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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FIBRILLAR PROCOLLAGEN TYPE I C-PROPEPTIDE HOMO-TRIMER
 
Authors :  U. Sharma, D. J. S. Hulmes, N. Aghajari
Date :  19 May 16  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A (1x),D (1x),E (1x)
Biol. Unit 2:  A (1x),D (1x),E (1x)
Biol. Unit 3:  B,C,F  (1x)
Keywords :  Fibrillar Collagen, Extracellular Matrix, Fibrosis, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Sharma, L. Carrique, S. Vadon-Le Goff, N. Mariano, R. N. Georges, F. Delolme, P. Koivunen, J. Myllyharju, C. Moali, N. Aghajari, D. J. Hulmes
Structural Basis Of Homo- And Heterotrimerization Of Collagen I.
Nat Commun V. 8 14671 2017
PubMed-ID: 28281531  |  Reference-DOI: 10.1038/NCOMMS14671

(-) Compounds

Molecule 1 - COLLAGEN ALPHA-1(I) CHAIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: HEK 293T
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: COL1A1
    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): A (1x)  D (1x)E (1x) 
Biological Unit 2 (1x): A (1x)  D (1x)E (1x) 
Biological Unit 3 (1x):  BC  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:59 , ASN A:61 , GLN A:62 , CYS A:64 , ASP A:67binding site for residue CA A 301
02AC2SOFTWAREGLU A:79 , SER A:145 , CYS A:244 , LEU A:246binding site for residue GOL A 302
03AC3SOFTWAREASP B:59 , ASN B:61 , GLN B:62 , CYS B:64 , ASP B:67 , HOH F:408binding site for residue CA B 301
04AC4SOFTWAREASP B:160 , LYS B:168binding site for residue CL B 302
05AC5SOFTWAREHIS B:105 , LEU B:170 , LEU B:171 , ARG B:181 , ALA B:182 , GLU B:183 , TYR B:190 , HOH B:408 , HOH B:409 , HOH B:424binding site for residue GOL B 303
06AC6SOFTWAREGLN B:147 , ILE B:148 , THR B:149 , ASP B:239 , GLY B:241binding site for residue GOL B 304
07AC7SOFTWAREGLU B:79 , GLU B:143 , ALA B:144 , SER B:145 , LYS B:212 , CYS B:244 , HOH B:472binding site for residue GOL B 305
08AC8SOFTWAREARG B:39 , ARG C:39 , ARG F:39binding site for residue CL B 306
09AC9SOFTWAREHOH B:406 , ASP C:59 , ASN C:61 , GLN C:62 , CYS C:64 , ASP C:67binding site for residue CA C 301
10AD1SOFTWAREASP D:59 , ASN D:61 , GLN D:62 , CYS D:64 , ASP D:67binding site for residue CA D 301
11AD2SOFTWAREARG D:39binding site for residue CL D 302
12AD3SOFTWAREHOH A:412 , ASP E:59 , ASN E:61 , GLN E:62 , CYS E:64 , ASP E:67binding site for residue CA E 301
13AD4SOFTWAREGLU E:79 , GLU E:143 , ALA E:144 , SER E:145 , LYS E:212 , CYS E:244binding site for residue GOL E 302
14AD5SOFTWAREHOH C:402 , ASP F:59 , ASN F:61 , GLN F:62 , CYS F:64 , ASP F:67binding site for residue CA F 301

(-) SS Bonds  (24, 24)

Asymmetric Unit
No.Residues
1A:41 -A:73
2A:47 -E:64
3A:64 -D:47
4A:81 -A:244
5A:152 -A:197
6B:41 -B:73
7B:47 -C:64
8B:64 -F:47
9B:81 -B:244
10B:152 -B:197
11C:41 -C:73
12C:47 -F:64
13C:81 -C:244
14C:152 -C:197
15D:41 -D:73
16D:64 -E:47
17D:81 -D:244
18D:152 -D:197
19E:41 -E:73
20E:81 -E:244
21E:152 -E:197
22F:41 -F:73
23F:81 -F:244
24F:152 -F:197

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:219 -Pro A:220
2Leu B:219 -Pro B:220
3Leu C:219 -Pro C:220
4Leu D:219 -Pro D:220
5Lys E:101 -Asp E:102
6Asp E:102 -Lys E:103
7Leu E:219 -Pro E:220
8Leu F:219 -Pro F:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K31)

(-) Exons   (0, 0)

(no "Exon" information available for 5K31)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee.....hhhhheeeeee....eeee.....eeeee..............hhhhhh.............hhhhhhhhhhhhhhh...eeeeeeeeee.................eee.....ee..........eeeee........eeeeeeeeee.hhhhh...eee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k31 A   6 VRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQQITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL 246
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245 


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee.....hhhhheeeeee....eeee.....eeeee..............hhhhhh.............hhhhhhhhhhhhhhh..eeeeeeeeeee.................eeee....ee..........eeeee........eeeeeeeeee.hhhhh.eeeee.........eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k31 B   8 DRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQQITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL 246
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         


Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee.....hhhhheeeeee....eeee.....eeeee..............hhhhhh.............hhhhhhhhhhhhhhh...eeeeeeeeee.................eeee....ee....hhhhh.eeeee........eeeeeeeeee.hhhhh.eeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k31 C   9 RDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQQITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL 246
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238        


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee.....hhhhheeeeee....eeee.....eeeee..............hhhhhh.............hhhhhhhhhhhhhhh...eeeeeeeeee.................eee.....ee....hhhhh.eeeee........eeeeeeeeee.hhhhh...eee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k31 D   8 DRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQQITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL 246
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         


Chain E from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee..........eeeeee....eeee.....eeeee..............hhhhhh.............hhhhhhhhhhhhhhh...eeeeeeeeee.................eee.....ee....hhhhh.eeeee........eeeeeeeeee.hhhhh...eee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k31 E   8 DRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQQITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL 246
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         


Chain F from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee.....hhhhheeeeee....eeee.....eeeee..............hhhhhh.............hhhhhhhhhhhhhhh...eeeeeeeeee.................eee.....ee..........eeeee.........eeeeeeeee.hhhhh...eee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k31 F   7 RDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVAQKNWYISKNPKDKRHVWFGESMTDGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQQITYHCKNSVAYMDQQTGNLKKALLLQGSNEIEIRAEGNSRFTYSVTVDGCTSHTGAWGKTVIEYKTTKSSRLPIIDVAPLDVGAPDQEFGFDVGPVCFL 246
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
   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 5K31)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K31)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K31)

(-) Gene Ontology  (71, 71)

Asymmetric Unit(hide GO term definitions)

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  5k31
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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 5cvb

(-) Related Entries Specified in the PDB File

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