[English] 日本語
Yorodumi
- PDB-9elz: CRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG2 FC FRAG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9elz
TitleCRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG2 FC FRAGMENT- FC-GAMMA RECEPTOR IIA COMPLEX H131 VARIANT
Components
  • IgG receptor IIA H131 variant Fc fragment
  • IgG2 Fc
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT / FC GAMMA RECEPTOR IIA / CD32A
Function / homology
Function and homology information


regulation of immune system process / IgG binding / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor III-A
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI162242 United States
CitationJournal: Front Immunol / Year: 2025
Title: Cross-species analysis of FcgRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque.
Authors: Tolbert, W.D. / Nhan, P.B. / Conley, H.E. / Ge, X. / Chandravanshi, M. / Lee, M. / Veilleux, J. / Korzeniowski, M. / Gottumukkala, S. / Ackerman, M.E. / Pollara, J. / Pazgier, M.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IgG2 Fc
B: IgG2 Fc
C: IgG receptor IIA H131 variant Fc fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5688
Polymers69,5853
Non-polymers3,9835
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.123, 128.123, 253.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-501-

MPD

-
Components

-
Antibody / Protein / Non-polymers , 3 types, 4 molecules ABC

#1: Antibody IgG2 Fc


Mass: 25078.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein IgG receptor IIA H131 variant Fc fragment


Mass: 19428.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: FCGR2B / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: F6TRF8
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

-
Sugars , 3 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-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: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, 0.1 M magnesium acetate, 0.1 M MOPS pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.95369 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2023
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 21259 / % possible obs: 98.2 % / Redundancy: 17.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.048 / Net I/σ(I): 17.9
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 807 / CC1/2: 0.48 / Rpim(I) all: 0.481 / % possible all: 77

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→28.92 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.306 1057 4.99 %
Rwork0.275 --
obs0.277 21202 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 268 0 5035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095162
X-RAY DIFFRACTIONf_angle_d1.3347045
X-RAY DIFFRACTIONf_dihedral_angle_d10.943778
X-RAY DIFFRACTIONf_chiral_restr0.07842
X-RAY DIFFRACTIONf_plane_restr0.01877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.40411190.38782051X-RAY DIFFRACTION82
3.31-3.480.37791450.3792480X-RAY DIFFRACTION99
3.48-3.70.38521160.32812546X-RAY DIFFRACTION100
3.7-3.990.34541250.31052550X-RAY DIFFRACTION100
3.99-4.390.26791440.27352537X-RAY DIFFRACTION100
4.39-5.020.26051440.23672558X-RAY DIFFRACTION100
5.02-6.310.30391320.27252629X-RAY DIFFRACTION100
6.31-28.920.29171320.24542794X-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)
14.8257-0.75060.09394.97070.50185.4143-0.5839-1.54681.6440.84250.2473-0.9401-0.25020.35560.04150.66840.335-0.41611.2551-0.49550.940550.6479.058
22.2901-0.03661.75991.8609-0.07355.2739-0.5914-1.14032.38690.25710.062-0.8162-1.4419-0.15820.55831.17730.1802-0.52861.4557-0.88582.186539.15271.80.154
35.3057-1.64743.46222.1101-1.62715.35370.51040.5016-0.2429-0.1801-0.30820.11080.5282-0.0391-0.20820.81070.17670.0531.0529-0.18740.277117.54641.108-30.843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 233:444 )
2X-RAY DIFFRACTION2(CHAIN B AND RESID 230:444 )
3X-RAY DIFFRACTION3(CHAIN C AND RESID -1:171 )

+
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