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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-PARVIN CH2 DOMAIN
 
Authors :  A. L. Stiegler, K. M. Draheim, X. Li, N. E. Chayen, D. A. Calderwood, T. J.
Date :  27 Mar 12  (Deposition) - 08 Aug 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Calponin Homology Domain, Protein-Protein Interaction, Ld Motif, Integrin Signaling, Focal Adhesion, Adaptor Protein, Paxillin And Integrin-Linked Kinase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Stiegler, K. M. Draheim, X. Li, N. E. Chayen, D. A. Calderwood, T. J. Boggon
Structural Basis For Paxillin Binding And Focal Adhesion Targeting Of Beta-Parvin.
J. Biol. Chem. V. 287 32566 2012
PubMed-ID: 22869380  |  Reference-DOI: 10.1074/JBC.M112.367342

(-) Compounds

Molecule 1 - BETA-PARVIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL CALPONIN HOMOLOGY DOMAIN
    Gene: PARVB, CGI-56
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AFFIXIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 17)

Asymmetric Unit (1, 17)
No.NameCountTypeFull Name
1EDO17Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:284 , HOH A:504 , HOH A:513BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWAREASP A:345 , LEU A:346 , LYS A:347 , HOH A:514BINDING SITE FOR RESIDUE EDO A 402
03AC3SOFTWAREGLU A:274 , HOH A:540BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREASP A:247 , PRO A:250 , HOH A:501 , GLU C:277 , GLU C:279BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREGLN B:281 , ASP B:284 , TYR B:287 , HOH B:503 , HOH B:533BINDING SITE FOR RESIDUE EDO B 401
06AC6SOFTWAREGLN C:281 , ASP C:284 , TYR C:287 , HOH C:521 , HOH C:533BINDING SITE FOR RESIDUE EDO C 401
07AC7SOFTWAREHIS C:303 , HIS C:317BINDING SITE FOR RESIDUE EDO C 402
08AC8SOFTWAREGLN D:281 , ASP D:284 , VAL D:286BINDING SITE FOR RESIDUE EDO D 401
09AC9SOFTWARESER D:311 , PHE D:312 , LYS D:315 , ASN E:269 , ASN E:272 , GLU E:274BINDING SITE FOR RESIDUE EDO D 402
10BC1SOFTWAREGLU B:277 , HOH B:517 , LEU D:278 , GLU D:279BINDING SITE FOR RESIDUE EDO D 403
11BC2SOFTWAREGLN D:314BINDING SITE FOR RESIDUE EDO D 404
12BC3SOFTWAREHOH B:527 , LEU D:253 , LYS D:257 , LEU D:346 , HOH D:525BINDING SITE FOR RESIDUE EDO D 405
13BC4SOFTWARETHR B:280 , PRO D:250 , ASP D:251 , HOH D:519BINDING SITE FOR RESIDUE EDO D 406
14BC5SOFTWAREGLN E:281 , ASP E:284 , HOH E:527BINDING SITE FOR RESIDUE EDO E 401
15BC6SOFTWARETHR F:280 , LYS F:315BINDING SITE FOR RESIDUE EDO F 401
16BC7SOFTWAREASP F:284 , VAL F:286 , TYR F:287 , HOH F:525BINDING SITE FOR RESIDUE EDO F 402
17BC8SOFTWARELYS F:270BINDING SITE FOR RESIDUE EDO F 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EDL)

(-) 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:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edl A 236 RFERDAFDTLFDHAPDKLSVVKKSLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEDYFVPLHHFYLTPESFDQKVHNVSFAFELMLDGGLKKPKARPEDVVNLDLKSTLRVLYNLFTKYKNVE 364
                                   245       255       265       275       285       295       305       315       325       335       345       355         


Chain B from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edl B 237 FERDAFDTLFDHAPDKLSVVKKSLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEDYFVPLHHFYLTPESFDQKVHNVSFAFELMLDGGLKKPKARPEDVVNLDLKSTLRVLYNLFTKYKNVE 364
                                   246       256       266       276       286       296       306       316       326       336       346       356        


Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edl C 238 ERDAFDTLFDHAPDKLSVVKKSLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEDYFVPLHHFYLTPESFDQKVHNVSFAFELMLDGGLKKPKARPEDVVNLDLKSTLRVLYNLFTKYKNVE 364
                                   247       257       267       277       287       297       307       317       327       337       347       357       


Chain D from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edl D 238 ERDAFDTLFDHAPDKLSVVKKSLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEDYFVPLHHFYLTPESFDQKVHNVSFAFELMLDGGLKKPKARPEDVVNLDLKSTLRVLYNLFTKYKNVE 364
                                   247       257       267       277       287       297       307       317       327       337       347       357       


Chain E from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edl E 237 FERDAFDTLFDHAPDKLSVVKKSLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEDYFVPLHHFYLTPESFDQKVHNVSFAFELMLDGGLKKPKARPEDVVNLDLKSTLRVLYNLFTKYKNVE 364
                                   246       256       266       276       286       296       306       316       326       336       346       356        


Chain F from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4edl F 238 ERDAFDTLFDHAPDKLSVVKKSLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLLEDYVPLHHFYLTPESFDQKVHNVSFAFELMLDGGLKKPKARPEDVVNLDLKSTLRVLYNLFTKYKNVE 364
                                   247       257       267       277       287       297||     308       318       328       338       348       358      
                                                                                      298|                                                                
                                                                                       300
   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 4EDL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

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        PARVB_HUMAN | Q9HBI1: 4edm 4edn

(-) Related Entries Specified in the PDB File

4edm 4edn