5e6i

Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2

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

TCR alpha chain,Human nkt tcr alpha chain

Homo sapiens

UniProt K7N5M3

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 beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name K7N5M3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 114–208; UniProt 116–210 Author chain F; PDBConstruct 114–208; UniProt 116–210 Author chain G; PDBConstruct 114–208; UniProt 116–210 Author chain P; PDBConstruct 114–208; UniProt 116–210

T-cell receptor beta-2 chain C region

Homo sapiens

UniProt A0A087WZ08

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A087WZ08_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–243; UniProt 19–262 Author chain H; PDBConstruct 1–243; UniProt 19–262 Author chain L; PDBConstruct 1–243; UniProt 19–262 Author chain Q; PDBConstruct 1–243; UniProt 19–262

HLA class I histocompatibility antigen, A-2 alpha chain

Homo sapiens

UniProt P01892

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) Beta-2-microglobulin × 1 (P61769) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name 1A02_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 2–276; UniProt 25–299 Author chain I; PDBConstruct 2–276; UniProt 25–299 Author chain M; PDBConstruct 2–276; UniProt 25–299 Author chain R; PDBConstruct 2–276; UniProt 25–299

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 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Matrix protein 1 × 1 (E9P5U1) Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Matrix protein 1 × 1 (E9P5U1) 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 4
Chains and sequence ranges Author chain D; PDBConstruct 2–100; UniProt 21–119 Author chain J; PDBConstruct 2–100; UniProt 21–119 Author chain N; PDBConstruct 2–100; UniProt 21–119 Author chain U; PDBConstruct 2–100; UniProt 21–119

Matrix protein 1

OrganismNot specified

UniProt E9P5U1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 TCR alpha chain,Human nkt tcr alpha chain × 1 (K7N5M3) T-cell receptor beta-2 chain C region × 1 (A0A087WZ08) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name E9P5U1_9INFA
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–9; UniProt 2–10 Author chain K; PDBConstruct 1–9; UniProt 2–10 Author chain O; PDBConstruct 1–9; UniProt 2–10 Author chain T; PDBConstruct 1–9; UniProt 2–10

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_id5e6i
Deposition date deposition_date2015-10-09
Structure title titleCrystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2
Keywords keywordsImmune system, TCR, HLA-A2, Flu, Complex; 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.

5e6i__assembly_1__model_1

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

Download this curve (.dat)

5e6i__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.

5e6i__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)37.52 Å
Rg (electron density)37.71 Å
Total Rg37.83 Å
Atom count6325
Residues806
Excluded volume110880 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5e6i__assembly_1__model_1 pentameric (5) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5e6i__assembly_2__model_1 pentameric (5) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5e6i__assembly_3__model_1 pentameric (5) Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5e6i__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 (5)

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6. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id5e6iA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iC01
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_id5e6iC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iI01
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_id5e6iI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iM01
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_id5e6iM02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iN00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iP01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iP02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iQ01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iQ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iR01
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_id5e6iR02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e6iU00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)