[English] 日本語
Yorodumi
- EMDB-75133: FcgRIIa in complex with IV.3 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75133
TitleFcgRIIa in complex with IV.3 Fab
Map dataThe map of FcgRIIa-IV.3 Fab complex
Sample
  • Complex: fcgRIIa-IV.3 Fab complex
    • Complex: fcgRIIa
      • Protein or peptide: Low affinity immunoglobulin gamma Fc region receptor II-a
    • Complex: IV.3 Fab
      • Protein or peptide: IV.3 Fab heavy chain
      • Protein or peptide: IV.3 Fab light chain
Keywordsplatelet / FcgRIIa / mAb IV.3 / IMMUNE SYSTEM
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
Low affinity immunoglobulin gamma Fc region receptor II-a
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsColler BS / Wang JL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL019278-48 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanistic Basis for the Selective Recognition of the Fcγ Receptor IIa by Monoclonal Antibody IV.3.
Authors: Jialing Wang / Sabina Novack / Jihong Li / Emily G Niejadlik / Stylianos Bournazos / Barry S Coller / Marta Filizola
Abstract: The monoclonal antibody IV.3 selectively binds the platelet Fcγ receptor IIa (FcγRIIa), potently blocking immune complex engagement without cross-reacting with the closely-related FcγRIIb. This ...The monoclonal antibody IV.3 selectively binds the platelet Fcγ receptor IIa (FcγRIIa), potently blocking immune complex engagement without cross-reacting with the closely-related FcγRIIb. This specificity has made IV.3 invaluable for dissecting FcγRIIa-mediated activation in diverse conditions, including infection, autoimmunity, thromboinflammation, and platelet-mediated thrombosis. We combined cryogenic electron microscopy, surface plasmon resonance, alchemical free energy calculations, and molecular dynamics simulations to elucidate IV.3's binding sites on FcγRIIa and the mechanistic basis of IV.3 specificity. We find that IV.3 engages a broader FcγRIIa epitope than previously recognized, extending beyond residues H/R134 and L135 (R and S in FcγRIIb). Simulations of FcγIIa-R134 variants bearing either L135 or S135 reveal that IV.3 specificity arises from hydrophobic stabilization mediated by L135 and disruption of an R134-specific interaction network in the presence of S135. These findings provide a mechanistic framework for rational design of FcγRIIa-targeted therapeutics.
History
DepositionJan 16, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75133.png

Downloads & links

-
Map

FileDownload / File: emd_75133.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map of FcgRIIa-IV.3 Fab complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-6.2420034 - 8.183313
Average (Standard dev.)0.00083191274 (±0.109397516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 240.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half A map of FcgRIIa-IV.3 Fab complex

Fileemd_75133_half_map_1.map
AnnotationHalf A map of FcgRIIa-IV.3 Fab complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half A map of FcgRIIa-IV.3 Fab complex

Fileemd_75133_half_map_2.map
AnnotationHalf A map of FcgRIIa-IV.3 Fab complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : fcgRIIa-IV.3 Fab complex

EntireName: fcgRIIa-IV.3 Fab complex
Components
  • Complex: fcgRIIa-IV.3 Fab complex
    • Complex: fcgRIIa
      • Protein or peptide: Low affinity immunoglobulin gamma Fc region receptor II-a
    • Complex: IV.3 Fab
      • Protein or peptide: IV.3 Fab heavy chain
      • Protein or peptide: IV.3 Fab light chain

-
Supramolecule #1: fcgRIIa-IV.3 Fab complex

SupramoleculeName: fcgRIIa-IV.3 Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 750 KDa

-
Supramolecule #2: fcgRIIa

SupramoleculeName: fcgRIIa / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: IV.3 Fab

SupramoleculeName: IV.3 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Low affinity immunoglobulin gamma Fc region receptor II-a

MacromoleculeName: Low affinity immunoglobulin gamma Fc region receptor II-a
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.528963 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QAAAPPKAVL KLEPPWINVL QEDSVTLTCQ GARSPESDSI QWFHNGNLIP THTQPSYRFK ANNNDSGEYT CQTGQTSLSD PVHLTVLSE WLVLQTPHLE FQEGETIMLR CHSWKDKPLV KVTFFQNGKS QKFSHLDPTF SIPQANHSHS GDYHCTGNIG Y TLFSSKPV TITVQVPSMG SSSPMGI

UniProtKB: Low affinity immunoglobulin gamma Fc region receptor II-a

-
Macromolecule #2: IV.3 Fab heavy chain

MacromoleculeName: IV.3 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.493609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGAHSQ IQLVQSGPEL KKPGETVKIS CKASGYTFTN YGMNWVKQAP GKGLKWMGWL NTYTGESIYP DDFKGRFAF SSETSASTAY LQINNLKNED MATYFCARGD YGYDDPLDYW GQGTSVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV ...String:
MGWSCIILFL VATATGAHSQ IQLVQSGPEL KKPGETVKIS CKASGYTFTN YGMNWVKQAP GKGLKWMGWL NTYTGESIYP DDFKGRFAF SSETSASTAY LQINNLKNED MATYFCARGD YGYDDPLDYW GQGTSVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVV

-
Macromolecule #3: IV.3 Fab light chain

MacromoleculeName: IV.3 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.928209 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSD IVMTQAAPSV PVTPGESVSI SCRSSKSLLH TNGNTYLHWF LQRPGQSPQL LIYRMSVLAS GVPDRFSGS GSGTAFTLSI SRVEAEDVGV FYCMQHLEYP LTFGAGTKLE LKRTVDAPSV FIFPPSDEQL KSGTASVVCL L NNFYPREA ...String:
MGWSCIILFL VATATGVHSD IVMTQAAPSV PVTPGESVSI SCRSSKSLLH TNGNTYLHWF LQRPGQSPQL LIYRMSVLAS GVPDRFSGS GSGTAFTLSI SRVEAEDVGV FYCMQHLEYP LTFGAGTKLE LKRTVDAPSV FIFPPSDEQL KSGTASVVCL L NNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.4.0) / Number images used: 392060
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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