7V7K

Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoST)

• PDB DOI: https://doi.org/10.2210/pdb7V7K/pdb

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


• Deposited: 2021-08-21 Released: 2022-08-24 
• Deposition Author(s): Niu, J., Xu, L., Meng, B., Han, Y.B., Yang, B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 49.95 kDa 
• Atom Count: 3,605 
• Modelled Residue Count: 441 
• Deposited Residue Count: 459 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16A fab light chain	A	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
16A fab heavy chain	B	229	Mus musculus	Mutation(s): 0

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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P15941-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGA (Subject of Investigation/LOI)	D [auth C], E [auth C]	2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.052	α = 90
b = 136.622	β = 90
c = 80.993	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Niu, J., Xu, L., Meng, B., Han, Y.B., Yang, B.

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

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary