7V4W | pdb_00007v4w

Crystal structure of Antibody 16A in complex with MUC1 peptide

PDB DOI: https://doi.org/10.2210/pdb7V4W/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Trichopalpus nigribasis
Mutation(s): No

Deposited: 2021-08-15 Released: 2022-08-17
Deposition Author(s): Niu, J., Xu, L., Meng, B., Han, Y.B., Yang, B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Site-specific GalNAc modification on a MUC1 neoantigen epitope forms a basis for high-affinity antibody binding

Han, Y.B., Xu, L.

To be published.

Macromolecule Content

Total Structure Weight: 49.51 kDa
Atom Count: 3,574
Modeled Residue Count: 433
Deposited Residue Count: 459
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16A Fab Light chain	A	217	Mus musculus	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
16A Fab Heavy chain	B	229	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-1 subunit alpha	C	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens) Explore P15941 Go to UniProtKB: P15941
PHAROS: P15941 GTEx: ENSG00000185499
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15941
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.557	α = 90
b = 63.37	β = 97.124
c = 88.681	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-08-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2022-08-17
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

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.