[English] 日本語
Yorodumi
- PDB-8h7j: The crystal structure of CD163 SRCR5-9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h7j
TitleThe crystal structure of CD163 SRCR5-9
ComponentsScavenger receptor cysteine-rich type 1 protein M130
KeywordsENDOCYTOSIS / CD163 / arterivirus receptor / SRCR / long-range SRCR repeat / putative arterivirus interaction domains
Function / homology
Function and homology information


acute-phase response / virus receptor activity / external side of plasma membrane / extracellular region
Similarity search - Function
SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain
Similarity search - Domain/homology
Scavenger receptor cysteine-rich type 1 protein M130
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, Z.P. / Li, R. / Ma, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: The crystal structure of CD163 SRCR5-9
Authors: Ma, H.F. / Li, R. / Luo, Z.P.
History
DepositionOct 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Scavenger receptor cysteine-rich type 1 protein M130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8646
Polymers60,5161
Non-polymers2,3485
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.328, 60.085, 85.424
Angle α, β, γ (deg.)90.000, 114.120, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Scavenger receptor cysteine-rich type 1 protein M130


Mass: 60516.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CD163, M130 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q2VL90
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-2-3/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 4000, 0.15M potassium sodium tartrate tetra-hydrate pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20350 / % possible obs: 98.7 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.059 / Net I/σ(I): 21.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.552 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1962 / CC1/2: 0.761 / Rpim(I) all: 0.779 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JFB

5jfb


Resolution: 2.5→48.487 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.676 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 1.026 / ESU R Free: 0.268
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2123 936 4.811 %
Rwork0.1822 18519 -
all0.184 --
obs-19455 94.031 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 59.455 Å2
Baniso -1Baniso -2Baniso -3
1--0.066 Å2-0 Å20.067 Å2
2---0.411 Å20 Å2
3---0.297 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 156 111 4397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124415
X-RAY DIFFRACTIONr_bond_other_d0.0090.0163670
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6486004
X-RAY DIFFRACTIONr_angle_other_deg0.5521.578612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6835554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.186527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88910640
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.66910188
X-RAY DIFFRACTIONr_chiral_restr0.0630.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.025083
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02858
X-RAY DIFFRACTIONr_nbd_refined0.1460.2583
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23283
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22148
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.10.22203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.218
X-RAY DIFFRACTIONr_nbd_other0.1690.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.29
X-RAY DIFFRACTIONr_mcbond_it9.90811.9612219
X-RAY DIFFRACTIONr_mcbond_other9.88511.962219
X-RAY DIFFRACTIONr_mcangle_it12.18522.3922772
X-RAY DIFFRACTIONr_mcangle_other12.18422.3962773
X-RAY DIFFRACTIONr_scbond_it12.50213.6342196
X-RAY DIFFRACTIONr_scbond_other12.49913.6372197
X-RAY DIFFRACTIONr_scangle_it15.44724.8033232
X-RAY DIFFRACTIONr_scangle_other15.44424.8063233
X-RAY DIFFRACTIONr_lrange_it16.699120.51317963
X-RAY DIFFRACTIONr_lrange_other16.707120.5617930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5610.287460.221911X-RAY DIFFRACTION64.1421
2.561-2.6310.227610.2151167X-RAY DIFFRACTION82.638
2.631-2.7070.26620.2071229X-RAY DIFFRACTION89.4664
2.707-2.790.263630.2011248X-RAY DIFFRACTION95.0689
2.79-2.8820.21590.1821275X-RAY DIFFRACTION98.0882
2.882-2.9820.263640.1811226X-RAY DIFFRACTION98.9264
2.982-3.0950.247510.1871193X-RAY DIFFRACTION98.8871
3.095-3.220.221690.1721143X-RAY DIFFRACTION97.8998
3.22-3.3630.253520.181085X-RAY DIFFRACTION96.6837
3.363-3.5260.164590.1671048X-RAY DIFFRACTION99.5504
3.526-3.7160.17520.1651021X-RAY DIFFRACTION99.6286
3.716-3.940.207480.16947X-RAY DIFFRACTION99.2024
3.94-4.210.17500.155896X-RAY DIFFRACTION99.1614
4.21-4.5440.154430.156827X-RAY DIFFRACTION98.3051
4.544-4.9740.18330.152771X-RAY DIFFRACTION96.6346
4.974-5.5530.211310.184714X-RAY DIFFRACTION99.866
5.553-6.3980.297360.228624X-RAY DIFFRACTION100
6.398-7.8030.214230.206531X-RAY DIFFRACTION98.227

+
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