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- PDB-5cvb: Crystal structure of the type IX collagen NC2 hetero-trimerizatio... -

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Basic information

Entry
Database: PDB / ID: 5cvb
TitleCrystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment a1a1a1 of type I collagen
Components
  • Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain
  • Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain
  • Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
KeywordsSTRUCTURAL PROTEIN / collagen / hetero-trimerization / chain stagger / chain register / triple helix
Function / homology
Function and homology information


collagen type IX trimer / cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization ...collagen type IX trimer / cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / Defective VWF binding to collagen type I / platelet-derived growth factor binding / bone trabecula formation / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / intramembranous ossification / embryonic skeletal system development / Extracellular matrix organization / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / endochondral ossification / Platelet Adhesion to exposed collagen / NCAM1 interactions / cellular response to fibroblast growth factor stimulus / collagen fibril organization / negative regulation of cell-substrate adhesion / response to steroid hormone / face morphogenesis / Scavenging by Class A Receptors / skin development / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Syndecan interactions / GP1b-IX-V activation signalling / blood vessel development / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / protein localization to nucleus / Non-integrin membrane-ECM interactions / ECM proteoglycans / response to hyperoxia / Integrin cell surface interactions / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / cellular response to retinoic acid / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / response to cAMP / visual perception / ossification / extracellular matrix organization / secretory granule / skeletal system development / Cell surface interactions at the vascular wall / cellular response to glucose stimulus / animal organ morphogenesis / sensory perception of sound / cellular response to amino acid stimulus / response to insulin / response to hydrogen peroxide / cellular response to mechanical stimulus / osteoblast differentiation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein transport / positive regulation of canonical Wnt signaling pathway / response to estradiol / cellular response to tumor necrosis factor / carbohydrate binding / collagen-containing extracellular matrix / protease binding / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
: / Thrombospondin N-terminal -like domains. / 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 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain ...: / Thrombospondin N-terminal -like domains. / 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 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Collagen alpha-1(I) chain / Collagen alpha-1(IX) chain / Collagen alpha-3(IX) chain / Collagen alpha-2(IX) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.249 Å
AuthorsBoudko, S.P. / Bachinger, H.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Shriners Hospitals for Children United States
CitationJournal: Sci Rep / Year: 2016
Title: Structural insight for chain selection and stagger control in collagen.
Authors: Boudko, S.P. / Bachinger, H.P.
History
DepositionJul 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain
B: Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain
C: Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
D: Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain
E: Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain
F: Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,52511
Polymers42,0656
Non-polymers4605
Water1,72996
1
A: Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain
B: Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain
C: Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2175
Polymers21,0323
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-72 kcal/mol
Surface area11500 Å2
MethodPISA
2
D: Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain
E: Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain
F: Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3096
Polymers21,0323
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-71 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.770, 64.460, 65.390
Angle α, β, γ (deg.)90.000, 112.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain / Alpha-1 type I collagen


Mass: 7161.650 Da / Num. of mol.: 2 / Fragment: UNP Residues 572-583,UNP Residues 754-789
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A1, COL9A1 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P02452, UniProt: P20849
#2: Protein Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain / Alpha-1 type I collagen


Mass: 6871.765 Da / Num. of mol.: 2 / Fragment: UNP Residues 572-583,UNP Residues 517-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A1, COL9A2 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P02452, UniProt: Q14055
#3: Protein Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain / Alpha-1 type I collagen


Mass: 6999.000 Da / Num. of mol.: 2 / Fragment: UNP Residues 572-583,UNP Residues 517-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A1, COL9A3 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P02452, UniProt: Q14050
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.1M BisTris, 14% PEG MME 5,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97866, 0.97887, 0.96338
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 23, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978661
20.978871
30.963381
ReflectionRedundancy: 6.7 % / Number: 116869 / Rmerge(I) obs: 0.115 / Χ2: 1.16 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 17539 / % possible obs: 92.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.15010.0852.5877.4
4.856.110.0962.0987.6
4.234.8510.0811.6387.6
3.854.2310.0831.4017.6
3.573.8510.11.3697.6
3.363.5710.1091.3737.6
3.193.3610.1251.1017.7
3.053.1910.1470.9467.7
2.943.0510.1630.8247.7
2.832.9410.1410.7817.6
2.752.8310.1570.8687.6
2.672.7510.2360.7147.2
2.62.6710.2480.636.7
2.532.610.2890.6265.9
2.482.5310.330.8395.2
2.422.4810.3360.6764.5
2.382.4210.2910.5954.3
2.332.3810.3080.6334.1
2.292.3310.3010.5394
2.252.2910.3631.1013.6
ReflectionResolution: 2.249→47.76 Å / Num. obs: 17539 / % possible obs: 92.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Χ2: 1.161 / Net I/av σ(I): 14.905 / Net I/σ(I): 10.1 / Num. measured all: 116869
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.293.60.3635080.7860.1980.4171.10154.7
2.29-2.3340.3015910.8930.1570.3410.53962.9
2.33-2.384.10.3086590.8820.1570.3480.63369.7
2.38-2.424.30.2917610.9110.1460.3270.59580.5
2.42-2.484.50.3368240.9190.1670.3770.67688.2
2.48-2.535.20.339040.9110.1610.3690.83995.5
2.53-2.65.90.2899260.9640.1280.3160.62698.5
2.6-2.676.70.2489310.9810.1030.2690.6399.7
2.67-2.757.20.2369510.9920.0940.2540.714100
2.75-2.837.60.1579470.9980.0610.1690.868100
2.83-2.947.60.1419360.9990.0540.1510.781100
2.94-3.057.70.1639560.9950.0630.1750.824100
3.05-3.197.70.1479390.9910.0570.1580.946100
3.19-3.367.70.1259370.9930.0480.1341.101100
3.36-3.577.60.1099460.9940.0420.1171.373100
3.57-3.857.60.19630.9930.0390.1071.369100
3.85-4.237.60.0839400.9950.0320.0891.401100
4.23-4.857.60.0819630.9950.0310.0871.638100
4.85-6.17.60.0969610.9950.0370.1032.098100
6.1-47.767.40.0859960.9980.0330.0912.587100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.249→47.753 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2776 1666 9.95 %
Rwork0.2269 --
obs0.232 16750 88.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.09 Å2 / Biso mean: 43.971 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 2.249→47.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 30 96 2775
Biso mean--41.39 38.73 -
Num. residues----388

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