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

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Basic information

Entry
Database: PDB / ID: 5cti
TitleCrystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment a2a1a1 of type I collagen (native form)
Components
  • Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain
  • Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
  • Collagen alpha-2(I) chain,Collagen alpha-2(IX) chain
KeywordsSTRUCTURAL PROTEIN / collagen / hetero-trimerization / chain stagger / chain register / triple helix
Function / homology
Function and homology information


collagen type IX trimer / collagen type I trimer / cellular response to vitamin E / tooth mineralization / protein heterotrimerization / cellular response to fluoride / Anchoring fibril formation / intramembranous ossification / Crosslinking of collagen fibrils / collagen biosynthetic process ...collagen type IX trimer / collagen type I trimer / cellular response to vitamin E / tooth mineralization / protein heterotrimerization / cellular response to fluoride / Anchoring fibril formation / intramembranous ossification / Crosslinking of collagen fibrils / collagen biosynthetic process / extracellular matrix assembly / 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 / extracellular matrix structural constituent conferring tensile strength / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Extracellular matrix organization / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / skin morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / Signaling by PDGF / Platelet Adhesion to exposed collagen / NCAM1 interactions / collagen fibril organization / response to steroid hormone / face morphogenesis / odontogenesis / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Scavenging by Class A Receptors / GP1b-IX-V activation signalling / Syndecan interactions / blood vessel development / SMAD binding / bone mineralization / Platelet Aggregation (Plug Formation) / RUNX2 regulates osteoblast differentiation / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / negative regulation of cell-substrate adhesion / response to cAMP / response to hyperoxia / protein localization to nucleus / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / GPVI-mediated activation cascade / Rho protein signal transduction / cellular response to retinoic acid / cellular response to fibroblast growth factor stimulus / visual perception / transforming growth factor beta receptor signaling pathway / secretory granule / cellular response to epidermal growth factor stimulus / animal organ morphogenesis / skeletal system development / Cell surface interactions at the vascular wall / cellular response to amino acid stimulus / cellular response to glucose stimulus / response to hydrogen peroxide / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / sensory perception of sound / cellular response to mechanical stimulus / response to insulin / regulation of blood pressure / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / osteoblast differentiation / cellular response to tumor necrosis factor / positive regulation of canonical Wnt signaling pathway / response to estradiol / protein transport / : / carbohydrate binding / protease binding / Interleukin-4 and Interleukin-13 signaling / protein-macromolecule adaptor activity / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein 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 / Thrombospondin N-terminal -like domains. / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. ...Fibrillar collagen, C-terminal / : / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / Thrombospondin N-terminal -like domains. / : / 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-2(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 / MOLECULAR REPLACEMENT / Resolution: 1.8994 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 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 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
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-2(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)21,1926
Polymers20,9163
Non-polymers2763
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-70 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.777, 55.912, 61.660
Angle α, β, γ (deg.)90.000, 92.350, 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: 7020.964 Da / Num. of mol.: 1 / 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): BL21(DE3) / References: UniProt: P02452, UniProt: P20849
#2: Protein Collagen alpha-2(I) chain,Collagen alpha-2(IX) chain / Alpha-2 type I collagen


Mass: 6895.721 Da / Num. of mol.: 1 / Fragment: UNP Residues 484-495,UNP Residues 517-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A2, COL9A2 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08123, 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.: 1 / 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): BL21(DE3) / References: UniProt: P02452, UniProt: Q14050
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 0.2 M sodium acetate, 17% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 724 / Detector: CCD / Date: Jan 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8994→50 Å / Num. obs: 14864 / % possible obs: 99.1 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.068 / Χ2: 1.607 / Net I/av σ(I): 40.585 / Net I/σ(I): 15.3 / Num. measured all: 176334
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8994-1.9340.4197001.794.7
1.93-1.975.20.3727251.82596.8
1.97-2.016.20.2987111.70895.4
2.01-2.057.40.267061.71797.5
2.05-2.098.50.247501.55898.6
2.09-2.1410.60.1987671.5299.4
2.14-2.1912.90.1877041.58799.6
2.19-2.2513.20.1677471.539100
2.25-2.3213.30.1527771.53100
2.32-2.3913.50.1347311.504100
2.39-2.4813.80.127401.513100
2.48-2.58140.1137541.544100
2.58-2.714.10.1067431.56100
2.7-2.8414.10.0737571.536100
2.84-3.0214.10.0677421.51100
3.02-3.2514.20.0597481.494100
3.25-3.5814.20.0457581.54100
3.58-4.0914.30.0377581.522100
4.09-5.1614.30.0337631.608100
5.16-5013.90.0437832.39199.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CTD

5ctd


Resolution: 1.8994→30.804 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 1484 10 %
Rwork0.1595 13352 -
obs0.1634 14836 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.42 Å2 / Biso mean: 26.6441 Å2 / Biso min: 6.69 Å2
Refinement stepCycle: final / Resolution: 1.8994→30.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 42 145 1622
Biso mean--44.43 33.07 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111524
X-RAY DIFFRACTIONf_angle_d1.4562083
X-RAY DIFFRACTIONf_chiral_restr0.047197
X-RAY DIFFRACTIONf_plane_restr0.008306
X-RAY DIFFRACTIONf_dihedral_angle_d13.445618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8994-1.96070.27841250.221171129695
1.9607-2.03070.22161420.16941151129396
2.0307-2.1120.19591270.16241199132698
2.112-2.20810.211390.144312101349100
2.2081-2.32450.18231370.143612441381100
2.3245-2.47010.20281300.140612061336100
2.4701-2.66070.19081430.152912201363100
2.6607-2.92830.19511320.15411216134899
2.9283-3.35150.20051360.168212261362100
3.3515-4.22090.181310.148512461377100
4.2209-30.80810.19791420.174812631405100

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