9d95

TRAV35/TRBV20 TCR - HLA-B38 complex

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

MHC class I antigen

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEXAETHYLENE GLYCOL × 1 water × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 HEXAETHYLENE GLYCOL × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E5FQ58_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 25–300 Author chain F； PDBConstruct 1–276； UniProt 25–300 Author chain K； PDBConstruct 1–276； UniProt 25–300 Author chain P； PDBConstruct 1–276； UniProt 25–300

Beta-2-microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEXAETHYLENE GLYCOL × 1 water × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 HEXAETHYLENE GLYCOL × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Epstein-Barr nuclear antigen 2 × 1 （P12978） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–100； UniProt 21–119 Author chain G； PDBConstruct 2–100； UniProt 21–119 Author chain L； PDBConstruct 2–100； UniProt 21–119 Author chain Q； PDBConstruct 2–100； UniProt 21–119

Epstein-Barr nuclear antigen 2

human gammaherpesvirus 4

UniProt P12978

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEXAETHYLENE GLYCOL × 1 water × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 HEXAETHYLENE GLYCOL × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） T cell receptor alpha chain × 1 T cell receptor beta chain × 1 SULFATE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EBNA2_EBVB9
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 14–23 Author chain H； PDBConstruct 1–10； UniProt 14–23 Author chain M； PDBConstruct 1–10； UniProt 14–23 Author chain R； PDBConstruct 1–10； UniProt 14–23

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9d95
Deposition date deposition_date	2024-08-21
Last revision last_revision	2025-09-03
Structure title title	TRAV35/TRBV20 TCR - HLA-B38 complex
Keywords keywords	TCR - peptide - HLA complex T cell Human Leucocyte Antigen Epstein Barr virus, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9d95__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9d95__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9d95__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	36.77 Å
Rg (electron density)	37.05 Å
Total Rg	37.07 Å
Atom count	6476
Residues	820
Excluded volume	113450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9d95__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9d95__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9d95__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9d95__assembly_4__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	MHC class I antigen
Molecular weight formula_weight	32029.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F,K,P
Atom count atom_count	25533

GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQICKTNTQTYRENLRIALRYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQFAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRTYLEGTCVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11879.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G,L,Q

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Epstein-Barr nuclear antigen 2
Molecular weight formula_weight	1176.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H,M,R

YHLIVDTDSL

Source Source

Source organism organism	human gammaherpesvirus 4
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	synthetic construct

Entity 4 Entity 4 polymer

Description description	T cell receptor alpha chain
Molecular weight formula_weight	23604.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I,N,S

GQQLNQSPQSMFIQEGEDVSMNCTSSSIFNTWLWYKQDPGEGPVLLIALYKAGELTSNGRLTAQFGITRKDSFLNISASIPSDVGIYFCAGRDEGTYKYIFGTGTRLKVLANIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSGSGLEVLFQ

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	T cell receptor beta chain
Molecular weight formula_weight	28660.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J,O,T

GAVVSQHPSRVICKSGTSVKIECRSLDFQATTMFWYRQFPKKSLMLMATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSARDLQGVNYGYTFGSGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADGSGLEVLFQ

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 8 Entity 8 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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Unit-cell length a length_a	102.789 Å
Unit-cell length b length_b	124.060 Å
Unit-cell length c length_c	332.542 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.2038
R_work r_work	0.2021
R_free r_free	0.2351

TRAV35/TRBV20 TCR - HLA-B38 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Epstein-Barr nuclear antigen 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9d95__assembly_1__model_1

9d95__assembly_1__model_1 | I(q)

9d95__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)