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3pqy

Crystal Structure of 6218 TCR in complex with the H2Db-PA224

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

H-2 class I histocompatibility antigen, D-B alpha chain

Mus musculus

UniProt P01899

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 5 Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 4 Consistent with protein count
2 Insufficient information Heteromer Protein 5 Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 1 Consistent with protein count
3 Insufficient information Heteromer Protein 5 Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 Consistent with protein count
4 Insufficient information Heteromer Protein 5 Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 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
1bz9 1bz9 1ce6 1ffn 1ffn 1ffo 1ffo 1ffp 1ffp 1fg2 1fg2 1fg2

203 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HA11_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–275； UniProt 26–300 Author chain F； PDBConstruct 1–275； UniProt 26–300 Author chain K； PDBConstruct 1–275； UniProt 26–300 Author chain P； PDBConstruct 1–275； UniProt 26–300

Beta-2-microglobulin

Mus musculus

UniProt P01887

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 4 Consistent with protein count
2 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 1 Consistent with protein count
3 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 Consistent with protein count
4 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6i8c

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1bii 1bqh 1bqh 1bz9 1bz9 1cd1 1cd1 1ddh 1ffn 1ffn 1ffo 1ffo

483 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name B2MG_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–99； UniProt 21–119 Author chain G； PDBConstruct 1–99； UniProt 21–119 Author chain L； PDBConstruct 1–99； UniProt 21–119 Author chain Q； PDBConstruct 1–99； UniProt 21–119

T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain

Homo sapiens

UniProt A0A075B6C4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 4 Consistent with protein count
2 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 1 Consistent with protein count
3 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 Consistent with protein count
4 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 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
3pqy 3pqy 3pqy 3pqy 7n4k 7n5c 7n5p

7 assemblies

View Construct and Data Evidence
UniProt name A0A075B6C4_MOUSE
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–88； UniProt 20–107 Author chain I； PDBConstruct 1–88； UniProt 20–107 Author chain N； PDBConstruct 1–88； UniProt 20–107 Author chain S； PDBConstruct 1–88； UniProt 20–107

T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain

Homo sapiens

UniProt K7N5N2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 4 Consistent with protein count
2 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 1 Consistent with protein count
3 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 Consistent with protein count
4 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor beta, variable 29,Human nkt tcr beta chain × 1 （A0A0G2LB96,K7N5M4） water × 3 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
3pqy 3pqy 3pqy 3pqy 5nht 5wkf 5wkf 5wkh 5wkh 6at6 6py2 6q3s

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name K7N5N2_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 109–195； UniProt 115–201 Author chain I； PDBConstruct 109–195； UniProt 115–201 Author chain N； PDBConstruct 109–195； UniProt 115–201 Author chain S； PDBConstruct 109–195； UniProt 115–201

T cell receptor beta, variable 29,Human nkt tcr beta chain

Homo sapiens

UniProt A0A0G2LB96

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 4 Consistent with protein count
2 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 1 Consistent with protein count
3 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 3 Consistent with protein count
4 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 3 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
3pqy 3pqy 3pqy 3pqy 7n4k 7n5c 7n5p

7 assemblies

View Construct and Data Evidence
UniProt name A0A0G2LB96_MOUSE
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–94； UniProt 20–113 Author chain J； PDBConstruct 1–94； UniProt 20–113 Author chain O； PDBConstruct 1–94； UniProt 20–113 Author chain T； PDBConstruct 1–94； UniProt 20–113

T cell receptor beta, variable 29,Human nkt tcr beta chain

Homo sapiens

UniProt K7N5M4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 4 Consistent with protein count
2 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 1 Consistent with protein count
3 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 3 Consistent with protein count
4 Insufficient information Heteromer Protein 5 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） 10-mer peptide from RNA-directed RNA polymerase × 1 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain × 1 （A0A075B6C4,K7N5N2） water × 3 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
3pqy 3pqy 3pqy 3pqy 4mnh 4mnh 5brz 5bs0 5men 5wlg 5wlg 6at6

30 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name K7N5M4_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 98–240； UniProt 107–249 Author chain J； PDBConstruct 98–240； UniProt 107–249 Author chain O； PDBConstruct 98–240； UniProt 107–249 Author chain T； PDBConstruct 98–240； UniProt 107–249

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_id3pqy
Deposition date deposition_date2010-11-28
Structure title titleCrystal Structure of 6218 TCR in complex with the H2Db-PA224
Keywords keywordsH2Db, influenza, TCR, T cell, PA epitope, repertoire, viral immunity, chimeric TCR, 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.

3pqy__assembly_1__model_1

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

Download this curve (.dat)

3pqy__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.

3pqy__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）38.37 Å
Rg (electron density)39.02 Å
Total Rg39.10 Å
Atom count6562
Residues812
Excluded volume115410 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3pqy__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3pqy__assembly_2__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3pqy__assembly_3__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3pqy__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 (6)

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6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id3pqyA01
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_id3pqyA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyF01
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_id3pqyF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyJ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyK01
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_id3pqyK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyN02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyO01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyO02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyP01
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_id3pqyP02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyQ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyS01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyS02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyT01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3pqyT02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)