[English] 日本語
Yorodumi
- PDB-5cti: Crystal structure of the type IX collagen NC2 hetero-trimerizatio... -

+
Open data


ID or keywords:

Loading...

-
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 / Crosslinking of collagen fibrils / collagen biosynthetic process / extracellular matrix assembly ...collagen type IX trimer / collagen type I trimer / cellular response to vitamin E / tooth mineralization / protein heterotrimerization / cellular response to fluoride / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / extracellular matrix assembly / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Defective VWF binding to collagen type I / platelet-derived growth factor binding / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / bone trabecula formation / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / intramembranous ossification / Extracellular matrix organization / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / Collagen biosynthesis and modifying enzymes / skin morphogenesis / collagen metabolic process / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / endochondral ossification / Platelet Adhesion to exposed collagen / NCAM1 interactions / collagen fibril organization / face morphogenesis / response to steroid hormone / odontogenesis / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / MET activates PTK2 signaling / Scavenging by Class A Receptors / GP1b-IX-V activation signalling / Syndecan interactions / blood vessel development / SMAD binding / bone mineralization / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / cellular response to fibroblast growth factor stimulus / negative regulation of cell-substrate adhesion / protein localization to nucleus / Rho protein signal transduction / ECM proteoglycans / response to hyperoxia / Integrin cell surface interactions / positive regulation of epithelial to mesenchymal transition / response to cAMP / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / cellular response to retinoic acid / visual perception / cellular response to epidermal growth factor stimulus / transforming growth factor beta receptor signaling pathway / secretory granule / animal organ morphogenesis / skeletal system development / Cell surface interactions at the vascular wall / response to insulin / cellular response to amino acid stimulus / sensory perception of sound / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to glucose stimulus / response to hydrogen peroxide / regulation of blood pressure / cellular response to mechanical stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / protein transport / cellular response to tumor necrosis factor / response to estradiol / carbohydrate binding / protease binding / : / protein-macromolecule adaptor activity / Interleukin-4 and Interleukin-13 signaling / positive regulation of cell migration / endoplasmic reticulum lumen / response to xenobiotic stimulus / positive regulation of DNA-templated transcription / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding
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. ...: / 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-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more