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7pbe

Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope

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

MHC class I antigen

Homo sapiens

UniProt A0A5B8RNS7

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） Spike protein S1 × 1 （P0DTC2） Human T-cell Receptor YLQ36, alpha chain × 1 Human T-cell Receptor YLQ36, beta chain × 1 DI(HYDROXYETHYL)ETHER × 1 SULFATE ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Beta-2-microglobulin × 1 （P61769） Spike protein S1 × 1 （P0DTC2） Human T-cell Receptor YLQ36, alpha chain × 1 Human T-cell Receptor YLQ36, beta chain × 1 DI(HYDROXYETHYL)ETHER × 1 SULFATE ION × 2 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
4gkn 4gkn 6tmo 6trn 6tro 6uz1 6uz1 6vm7 6vm8 6vm9 6vma 6vmc

44 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name A0A5B8RNS7_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

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 （A0A5B8RNS7） Spike protein S1 × 1 （P0DTC2） Human T-cell Receptor YLQ36, alpha chain × 1 Human T-cell Receptor YLQ36, beta chain × 1 DI(HYDROXYETHYL)ETHER × 1 SULFATE ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 MHC class I antigen × 1 （A0A5B8RNS7） Spike protein S1 × 1 （P0DTC2） Human T-cell Receptor YLQ36, alpha chain × 1 Human T-cell Receptor YLQ36, beta chain × 1 DI(HYDROXYETHYL)ETHER × 1 SULFATE ION × 2 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 2
Chains and sequence ranges Author chain B； PDBConstruct 2–100； UniProt 21–119 Author chain G； PDBConstruct 2–100； UniProt 21–119

Spike protein S1

OrganismNot specified

UniProt P0DTC2

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 （A0A5B8RNS7） Beta-2-microglobulin × 1 （P61769） Human T-cell Receptor YLQ36, alpha chain × 1 Human T-cell Receptor YLQ36, beta chain × 1 DI(HYDROXYETHYL)ETHER × 1 SULFATE ION × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 MHC class I antigen × 1 （A0A5B8RNS7） Beta-2-microglobulin × 1 （P61769） Human T-cell Receptor YLQ36, alpha chain × 1 Human T-cell Receptor YLQ36, beta chain × 1 DI(HYDROXYETHYL)ETHER × 1 SULFATE ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
7b62 7fg7 7my8 7p5g 7p5q 7p5s 7r95 7tpk 7v22 7xiz 9n2l 9wsp

12 assemblies

Homodimer
7wxz 7wxz 7y9n 7zr2

4 assemblies

Homotetramer
6lvn 7owx

2 assemblies

Other homooligomers
6lxt 6lxt 6m1v 6x29 6x2a 6x2b 6x2c 6x45 6xs6 6zgg 6zgh 7a93

103 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
10mu 11hk 11hl 11hn 11hw 6lzg 6m0j 6m17 6vsb 6vw1 6vw1 6vxx

2353 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SPIKE_SARS2
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–9； UniProt 269–277 Author chain H； PDBConstruct 1–9； UniProt 269–277

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_id7pbe
Deposition date deposition_date2021-08-02
Structure title titleEmergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope
Keywords keywordsMHC I, A02, Wuhan epitope, SARS-COV-2, Spike protein, 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.

7pbe__assembly_1__model_1

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

Download this curve (.dat)

7pbe__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.

7pbe__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）37.47 Å
Rg (electron density)37.79 Å
Total Rg37.89 Å
Atom count6704
Residues826
Excluded volume117180 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7pbe__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 7pbe__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 (7)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7pbeA01
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_id7pbeA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7pbeF01
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_id7pbeF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)