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- PDB-1u5m: Structure of a Chordin-like Cysteine-rich Repeat (VWC module) fro... -

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Basic information

Entry
Database: PDB / ID: 1u5m
TitleStructure of a Chordin-like Cysteine-rich Repeat (VWC module) from Collagen IIA
Componentsalpha 1 type II collagen isoform 1
KeywordsSTRUCTURAL PROTEIN / 5 disulfide bonds / two sub-domain architecture / beta-sheet
Function / homology
Function and homology information


collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development / limb bud formation / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / Signaling by PDGF / endochondral ossification / NCAM1 interactions / collagen fibril organization / cartilage development / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / cartilage condensation / inner ear morphogenesis / roof of mouth development / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / skeletal system development / central nervous system development / sensory perception of sound / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / protein homodimerization activity / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / Complement Module, domain 1 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / Complement Module, domain 1 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Complement Module; domain 1 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Ribbon / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / semi-automated assignment, torsion angle dynamics
AuthorsO'Leary, J.M. / Hamilton, J.m. / Deane, C.M. / Valeyev, N.V. / Sandell, L.J. / Downing, A.K.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA
Authors: O'Leary, J.M. / Hamilton, J.M. / Deane, C.M. / Valeyev, N.V. / Sandell, L.J. / Downing, A.K.
#1: Journal: PROTEIN EXPR.PURIF. / Year: 2004
Title: Identification and removal of O-linked and non-covalently linked sugars from recombinant protein produced using Pichia pastoris
Authors: O'Leary, J.M. / Radcliffe, C.M. / Willis, A.C. / Dwek, R.A. / Rudd, P.M. / Downing, A.K.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha 1 type II collagen isoform 1


Theoretical massNumber of molelcules
Total (without water)7,9811
Polymers7,9811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600target function
RepresentativeModel #1,2closest to the average

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Components

#1: Protein alpha 1 type II collagen isoform 1 / collagen II / alpha-1 polypeptide / cartilage collagen / chondrocalcin / included / COL11A3 / formerly


Mass: 7981.009 Da / Num. of mol.: 1 / Fragment: Exon2 / Mutation: T67A, T71A, S73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL2A1 / Plasmid: pPICK9K-CRcolIIA / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P02458

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HMQC-J
1312D NOESY
NMR detailsText: Sequential assignments were made using triple resonance techniques. Disulfide bond connectivity was determined using NOESY data acquired at different temperatures.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM U-15N exon2; 50mM phosphate buffer; 0.02% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM U-15N exon2; 50mM phosphate buffer; 0.02% NaN3; 99.9% D2O99.9% D2O
30.8mM U-15N,13C exon2; 50mM phosphate buffer; 0.02% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM potassium phosphate / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA6001
GE OMEGAGEOMEGA7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guntert, P.structure solution
CYANA1.0.6Guntert, P.refinement
RefinementMethod: semi-automated assignment, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 20

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