4ZSO | pdb_00004zso

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.226 (Depositor), 0.226 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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

Find similar proteins by:

| 3D Structure

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

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q68D85
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E Focus chain F	Go to GlyGen: Q68D85-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

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

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth D]	K [auth B], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain L [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth D]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F]	M [auth E], N [auth F]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain M [auth E] Focus chain N [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.257 (Depositor), 0.257 (DCC)
R-Value Work: 0.226 (Depositor), 0.226 (DCC)
R-Value Observed: 0.226 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Xu, X.

Li, Y.

Mariuzza, R.A.

Revision History (Full details and data files)

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