ckg 4ckh 4f1p 4nsw

(-) Related Entries Specified in the PDB File

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