9LOC | pdb_00009loc

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

PDB DOI: https://doi.org/10.2210/pdb9LOC/pdb
EM Map EMD-63244: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-01-23 Released: 2025-11-26
Deposition Author(s): Chen, S.H., Xiao, J.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Chen, S.H., Xiao, J.Y.

To be published.

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fc receptor-like protein 5	A	860	Homo sapiens	Mutation(s): 0 Gene Names: FCRL5, FCRH5, IRTA2, UNQ503/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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96RD9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q96RD9-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain	B, C, D, E, F B, C, D, E, F, G, H, I, J, K, L, M	250	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5 Go to UniProtKB: P0DOX5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DOX5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	6		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G39203UC GlyCosmos: G39203UC GlyGen: G39203UC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth H] SDF format, chain W [auth I] SDF format, chain X [auth J] SDF format, chain Y [auth K] SDF format, chain Z [auth L] MOL2 format, chain AA [auth M] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth H] MOL2 format, chain W [auth I] MOL2 format, chain X [auth J] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth L] mmCIF format, chain AA [auth M] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain V [auth H] mmCIF format, chain W [auth I] mmCIF format, chain X [auth J] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth L]	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		Interactions Focus chain AA [auth M] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth M] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L]