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(-) Description

Title :  STRUCTURE OF A CHORDIN-LIKE CYSTEINE-RICH REPEAT (VWC MODULE) FROM COLLAGEN IIA
 
Authors :  J. M. O'Leary, J. M. Hamilton, C. M. Deane, N. V. Valeyev, L. J. Sandell, A. K. Downing
Date :  28 Jul 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  5 Disulfide Bonds, Two Sub-Domain Architecture, Beta-Sheet, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. O'Leary, J. M. Hamilton, C. M. Deane, N. V. Valeyev, L. J. Sandell, A. K. Downing
Solution Structure And Dynamics Of A Prototypical Chordin-Like Cysteine-Rich Repeat (Von Willebrand Factor Type C Module) From Collagen Iia
J. Biol. Chem. V. 279 53857 2004
PubMed-ID: 15466413  |  Reference-DOI: 10.1074/JBC.M409225200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA 1 TYPE II COLLAGEN ISOFORM 1
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICK9K-CRCOLIIA
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: EXON2
    Gene: COL2A1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COLLAGEN II, ALPHA-1 POLYPEPTIDE

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1U5M)

(-) Sites  (0, 0)

(no "Site" information available for 1U5M)

(-) SS Bonds  (5, 5)

NMR Structure
No.Residues
1A:10 -A:33
2A:28 -A:61
3A:31 -A:40
4A:45 -A:62
5A:51 -A:65

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063891C57YCO2A1_HUMANDisease (STL1O)121912898AC33Y
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFC_2PS50184 VWFC domain profile.CO2A1_HUMAN32-90  1A:8-66
2VWFC_1PS01208 VWFC domain signature.CO2A1_HUMAN52-89  1A:28-65

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003805181bENSE00002177316chr12:48398269-48398020250CO2A1_HUMAN1-29291A:1-55
1.4aENST000003805184aENSE00001661130chr12:48393908-48393702207CO2A1_HUMAN29-98701A:5-7369
1.5bENST000003805185bENSE00001672257chr12:48392214-4839219817CO2A1_HUMAN98-10360--
1.6ENST000003805186ENSE00001650589chr12:48391984-4839195233CO2A1_HUMAN104-114110--
1.7ENST000003805187ENSE00001613103chr12:48391847-4839181533CO2A1_HUMAN115-125110--
1.8ENST000003805188ENSE00001683942chr12:48391707-4839165454CO2A1_HUMAN126-143180--
1.9bENST000003805189bENSE00001713001chr12:48391490-48391389102CO2A1_HUMAN144-177340--
1.10ENST0000038051810ENSE00001749051chr12:48390408-4839033178CO2A1_HUMAN178-203260--
1.11ENST0000038051811ENSE00001805624chr12:48389702-4838965845CO2A1_HUMAN204-218150--
1.12ENST0000038051812ENSE00001641870chr12:48389546-4838949354CO2A1_HUMAN219-236180--
1.13ENST0000038051813ENSE00001626662chr12:48389091-4838903854CO2A1_HUMAN237-254180--
1.14ENST0000038051814ENSE00001716055chr12:48388260-4838820754CO2A1_HUMAN255-272180--
1.15ENST0000038051815ENSE00001598832chr12:48387830-4838777754CO2A1_HUMAN273-290180--
1.16ENST0000038051816ENSE00001606284chr12:48387645-4838759254CO2A1_HUMAN291-308180--
1.17ENST0000038051817ENSE00001752481chr12:48387285-4838724145CO2A1_HUMAN309-323150--
1.18ENST0000038051818ENSE00001729865chr12:48386714-4838666154CO2A1_HUMAN324-341180--
1.19ENST0000038051819ENSE00001774985chr12:48383588-4838354445CO2A1_HUMAN342-356150--
1.20ENST0000038051820ENSE00001763552chr12:48383064-4838301154CO2A1_HUMAN357-374180--
1.22ENST0000038051822ENSE00001668796chr12:48381492-4838139499CO2A1_HUMAN375-407330--
1.23ENST0000038051823ENSE00001662817chr12:48381096-4838105245CO2A1_HUMAN408-422150--
1.24ENST0000038051824ENSE00001723909chr12:48380959-4838086199CO2A1_HUMAN423-455330--
1.25ENST0000038051825ENSE00001692548chr12:48380671-4838061854CO2A1_HUMAN456-473180--
1.26ENST0000038051826ENSE00001740201chr12:48380226-48380119108CO2A1_HUMAN474-509360--
1.27ENST0000038051827ENSE00001767237chr12:48379748-4837969554CO2A1_HUMAN510-527180--
1.28ENST0000038051828ENSE00001599090chr12:48379609-4837951199CO2A1_HUMAN528-560330--
1.29ENST0000038051829ENSE00001757919chr12:48379370-4837931754CO2A1_HUMAN561-578180--
1.30ENST0000038051830ENSE00001716482chr12:48378876-4837877899CO2A1_HUMAN579-611330--
1.31ENST0000038051831ENSE00001622932chr12:48378382-4837832954CO2A1_HUMAN612-629180--
1.32ENST0000038051832ENSE00001644701chr12:48377923-4837787054CO2A1_HUMAN630-647180--
1.33bENST0000038051833bENSE00001796614chr12:48377519-4837746654CO2A1_HUMAN648-665180--
1.34ENST0000038051834ENSE00001710088chr12:48377221-4837716854CO2A1_HUMAN666-683180--
1.35ENST0000038051835ENSE00001621432chr12:48376920-4837687645CO2A1_HUMAN684-698150--
1.36ENST0000038051836ENSE00001633545chr12:48376729-4837663199CO2A1_HUMAN699-731330--
1.37ENST0000038051837ENSE00001803753chr12:48376392-48376285108CO2A1_HUMAN732-767360--
1.38aENST0000038051838aENSE00001681804chr12:48375943-4837589054CO2A1_HUMAN768-785180--
1.39ENST0000038051839ENSE00001607745chr12:48375612-4837555954CO2A1_HUMAN786-803180--
1.40ENST0000038051840ENSE00001635649chr12:48375179-4837512654CO2A1_HUMAN804-821180--
1.41ENST0000038051841ENSE00001669107chr12:48374751-4837469854CO2A1_HUMAN822-839180--
1.42ENST0000038051842ENSE00001772729chr12:48374444-48374337108CO2A1_HUMAN840-875360--
1.43ENST0000038051843ENSE00001591943chr12:48373845-4837379254CO2A1_HUMAN876-893180--
1.44ENST0000038051844ENSE00001766798chr12:48373347-4837329454CO2A1_HUMAN894-911180--
1.45ENST0000038051845ENSE00001647246chr12:48372541-48372380162CO2A1_HUMAN912-965540--
1.46ENST0000038051846ENSE00001632799chr12:48372181-48372074108CO2A1_HUMAN966-1001360--
1.47ENST0000038051847ENSE00001687971chr12:48371900-48371793108CO2A1_HUMAN1002-1037360--
1.48ENST0000038051848ENSE00001745083chr12:48371436-4837138354CO2A1_HUMAN1038-1055180--
1.49ENST0000038051849ENSE00001771216chr12:48371210-48371103108CO2A1_HUMAN1056-1091360--
1.50ENST0000038051850ENSE00001800326chr12:48370938-4837088554CO2A1_HUMAN1092-1109180--
1.51ENST0000038051851ENSE00001628024chr12:48370702-48370595108CO2A1_HUMAN1110-1145360--
1.52ENST0000038051852ENSE00001632016chr12:48370350-4837029754CO2A1_HUMAN1146-1163180--
1.53ENST0000038051853ENSE00001755795chr12:48369853-48369746108CO2A1_HUMAN1164-1199360--
1.54ENST0000038051854ENSE00001632936chr12:48369388-48369100289CO2A1_HUMAN1200-1296970--
1.55ENST0000038051855ENSE00001165399chr12:48368645-48368458188CO2A1_HUMAN1296-1358630--
1.56ENST0000038051856ENSE00001005948chr12:48368114-48367872243CO2A1_HUMAN1359-1439810--
1.57bENST0000038051857bENSE00001521209chr12:48367336-48366748589CO2A1_HUMAN1440-1487480--

(-) Sequences/Alignments

NMR Structure
   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:73
 aligned with CO2A1_HUMAN | P02458 from UniProtKB/Swiss-Prot  Length:1487

    Alignment length:73
                                    34        44        54        64        74        84        94   
           CO2A1_HUMAN   25 GQDVQEAGSCVQDGQRYNDKDVWKPEPCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCPICPTDLATAS 97
               SCOP domains d1u5ma_ A: Collagen alpha 1(II) chain precursor                           SCOP domains
               CATH domains --------1u5mA01 A:9-44                      ----------------------------- CATH domains
               Pfam domains ---------VWC-1u5mA01 A:10-65                                     -------- Pfam domains
         Sec.struct. author .........ee....ee....ee.....eeeeee..eeeeee............................... Sec.struct. author
                 SAPs(SNPs) --------------------------------Y---------------------------------------- SAPs(SNPs)
                PROSITE (1) -------VWFC_2  PDB: A:8-66 UniProt: 32-90                         ------- PROSITE (1)
                PROSITE (2) ---------------------------VWFC_1  PDB: A:28-65 UniProt: 52-89   -------- PROSITE (2)
           Transcript 1 (1) 1.1b -------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.4a  PDB: A:5-73 UniProt: 29-98 [INCOMPLETE]                    Transcript 1 (2)
                  1u5m A  1 YVEFQEAGSCVQDGQRYNDKDVWKPEPCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCPICPADLAAAA 73
                                    10        20        30        40        50        60        70
   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  (1, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: FnI-like (2)

(-) Gene Ontology  (44, 44)

NMR Structure(hide GO term definitions)
Chain A   (CO2A1_HUMAN | P02458)
molecular function
    GO:0005201    extracellular matrix structural constituent    The action of a molecule that contributes to the structural integrity of the extracellular matrix.
    GO:0030020    extracellular matrix structural constituent conferring tensile strength    A constituent of the extracellular matrix that enables the matrix to resist longitudinal stress.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
biological process
    GO:0060348    bone development    The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
    GO:0001502    cartilage condensation    The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0060351    cartilage development involved in endochondral bone morphogenesis    The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones.
    GO:0071773    cellular response to BMP 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 a bone morphogenetic protein (BMP) stimulus.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0002062    chondrocyte differentiation    The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
    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:0060272    embryonic skeletal joint morphogenesis    The process in which the anatomical structures of skeletal joints are generated and organized during the embryonic phase. A skeletal joint is the connecting structure between the bones of the skeleton.
    GO:0001958    endochondral ossification    Replacement ossification wherein bone tissue replaces cartilage.
    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:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0048839    inner ear development    The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0060174    limb bud formation    The process pertaining to the initial formation of a limb bud from unspecified parts. This process begins with the formation of a local condensation of mesenchyme cells within the prospective limb field, and ends when a limb bud is recognizable.
    GO:0035108    limb morphogenesis    The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping.
    GO:2001240    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:0030903    notochord development    The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0071599    otic vesicle development    The process whose specific outcome is the progression of the otic vesicle over time, from its formation to the mature structure. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0006029    proteoglycan metabolic process    The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    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:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    GO:0001894    tissue homeostasis    A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    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:0005585    collagen type II trimer    A collagen homotrimer of alpha1(II) chains; type II collagen triple helices associate to form fibrils.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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  1u5m
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  CO2A1_HUMAN | P02458
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 Related Entries

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

UniProtKB/Swiss-Prot
        CO2A1_HUMAN | P02458: 2fse 2seb 5nir

(-) Related Entries Specified in the PDB File

1fbr PAIR OF FIBRONECTIN TYPE I DOMAINS