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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYPE IX COLLAGEN NC2 HETERO-TRIMERIZATION DOMAIN WITH A GUEST FRAGMENT A1A1A1 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 :  2.25
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-1(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 572-583,UNP RESIDUES 754-789
    Gene: COL1A1, COL9A1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-1 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, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:54 , HIS A:55 , VAL B:45 , GLN C:19 , ALA C:20binding site for residue GOL A 101
2AC2SOFTWAREGLN C:58 , HOH C:202 , HOH C:206binding site for residue GOL C 101
3AC3SOFTWAREASP A:41 , GLN E:55 , GLU E:58 , SER F:53 , ALA F:57binding site for residue GOL F 101
4AC4SOFTWARETHR A:40 , ASP A:41 , ARG C:43 , GLN E:55 , GLY F:49 , HOH F:215 , HOH F:216binding site for residue GOL F 102
5AC5SOFTWAREGLU C:46 , ALA E:60 , ALA F:60 , ARG F:64binding site for residue GOL F 103

(-) 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 5CVB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CVB)

(-) 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:66
                                                                                                 
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................................hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  5cvb A  2 SGPPGPPGPPGPPGARGQAGVmGFPGPPGPPGPPGRAPTDQHIKQVCmRVIQEHFAEmAASLKRPD 67
                                    11        21 |      31        41       |51       |61      
                                                23-MSE                    49-MSE    59-MSE    


Chain B from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  5cvb B  2 SGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGRDATDQHIVDVALKMLQEQLAEVAV 61
                                    11        21        31        41        51        61


Chain C from PDB  Type:PROTEIN  Length:67
                                                                                                  
               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
                  5cvb C  1 GSGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGKEASEQRIRELCGGMISEQIAQLAAHLRKPL 67
                                    10        20        30        40        50        60       


Chain D from PDB  Type:PROTEIN  Length:67
                                                                                                  
               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
                  5cvb D  2 SGPPGPPGPPGPPGARGQAGVmGFPGPPGPPGPPGRAPTDQHIKQVCmRVIQEHFAEmAASLKRPDS 68
                                    11        21 |      31        41       |51       |61       
                                                23-MSE                    49-MSE    59-MSE     


Chain E from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  5cvb E  2 SGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGRDATDQHIVDVALKMLQEQLAEVAV 61
                                    11        21        31        41        51        61


Chain F from PDB  Type:PROTEIN  Length:68
                                                                                                   
               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
                  5cvb F  1 GSGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGKEASEQRIRELCGGMISEQIAQLAAHLRKPLA 68
                                    10        20        30        40        50        60
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5CVB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (77, 98)

Asymmetric Unit(hide GO term definitions)

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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 5cva 5k31
        CO9A1_HUMAN | P20849: 2uur 5ctd 5cti 5cva
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        CO9A3_HUMAN | Q14050: 5ctd 5cti 5cva

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