4R0L

Anti-canine CD28 antibody, 1C6, bound canine CD28

PDB DOI: https://doi.org/10.2210/pdb4R0L/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Canis lupus familiaris
Expression System: Escherichia coli BL21(DE3), Homo sapiens
Mutation(s): No

Deposited: 2014-07-31 Released: 2015-07-08
Deposition Author(s): Gewe, M.M., Strong, R.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.293
R-Value Work: 0.256
R-Value Observed: 0.258

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Anti-CD28 Antibody-Initiated Cytokine Storm in Canines.

Rosinski, S.L., Storb, R., Strong, R.K., Sale, G.E., Stone, D.M., Gewe, M.M., Friend, D.J., Abrams, V.K., Randolph-Habecker, J., Graves, S.S.

(2015) Transplant Direct 1

PubMed: 25988188 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1097/TXD.0000000000000516
Primary Citation of Related Structures:
4R0L

PubMed Abstract:
CD28 signal blockade following T cell receptor activation is under intense investigation as a tolerance-inducing therapy for transplantation. Our goal is to produce a CD28-specific reagent as a therapy for the prevention of graft rejection and graft-versus-host disease in the canine model of allogeneic hematopoietic cell transplantation (HCT).

Organizational Affiliation

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle Washington, 98109 ; Department of Medicine, University of Washington, Seattle, Washington, 98195.

Macromolecule Content

Total Structure Weight: 85.64 kDa
Atom Count: 4,887
Modelled Residue Count: 686
Deposited Residue Count: 734
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 1C6 Heavy chain	A, D [auth H]	121	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
T-cell costimulatory molecule CD28	B [auth C], C [auth D]	129	Canis lupus familiaris	Mutation(s): 0 Gene Names: CD28
UniProt
Find proteins for Q9N0N8 (Canis lupus familiaris) Explore Q9N0N8 Go to UniProtKB: Q9N0N8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9N0N8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 1C6 Light chain	E [auth L], F [auth B]	117	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
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	G [auth E], I [auth G]	3		N-Glycosylation	Interactions Focus chain G [auth E] Focus chain I [auth G] Interactions & Density Focus chain G [auth E] Focus chain I [auth G]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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 [auth F]	2		N-Glycosylation	Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D]	J [auth C], K [auth C], L [auth C], M [auth D], N [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.293
R-Value Work: 0.256
R-Value Observed: 0.258
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.783	α = 90
b = 86.783	β = 90
c = 205.804	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-08

Deposition Author(s):

Gewe, M.M.

Strong, R.K.

Revision History (Full details and data files)

Version 1.0: 2015-07-08
Type: Initial release
Version 1.1: 2016-08-03
Changes: Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary