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Title :  CRYSTAL STRUCTURE OF HUMAN TYPE III COLLAGEN G982-G1023 CONTAINING C-TERMINAL CYSTINE KNOT
 
Authors :  S. P. Boudko, J. Engel, K. Okuyama, K. Mizuno, H. P. Bachinger, M. A. Schumacher
Date :  01 Jul 08  (Deposition) - 30 Sep 08  (Release) - 05 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Collagen Iii, Cystine Knot, Triple Helix, Glycine, Mad Phasing, Alternative Splicing, Disease Mutation, Ehlers- Danlos Syndrome, Extracellular Matrix, Glycoprotein, Hydroxylation, Phosphoprotein, Polymorphism, Secreted, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. P. Boudko, J. Engel, K. Okuyama, K. Mizuno, H. P. Bachinger, M. A. Schumacher
Crystal Structure Of Human Type Iii Collagen Gly991-Gly1032 Cystine Knot-Containing Peptide Shows Both 7/2 And 10/3 Triple Helical Symmetries.
J. Biol. Chem. V. 283 32580 2008
PubMed-ID: 18805790  |  Reference-DOI: 10.1074/JBC.M805394200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLLAGEN ALPHA-1(III) CHAIN
    ChainsA, B, C
    EngineeredYES
    FragmentUNP RESIDUES 1158-1199
    MutationYES
    Other DetailsCHEMICALLY SYNTHESIZED PEPTIDE G982-G1023 BASED ON THE FRAGMENT 1158-1199 OF THE HUMAN COLLAGEN ALPHA-1(III) CHAIN, CO3A1_HUMAN, UNIPROT ENTRY P02461.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric/Biological Unit (2, 24)
No.NameCountTypeFull Name
1HYP21Mod. Amino Acid4-HYDROXYPROLINE
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3DMW)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:39 -B:40

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DMW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (16, 48)

Asymmetric/Biological Unit (16, 48)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_011154G1161VCO3A1_HUMANDisease (EDS4)587779473A/B/CG4V
02UniProtVAR_011155G1164ECO3A1_HUMANDisease (EDS4)587779431A/B/CG7E
03UniProtVAR_011156G1164RCO3A1_HUMANDisease (EDS4)587779553A/B/CG7R
04UniProtVAR_001798G1164SCO3A1_HUMANUnclassified  ---A/B/CG7S
05UniProtVAR_001799G1167VCO3A1_HUMANDisease (EDS4)587779578A/B/CG10V
06UniProtVAR_001800G1170DCO3A1_HUMANDisease (EDS4)587779465A/B/CG13D
07UniProtVAR_011157G1170VCO3A1_HUMANDisease (EDS4)587779465A/B/CG13V
08UniProtVAR_001801G1173ECO3A1_HUMANDisease (EDS4)121912918A/B/CG16E
09UniProtVAR_011158G1173RCO3A1_HUMANDisease (EDS4)587779521A/B/CG16R
10UniProtVAR_001802G1176VCO3A1_HUMANDisease (EDS4)  ---A/B/CG19V
11UniProtVAR_011159G1179RCO3A1_HUMANDisease (EDS4)587779574A/B/CG22R
12UniProtVAR_001803G1182ECO3A1_HUMANDisease (EDS4)111505097A/B/CG25E
13UniProtVAR_001804G1185DCO3A1_HUMANDisease (EDS4)121912917A/B/CG28D
14UniProtVAR_001805G1185VCO3A1_HUMANDisease (EDS4)121912917A/B/CG28V
15UniProtVAR_001806G1188ECO3A1_HUMANDisease (EDS4)112456072A/B/CG31E
16UniProtVAR_001807G1188RCO3A1_HUMANDisease (EDS4)587779504A/B/CG31R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DMW)

(-) Exons   (0, 0)

(no "Exon" information available for 3DMW)

(-) Sequences/Alignments

Asymmetric/Biological 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:37
 aligned with CO3A1_HUMAN | P02461 from UniProtKB/Swiss-Prot  Length:1466

    Alignment length:37
                                  1169      1179      1189       
         CO3A1_HUMAN   1160 IGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPC 1196
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..................................... Sec.struct. author
             SAPs(SNPs) (1) -V--E--V--D--E--V--R--E--D--E-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----R-----V--R-----------V--R-------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----S-------------------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                3dmw A    3 IGPpGPRGNRGERGSEGSpGHpGmpGPpGPpGApGPC   39
                               |    12        22 | ||  |32|  |   
                               |             21-HYP||  |  |  |   
                               6-HYP            24-HYP |  |  |   
                                                  26-MSE  |  |   
                                                   27-HYP |  |   
                                                      30-HYP |   
                                                         33-HYP  
                                                            36-HYP

Chain B from PDB  Type:PROTEIN  Length:37
 aligned with CO3A1_HUMAN | P02461 from UniProtKB/Swiss-Prot  Length:1466

    Alignment length:37
                                  1170      1180      1190       
         CO3A1_HUMAN   1161 GPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCC 1197
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..................................... Sec.struct. author
             SAPs(SNPs) (1) V--E--V--D--E--V--R--E--D--E--------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---R-----V--R-----------V--R--------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---S--------------------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                3dmw B    4 GPpGPRGNRGERGSEGSpGHpGmpGPpGPpGApGPCC   40
                              |     13       |23| ||  | 33  |    
                              6-HYP         21-HYP||  |  |  |    
                                               24-HYP |  |  |    
                                                 26-MSE  |  |    
                                                  27-HYP |  |    
                                                     30-HYP |    
                                                        33-HYP   
                                                           36-HYP

Chain C from PDB  Type:PROTEIN  Length:37
 aligned with CO3A1_HUMAN | P02461 from UniProtKB/Swiss-Prot  Length:1466

    Alignment length:37
                                  1168      1178      1188       
         CO3A1_HUMAN   1159 PIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGP 1195
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..................................... Sec.struct. author
             SAPs(SNPs) (1) --V--E--V--D--E--V--R--E--D--E------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----R-----V--R-----------V--R------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----S------------------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                3dmw C    2 PIGPpGPRGNRGERGSEGSpGHpGmpGPpGPpGApGP   38
                                |   11        21  | ||  31 |  |  
                                6-HYP         21-HYP||  |  |  |  
                                                 24-HYP |  |  |  
                                                   26-MSE  |  |  
                                                    27-HYP |  |  
                                                       30-HYP |  
                                                          33-HYP 
                                                             36-HYP

   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 3DMW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DMW)

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CO3A1_HUMAN | P02461)
molecular function
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0005201    extracellular matrix structural constituent    The action of a molecule that contributes to the structural integrity of the extracellular matrix.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0048407    platelet-derived growth factor binding    Interacting selectively and non-covalently with platelet-derived growth factor.
    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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0060414    aorta smooth muscle tissue morphogenesis    The process in which the structure of the smooth muscle tissue surrounding the aorta is generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body.
    GO:0001568    blood vessel development    The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    GO:0030199    collagen fibril organization    Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0050777    negative regulation of immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:2001223    negative regulation of neuron migration    Any process that stops, prevents or reduces the frequency, rate or extent of neuron migration.
    GO:0018149    peptide cross-linking    The formation of a covalent cross-link between or within protein chains.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0035025    positive regulation of Rho protein signal transduction    Any process that activates or increases the frequency, rate or extent of Rho protein signal transduction.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0034097    response to cytokine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0009314    response to radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0043588    skin development    The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    GO:0005586    collagen type III trimer    A collagen homotrimer of alpha1(III) chains; type III collagen triple helices associate to form fibrils.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CO3A1_HUMAN | P024612v53 4ae2 4aej 4ak3 4gyx

(-) Related Entries Specified in the PDB File

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