4ZSO

Crystal structure of a complex between B7-H6, a tumor cell ligand for natural cytotoxicity receptor NKp30, and an inhibitory antibody

• PDB DOI: https://doi.org/10.2210/pdb4ZSO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), unidentified baculovirus
• Mutation(s): No 


• Deposited: 2015-05-13 Released: 2016-05-18 
• Deposition Author(s): Xu, X., Li, Y., Mariuzza, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Crystal structure of a complex between B7-H6, a tumor cell ligand for natural cytotoxicity receptor NKp30, and an inhibitory antibody

Xu, X., Li, Y., Vivier, E., Chen, Q., Mariuzza, R.A.

To be published.

Biological Assembly 1  

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

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

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)

Macromolecule Content

• Total Structure Weight: 152.25 kDa 
• Atom Count: 10,273 
• Modelled Residue Count: 1,296 
• Deposited Residue Count: 1,372 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Light Chain	A, C	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Heavy Chain	B, D	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Natural cytotoxicity triggering receptor 3 ligand 1	E, F	253	Homo sapiens	Mutation(s): 0  Gene Names: NCR3LG1, B7H6
UniProt & NIH Common Fund Data Resources
Find proteins for Q68D85 (Homo sapiens) Explore Q68D85  Go to UniProtKB:  Q68D85
PHAROS:  Q68D85 GTEx:  ENSG00000188211
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q68D85-1

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth B], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	M [auth E], N [auth F]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.634	α = 90
b = 138.029	β = 90
c = 171.441	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Xu, X., Li, Y., Mariuzza, R.A.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary