[English] 日本語
Yorodumi
- PDB-5cj8: Human Osteoclast Associated Receptor (OSCAR) extracellular domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cj8
TitleHuman Osteoclast Associated Receptor (OSCAR) extracellular domain
ComponentsOsteoclast-associated immunoglobulin-like receptor
KeywordsIMMUNE SYSTEM / Immunoglobulin-like / monomer
Function / homology
Function and homology information


collagen receptor activity / 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 / Immunoglobulins / Immunoglobulin-like fold / 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: 2.015 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: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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


Theoretical massNumber of molelcules
Total (without water)20,3691
Polymers20,3691
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10030 Å2
Unit cell
Length a, b, c (Å)27.215, 46.464, 66.980
Angle α, β, γ (deg.)90.00, 93.25, 90.00
Int Tables number4
Space group name H-MP1211

-
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium fluoride, 20% w/v polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10875 / % possible obs: 99.8 % / Redundancy: 5.8 % / Net I/σ(I): 20.3

-
Processing

SoftwareName: PHENIX / Version: 1.7.3_928 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G0X, 1B6U

1g0x

1b6u


Resolution: 2.015→33.436 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 515 4.74 %
Rwork0.223 --
obs0.2247 10875 97.32 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.088 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2659 Å2-0 Å22.1303 Å2
2---3.3612 Å2-0 Å2
3---3.6271 Å2
Refinement stepCycle: LAST / Resolution: 2.015→33.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 0 67 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091456
X-RAY DIFFRACTIONf_angle_d1.3281993
X-RAY DIFFRACTIONf_dihedral_angle_d15.548532
X-RAY DIFFRACTIONf_chiral_restr0.09214
X-RAY DIFFRACTIONf_plane_restr0.007261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0149-2.21760.34481040.28272376X-RAY DIFFRACTION90
2.2176-2.53840.3491330.29542652X-RAY DIFFRACTION100
2.5384-3.19770.31061230.26452649X-RAY DIFFRACTION100
3.1977-33.44080.2091550.18222683X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.4784 Å / Origin y: 1.5404 Å / Origin z: 22.594 Å
111213212223313233
T0.2107 Å20.0021 Å2-0.0194 Å2-0.2686 Å2-0.0088 Å2--0.2451 Å2
L-0.0807 °2-0.1086 °2-0.4849 °2-0.728 °20.3315 °2--0.8866 °2
S0.0226 Å °-0.0183 Å °0.0102 Å °-0.0012 Å °0.0141 Å °-0.0338 Å °0.0921 Å °-0.0195 Å °-0 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