[English] 日本語
Yorodumi
- PDB-5cjb: Human Osteoclast Associated Receptor (OSCAR) in complex with a co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cjb
TitleHuman Osteoclast Associated Receptor (OSCAR) in complex with a collagen-like peptide
Components
  • Osteoclast-associated immunoglobulin-like receptor
  • collagen-like peptide
KeywordsIMMUNE SYSTEM/STRUCTURAL PROTEIN / Immunoglobulin-like / Collagen / IMMUNE SYSTEM-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


collagen receptor activity / immune response-regulating signaling pathway / osteoclast differentiation / specific granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / tertiary granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Osteoclast-associated immunoglobulin-like receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsGao, G.F. / Qi, J. / Shi, Y. / Haywood, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis of collagen recognition by human osteoclast-associated receptor and design of osteoclastogenesis inhibitors.
Authors: Haywood, J. / Qi, J. / Chen, C.C. / Lu, G. / Liu, Y. / Yan, J. / Shi, Y. / Gao, G.F.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Data collection / Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Osteoclast-associated immunoglobulin-like receptor
B: collagen-like peptide
C: collagen-like peptide
D: collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)27,0334
Polymers27,0334
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-18 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.940, 48.424, 118.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Osteoclast-associated immunoglobulin-like receptor / hOSCAR / Polymeric immunoglobulin receptor 3 / Poly-Ig receptor 3


Mass: 20369.395 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSCAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYS5
#2: Protein/peptide collagen-like peptide


Mass: 2221.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% polyvinyl alcohol type II, 0.2M potassium acetate pH 7, 0.1M HEPES NaOH

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. obs: 10822 / % possible obs: 99.7 % / Redundancy: 5.9 % / Net I/σ(I): 18.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CJ8

5cj8


Resolution: 2.398→37.438 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 521 4.81 %
Rwork0.222 --
obs0.224 10822 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.398→37.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 0 27 1858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091916
X-RAY DIFFRACTIONf_angle_d1.2322637
X-RAY DIFFRACTIONf_dihedral_angle_d14.054715
X-RAY DIFFRACTIONf_chiral_restr1.316276
X-RAY DIFFRACTIONf_plane_restr0.005346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.398-2.63920.33691530.31222488X-RAY DIFFRACTION100
2.6392-3.0210.31421230.27492562X-RAY DIFFRACTION100
3.021-3.80550.2621220.23582564X-RAY DIFFRACTION100
3.8055-37.44260.22751230.18312687X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.2318 Å / Origin y: -17.2181 Å / Origin z: -7.3802 Å
111213212223313233
T0.3168 Å20.0311 Å2-0.0015 Å2-0.3204 Å20.0041 Å2--0.3482 Å2
L1.0094 °20.0889 °20.3863 °2-0.8891 °2-0.1207 °2--0.7527 °2
S0.0006 Å °-0.0441 Å °-0.0804 Å °-0.0479 Å °0.0073 Å °0.0079 Å °0.0206 Å °0.0637 Å °0.0068 Å °
Refinement TLS groupSelection details: all

+
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