7VAC | pdb_00007vac

Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoST)

• PDB DOI: https://doi.org/10.2210/pdb7VAC/pdb

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


• Deposited: 2021-08-28 Released: 2022-08-31 
• 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: 3.50 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 149.22 kDa 
• Atom Count: 10,013 
• Modeled Residue Count: 1,319 
• Deposited Residue Count: 1,377 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14A fab light chain	A, C, E	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
14A fab heavy chain	B, D, F	229	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-1 subunit alpha	G, H, I	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)	J [auth G], K [auth G], L [auth H], M [auth H], N [auth I], O [auth I]	2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.92	α = 90
b = 206.848	β = 90
c = 225.405	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Niu, J., Xu, L., Meng, B., Han, Y.B., Yang, B.

---

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

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary