9D95 | pdb_00009d95

TRAV35/TRBV20 TCR - HLA-B38 complex

PDB DOI: https://doi.org/10.2210/pdb9D95/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, human gammaherpesvirus 4
Expression System: Escherichia coli, synthetic construct, Homo sapiens
Mutation(s): No

Deposited: 2024-08-21 Released: 2025-09-03
Deposition Author(s): Zhu, S., Petersen, J., Rossjohn, J.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.235 (Depositor), 0.234 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The ancient MHC class I molecule HLA-B*38:01 calibrates the immune system to protect against multiple sclerosis

Ladell, K., Zhu, S., Kaufmann, M., Vivian, J., Petersen, J., Rossjohn, J., Fugger, L., Price, D.

To be published.

Macromolecule Content

Total Structure Weight: 394.1 kDa
Atom Count: 25,533
Modeled Residue Count: 3,250
Deposited Residue Count: 3,424
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, F, K, P	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B, HLA-DRB1
UniProt
Find proteins for E5FQ58 (Homo sapiens) Explore E5FQ58 Go to UniProtKB: E5FQ58
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E5FQ58
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, G, L, Q	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Epstein-Barr nuclear antigen 2	C, H, M, R	10	human gammaherpesvirus 4	Mutation(s): 0 Gene Names: EBNA2, BYRF1
UniProt
Find proteins for P12978 (Epstein-Barr virus (strain B95-8)) Explore P12978 Go to UniProtKB: P12978
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12978
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha chain	D, I, N, S	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain D Focus chain I Focus chain N Focus chain S
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta chain	E, J, O, T	256	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth K] SDF format, chain MA [auth P] SDF format, chain Y [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth K] MOL2 format, chain MA [auth P] MOL2 format, chain Y [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth K] mmCIF format, chain MA [auth P] mmCIF format, chain Y [auth D]	AA [auth F], EA [auth K], MA [auth P], Y [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth K] Focus chain MA [auth P] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth K] Focus chain MA [auth P] Focus chain Y [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain DA [auth I] SDF format, chain HA [auth N] SDF format, chain IA [auth N] SDF format, chain JA [auth N] SDF format, chain KA [auth N] SDF format, chain LA [auth N] SDF format, chain OA [auth S] SDF format, chain PA [auth S] SDF format, chain QA [auth S] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth D] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth I] MOL2 format, chain HA [auth N] MOL2 format, chain IA [auth N] MOL2 format, chain JA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain LA [auth N] MOL2 format, chain OA [auth S] MOL2 format, chain PA [auth S] MOL2 format, chain QA [auth S] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth I] mmCIF format, chain HA [auth N] mmCIF format, chain IA [auth N] mmCIF format, chain JA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain LA [auth N] mmCIF format, chain OA [auth S] mmCIF format, chain PA [auth S] mmCIF format, chain QA [auth S] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D]	CA [auth I] DA [auth I] HA [auth N] IA [auth N] JA [auth N] CA [auth I], DA [auth I], HA [auth N], IA [auth N], JA [auth N], KA [auth N], LA [auth N], OA [auth S], PA [auth S], QA [auth S], V [auth D], W [auth D], X [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth I] Focus chain DA [auth I] Focus chain HA [auth N] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth S] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth I] Focus chain DA [auth I] Focus chain HA [auth N] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth S] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain FA [auth K] SDF format, chain GA [auth K] SDF format, chain NA [auth P] SDF format, chain U [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain NA [auth P] MOL2 format, chain U [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain NA [auth P] mmCIF format, chain U [auth A]	BA [auth F], FA [auth K], GA [auth K], NA [auth P], U [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth F] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain NA [auth P] Focus chain U [auth A] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain NA [auth P] Focus chain U [auth A]