9LOC | pdb_00009loc

Cryo-EM structure of human FcRL5 bound to IgG-Fc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9LOC

This is version 1.2 of the entry. See complete history

Literature

Human FcRL5 is an Fc receptor that simultaneously engages two IgGs.

Chen, S.Li, S.Zhang, Z.Xiao, J.

(2026) Sci Adv 12: eaeb8865-eaeb8865

  • DOI: https://doi.org/10.1126/sciadv.aeb8865
  • Primary Citation Related Structures: 
    9LOC, 9LOD

  • PubMed Abstract: 

    The Fc receptors play crucial roles in initiating the effector functions of immunoglobulins. FcRL5 is a prominent target in B cell malignancies and has been implicated as a receptor for immunoglobulin G (IgG). However, the molecular mechanism remained unclear. Here, we demonstrate that human FcRL5, but not its mouse counterpart, is a bona fide IgG-Fc (Fcγ) receptor that uniquely requires the presence of two Fcγ molecules in close proximity to form a robust interaction. Cryo-electron microscopy reveals that FcRL5 optimally engages two Fcγ molecules positioned at a 60° angle, with its D1-D2 domains binding to the first Fcγ molecule, while its D3 domain arches over the second Fcγ. This distinctive binding capability enables FcRL5 to specifically recognize IgG immune complexes (ICs), with the binding strength correlating with IgG concentration in the ICs. In addition, we demonstrate that FcRL5 can internalize the IgG polymer and IC. These results shed light on FcRL5 function and reveal a unique Fcγ-FcγR binding mode governed by avidity.


  • Organizational Affiliation
    • Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, P.R. China.

Macromolecule Content 

  • Total Structure Weight: 435.47 kDa 
  • Atom Count: 23,545 
  • Modeled Residue Count: 2,916 
  • Deposited Residue Count: 3,860 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fc receptor-like protein 5860Homo sapiensMutation(s): 0 
Gene Names: FCRL5FCRH5IRTA2UNQ503/PRO820
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RD9 (Homo sapiens)
Explore Q96RD9 
Go to UniProtKB:  Q96RD9
PHAROS:  Q96RD9
GTEx:  ENSG00000143297 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RD9
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q96RD9-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin gamma-1 heavy chain
B, C, D, E, F
B, C, D, E, F, G, H, I, J, K, L, M
250Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX5
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
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
N
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G39203UC
GlyCosmos: G39203UC
GlyGen: G39203UC

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth M]
O [auth A]
P [auth B]
Q [auth C]
R [auth D]
AA [auth M],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-21
    Changes: Data collection, Database references