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6avg

Crystal structure of the KFJ37 TCR-NY-ESO-1-HLA-B*07:02 complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 T-cell receptor alpha variable 4,TCR alpha chain × 1 （A0A0B4J268） T-cell receptor beta variable 9,TCR beta chain × 1 （A0A0B4J1U6） HLA class I histocompatibility antigen, B-7 alpha chain × 1 （P01889） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 T-cell receptor alpha variable 4,TCR alpha chain × 1 （A0A0B4J268） T-cell receptor beta variable 9,TCR beta chain × 1 （A0A0B4J1U6） HLA class I histocompatibility antigen, B-7 alpha chain × 1 （P01889） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1jnj 1lds 1py4 1py4 1py4 1py4 2d4d 2d4f 2vb5 2xks 2xku 2yxf

61 assemblies; showing the first 12

Homodimer
2x89 2x89 2z9t 3low 4r9h 4r9h 4ra3 4ra3 4rah 6m1b

10 assemblies

Homotetramer
2e8d 2f8o 3tlr 3tm6 3tm6 7afv

6 assemblies

Other homooligomers
3ciq 3ciq 3loz 6gk3 8a7o 8a7p 8a7q 8a7t

8 assemblies

Heteromeric or nucleic-acid complex
1a1m 1a1n 1a1o 1a6z 1a6z 1a9b 1a9b 1a9e 1agb 1agc 1agd 1age

1914 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–107； UniProt 13–119 Author chain H； PDBConstruct 1–107； UniProt 13–119

T-cell receptor alpha variable 4,TCR alpha chain

Homo sapiens

UniProt A0A0B4J268

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） T-cell receptor beta variable 9,TCR beta chain × 1 （A0A0B4J1U6） HLA class I histocompatibility antigen, B-7 alpha chain × 1 （P01889） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Beta-2-microglobulin × 1 （P61769） T-cell receptor beta variable 9,TCR beta chain × 1 （A0A0B4J1U6） HLA class I histocompatibility antigen, B-7 alpha chain × 1 （P01889） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6at6 6avf 6avg 6avg 7ndq 7ndu

6 assemblies

View Construct and Data Evidence
UniProt name A0A0B4J268_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–93； UniProt 18–109 Author chain C； PDBConstruct 2–93； UniProt 18–109

T-cell receptor beta variable 9,TCR beta chain

Homo sapiens

UniProt A0A0B4J1U6

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） T-cell receptor alpha variable 4,TCR alpha chain × 1 （A0A0B4J268） HLA class I histocompatibility antigen, B-7 alpha chain × 1 （P01889） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Beta-2-microglobulin × 1 （P61769） T-cell receptor alpha variable 4,TCR alpha chain × 1 （A0A0B4J268） HLA class I histocompatibility antigen, B-7 alpha chain × 1 （P01889） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6avg 6avg

2 assemblies

View Construct and Data Evidence
UniProt name A0A0B4J1U6_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 2–96； UniProt 20–114 Author chain E； PDBConstruct 2–96； UniProt 20–114

HLA class I histocompatibility antigen, B-7 alpha chain

Homo sapiens

UniProt P01889

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） T-cell receptor alpha variable 4,TCR alpha chain × 1 （A0A0B4J268） T-cell receptor beta variable 9,TCR beta chain × 1 （A0A0B4J1U6） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Beta-2-microglobulin × 1 （P61769） T-cell receptor alpha variable 4,TCR alpha chain × 1 （A0A0B4J268） T-cell receptor beta variable 9,TCR beta chain × 1 （A0A0B4J1U6） ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU × 1 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3vcl 4u1h 4u1k 4u1k 5eo0 5eo1 5wmn 5wmn 5wmo 5wmp 6at5 6avf

54 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name 1B07_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain F； PDBConstruct 1–362； UniProt 1–362 Author chain G； PDBConstruct 1–362； UniProt 1–362

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_id6avg
Deposition date deposition_date2017-09-02
Structure title titleCrystal structure of the KFJ37 TCR-NY-ESO-1-HLA-B*07:02 complex
Keywords keywordsHuman Leukocyte Antigen, Major histocompatibility complex, Immunoglobulin, T cell receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-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.

6avg__assembly_1__model_1

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

Download this curve (.dat)

6avg__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6avg__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）36.76 Å
Rg (electron density)37.14 Å
Total Rg37.27 Å
Atom count6579
Residues825
Excluded volume115040 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6avg__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6avg__assembly_2__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 (6)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id6avgA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6avgF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6avgG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6avgH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)