8YOT | pdb_00008yot

Nanobody in complex with LILRB3

PDB DOI: https://doi.org/10.2210/pdb8YOT/pdb
EM Map EMD-39457: EMDB EMDataResource

Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
Organism(s): Vicugna pacos, Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2024-03-13 Released: 2025-06-18
Deposition Author(s): Jin, C., Shi, Y.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Nanobody in complex with LILRB3

Jin, C., Shi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 131.99 kDa
Atom Count: 7,738
Modeled Residue Count: 1,002
Deposited Residue Count: 1,200
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	A, C	124	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LILRB3	B, D	476	Homo sapiens	Mutation(s): 0 Gene Names: LILRB3
UniProt & NIH Common Fund Data Resources
Find proteins for O75022 (Homo sapiens) Explore O75022 Go to UniProtKB: O75022
PHAROS: O75022 GTEx: ENSG00000204577
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75022
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2020YFA0509300

Revision History (Full details and data files)

Version 1.0: 2025-06-18
Type: Initial release
Version 1.1: 2025-07-23
Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.