6APN | pdb_00006apn

HLA-A*0201 single chain trimer with HPV.16 E7 peptide LLMGTLGIV

PDB DOI: https://doi.org/10.2210/pdb6APN/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-08-17 Released: 2018-08-22
Deposition Author(s): Finton, K.A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.260 (Depositor), 0.263 (DCC)
R-Value Work:
0.213 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Effects of HLA single chain trimer design on peptide presentation and stability

Finton, K.A.K.

To be published.

Macromolecule Content

Total Structure Weight: 100.18 kDa
Atom Count: 6,256
Modeled Residue Count: 767
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera	A, B	446	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P, HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P03129 (Human papillomavirus type 16) Explore P03129 Go to UniProtKB: P03129
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439
PHAROS: P04439 GTEx: ENSG00000206503
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P03129 P04439 P61769
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.260 (Depositor), 0.263 (DCC)
R-Value Work: 0.213 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.363	α = 90
b = 65.094	β = 96.25
c = 130.321	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-22
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.