1DLH | pdb_00001dlh

CRYSTAL STRUCTURE OF THE HUMAN CLASS II MHC PROTEIN HLA-DR1 COMPLEXED WITH AN INFLUENZA VIRUS PEPTIDE

PDB DOI: https://doi.org/10.2210/pdb1DLH/pdb

Classification: HISTOCOMPATIBILITY ANTIGEN
Organism(s): Homo sapiens, Influenza A virus (strain A/England/878/1969 H3N2)
Expression System: Spodoptera
Mutation(s): No

Deposited: 1994-02-15 Released: 1994-06-22
Deposition Author(s): Stern, L.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.304 (Depositor)
R-Value Work:
0.205 (Depositor)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide.

Stern, L.J., Brown, J.H., Jardetzky, T.S., Gorga, J.C., Urban, R.G., Strominger, J.L., Wiley, D.C.

(1994) Nature 368: 215-221

PubMed: 8145819 Search on PubMed
DOI: https://doi.org/10.1038/368215a0
Primary Citation Related Structures:
1DLH

PubMed Abstract:
An influenza virus peptide binds to HLA-DR1 in an extended conformation with a pronounced twist. Thirty-five per cent of the peptide surface is accessible to solvent and potentially available for interaction with the antigen receptor on T cells. Pockets in the peptide-binding site accommodate five of the thirteen side chains of the bound peptide, and explain the peptide specificity of HLA-DR1. Twelve hydrogen bonds between conserved HLA-DR1 residues and the main chain of the peptide provide a universal mode of peptide binding, distinct from the strategy used by class I histocompatibility proteins.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Harvard University, Cambridge Massachusetts 62138.

Macromolecule Content

Total Structure Weight: 90.39 kDa
Atom Count: 6,520
Modeled Residue Count: 762
Deposited Residue Count: 762
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (ALPHA CHAIN)	A, D	180	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903 Go to UniProtKB: P01903
PHAROS: P01903 GTEx: ENSG00000204287
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01903
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain D	Go to GlyGen: P01903-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (BETA CHAIN)	B, E	188	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911 Go to UniProtKB: P01911
PHAROS: P01911 GTEx: ENSG00000196126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01911
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain E	Go to GlyGen: P01911-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ENTEROTOXIN TYPE B PRECURSOR	C, F	13	Influenza A virus (strain A/England/878/1969 H3N2)	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P04664 (Influenza A virus (strain A/England/878/1969 H3N2)) Explore P04664 Go to UniProtKB: P04664
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04664
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	2		N-Glycosylation	Interactions Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G07375KG GlyCosmos: G07375KG GlyGen: G07375KG

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 L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B], K [auth D], L [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.304 (Depositor)
R-Value Work: 0.205 (Depositor)
R-Value Observed: 0.205 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.6	α = 90
b = 94.6	β = 90
c = 247.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1994-06-22

Deposition Author(s):

Stern, L.J.

Revision History (Full details and data files)

Version 1.0: 1994-06-22
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-11-13
Changes: Advisory, Data collection, Database references, Structure summary