7nme

Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR

Method: X-RAY DIFFRACTION Dmax: 133.2 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt A0A411J078

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–300 Not recorded Human MHC Class I, beta 2 microglobulin × 1 (P61769) GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU × 1 4C6 Human T-cell Receptor, alpha Chain × 1 4C6 Human T-cell Receptor, beta Chain × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;291 K;Molecular Dimensions Pact Premier C06: 0.1M PCTCP buffer, 25% PEG 1500, pH 9.0 Resolution 2.20 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

24 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A411J078_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300

Human MHC Class I, beta 2 microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded MHC class I antigen × 1 (A0A411J078) GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU × 1 4C6 Human T-cell Receptor, alpha Chain × 1 4C6 Human T-cell Receptor, beta Chain × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;291 K;Molecular Dimensions Pact Premier C06: 0.1M PCTCP buffer, 25% PEG 1500, pH 9.0 Resolution 2.20 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1313 other PDB entries and 1998 assemblies. Open the comparison page and filter oligomeric states

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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 7nme

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7nme
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7nme
Deposition date deposition_date2021-02-23
Structure title titleHuman MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR
Keywords keywordsMHC Class I, A24, Diabetes related super antigen, 4C6 TCR, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.29
Radius of gyration Rg (electron density) rg_electron37.45
Forward intensity I(0) i0146041000.00
Molecular weight molecular_weight93854.0 kDa
Excluded volume excluded_volume115860 ų
Envelope volume envelope_volume158120 ų
Hydration-shell volume shell_volume38420 ų
Envelope diameter envelope_diameter136.1
Shell Rg shell_rg39.34
Envelope Rg envelope_rg37.74
Shape Rg shape_rg37.44
Total Rg total_rg37.59
Total atoms total_atoms6614
Residues n_residues816
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax133.2
Rg (real space) rg_real37.87
Rg uncertainty (real space) rg_real_error1.96
I(0) (real space) i0_real1.4600e+08
I(0) uncertainty (real space) i0_real_error2.7310e+06
Rg (reciprocal space) rg_reciprocal37.51
I(0) (reciprocal space) i0_reciprocal146000000.0000
Solution quality estimate total_estimate0.7831
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.7
Skewness Skewness skewness0.649
Kurtosis Kurtosis kurtosis-0.212
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19170000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.585; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 0.739

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7nmeA01
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_id7nmeA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7nmeD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7nmeD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)