[English] 日本語
Yorodumi
- PDB-8cha: Fc gamma RIIa 27W/131H variant ectodomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cha
TitleFc gamma RIIa 27W/131H variant ectodomain
ComponentsLow affinity immunoglobulin gamma Fc region receptor II-a
KeywordsIMMUNE SYSTEM / FcgR / Fc receptor / antibody receptor / inflammation
Function / homology
Function and homology information


IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production ...IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / cell surface receptor signaling pathway / external side of plasma membrane / Neutrophil degranulation / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
3,6,9,12,15,18-HEXAOXAICOSANE / 1,2-DIMETHOXYETHANE / CITRATE ANION / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol / TRIETHYLENE GLYCOL / PHOSPHATE ION / Low affinity immunoglobulin gamma Fc region receptor II-a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsFoy, E.G. / Thomsen, M. / Goldman, A. / Robinson, J.I.
Funding support United Kingdom, European Union, Finland, 7items
OrganizationGrant numberCountry
Other private19764
Wellcome Trust091322/2/10/2 United Kingdom
European Research Council (ERC)708051European Union
Biotechnology and Biological Sciences Research Council (BBSRC)ALERT-13 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M021610/1 United Kingdom
Academy of Finland1252206 Finland
Medical Research Council (MRC, United Kingdom)MR/K015346/1 United Kingdom
CitationJournal: To Be Published
Title: Fc gamma RIIa 27W/131H variant ectodomain
Authors: Foy, E.G. / Thomsen, M. / Goldman, A. / Robinson, J.I.
History
DepositionFeb 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Low affinity immunoglobulin gamma Fc region receptor II-a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,39911
Polymers23,4401
Non-polymers1,95910
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint4 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.931, 76.526, 108.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Low affinity immunoglobulin gamma Fc region receptor II-a / IgG Fc receptor II-a / CDw32 / Fc-gamma RII-a / Fc-gamma-RIIa / FcRII-a


Mass: 23440.430 Da / Num. of mol.: 1 / Mutation: Q27W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2 / Variant: 27W/131H / Plasmid: pOPINTTG / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P12318
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

-
Non-polymers , 8 types, 120 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-16P / 3,6,9,12,15,18-HEXAOXAICOSANE


Mass: 294.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O6
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-DXE / 1,2-DIMETHOXYETHANE


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#8: Chemical ChemComp-FWN / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M sodium phosphate citrate, pH4.2, 41% (v/v) PEG 300
PH range: 4.0-5.0 / Temp details: constant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→41.82 Å / Num. obs: 19293 / % possible obs: 99 % / Redundancy: 6.1 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Net I/σ(I): 6.3
Reflection shellResolution: 1.81→1.875 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1867 / CC1/2: 0.45 / Rpim(I) all: 0.39 / Rrim(I) all: 0.83 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIXv1.13refinement
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RY4

3ry4


Resolution: 1.81→41.817 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 907 4.74 %
Rwork0.1928 --
obs0.1944 19122 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→41.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 127 111 1539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041523
X-RAY DIFFRACTIONf_angle_d0.7562087
X-RAY DIFFRACTIONf_dihedral_angle_d13.685900
X-RAY DIFFRACTIONf_chiral_restr0.048237
X-RAY DIFFRACTIONf_plane_restr0.005255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8103-1.92370.34821580.33092950X-RAY DIFFRACTION98
1.9237-2.07220.31881600.24472979X-RAY DIFFRACTION99
2.0722-2.28070.2661240.19553014X-RAY DIFFRACTION99
2.2807-2.61070.26451460.18823026X-RAY DIFFRACTION99
2.6107-3.28910.20661530.17073069X-RAY DIFFRACTION100
3.2891-41.8170.17641660.1733177X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8424-0.7859-0.62491.2340.46823.95590.04830.53740.0403-0.2067-0.0489-0.0308-0.11310.27390.01580.2113-0.0056-0.01360.2175-0.01150.14193.9735-15.5344-16.6012
24.10310.65250.13192.29890.00480.9947-0.0756-0.04820.28310.06310.02450.063-0.0583-0.04240.0570.15460.0125-0.00680.114-0.02030.187-8.8862-9.71582.8004
37.98055.37826.6933.99434.80136.3487-0.4638-1.21094.0235-0.3172-1.57924.0248-0.7041-0.42.06960.68190.01580.05830.2914-0.02680.6887-17.67850.70634.2337
42.0079-0.5620.25155.3479-0.94155.2234-0.00390.06760.14160.25290.0655-0.33840.0333-0.1731-0.12790.70460.25420.10751.0026-0.12690.7991-5.05631.658615.5827
57.3255-3.643-3.4352.80991.55781.9624-0.4054-0.53530.37710.36990.22380.48240.0629-0.39890.07240.2915-0.01410.01360.49970.11930.4721-5.1476-6.822-15.6772
625.48078.0353.92221.80881.99980.1515-0.4067-0.15720.75350.1002-0.3060.2984-0.1731-0.39520.5066-0.08750.07020.3357-0.05650.4941-26.9802-11.90644.7823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 201 )A201
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 4 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 203 )A202 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 208 )A208

+
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://pdbjlvh1.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