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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYPE IX COLLAGEN NC2 HETERO-TRIMERIZATION DOMAIN WITH A GUEST FRAGMENT A1A2A1 OF TYPE I COLLAGEN
 
Authors :  S. P. Boudko, H. P. Bachinger
Date :  25 Jul 15  (Deposition) - 10 Aug 16  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Collagen, Hetero-Trimerization, Chain Stagger, Chain Register, Triple Helix, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Boudko, H. P. Bachinger
Structural Insight For Chain Selection And Stagger Control In Collagen.
Sci Rep V. 6 37831 2016
PubMed-ID: 27897211  |  Reference-DOI: 10.1038/SREP37831

(-) Compounds

Molecule 1 - COLLAGEN ALPHA-2(I) CHAIN,COLLAGEN ALPHA-1(IX) CHAIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 484-495,UNP RESIDUES 754-789
    Gene: COL1A2, COL9A1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-2 TYPE I COLLAGEN
 
Molecule 2 - COLLAGEN ALPHA-1(I) CHAIN,COLLAGEN ALPHA-2(IX) CHAIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 572-583,UNP RESIDUES 517-552
    Gene: COL1A1, COL9A2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-1 TYPE I COLLAGEN
 
Molecule 3 - COLLAGEN ALPHA-1(I) CHAIN,COLLAGEN ALPHA-3(IX) CHAIN
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 572-583,UNP RESIDUES 517-553
    Gene: COL1A1, COL9A3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-1 TYPE I COLLAGEN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:54 , HIS A:55 , HOH A:203 , ALA C:20binding site for residue GOL A 101
2AC2SOFTWAREGLN F:58 , HOH F:203binding site for residue GOL F 101

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:48 -C:48
2D:48 -F:48

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CVA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CVA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CVA)

(-) Exons   (0, 0)

(no "Exon" information available for 5CVA)

(-) 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:64
                                                                                               
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  5cva A  3 GPPGPPGPPGPPGARGEPGNIGFPGPPGPPGPPGRAPTDQHIKQVCmRVIQEHFAEmAASLKRP 66
                                    12        22        32        42      | 52      | 62    
                                                                         49-MSE    59-MSE   


Chain B from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  5cva B  2 SGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGRDATDQHIVDVALKMLQEQLAEVAVSA 63
                                    11        21        31        41        51        61  


Chain C from PDB  Type:PROTEIN  Length:66
                                                                                                 
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................................hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  5cva C  2 SGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGKEASEQRIRELCGGMISEQIAQLAAHLRKPL 67
                                    11        21        31        41        51        61      


Chain D from PDB  Type:PROTEIN  Length:58
                                                                                         
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  5cva D 13 PPGARGEPGNIGFPGPPGPPGPPGRAPTDQHIKQVCmRVIQEHFAEmAASLKRPDSGA 70
                                    22        32        42      | 52      | 62        
                                                               49-MSE    59-MSE       


Chain E from PDB  Type:PROTEIN  Length:45
                                                                            
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  5cva E 15 GARGQAGVMGFPGPPGPPGPPGRDATDQHIVDVALKMLQEQLAEV 59
                                    24        34        44        54     


Chain F from PDB  Type:PROTEIN  Length:58
                                                                                         
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  5cva F 10 PPGPPGARGQAGVMGFPGPPGPPGPPGKEASEQRIRELCGGMISEQIAQLAAHLRKPL 67
                                    19        29        39        49        59
   Legend:   → Mismatch (orange background)
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  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 5CVA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CVA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CVA)

(-) Gene Ontology  (84, 129)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CO1A1_HUMAN | P02452: 1q7d 2llp 3ejh 3gxe 5ctd 5cti 5cvb 5k31
        CO1A2_HUMAN | P08123: 5ctd 5cti
        CO9A1_HUMAN | P20849: 2uur 5ctd 5cti 5cvb
        CO9A2_HUMAN | Q14055: 5ctd 5cti 5cvb
        CO9A3_HUMAN | Q14050: 5ctd 5cti 5cvb

(-) Related Entries Specified in the PDB File

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