7t5m

Structure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex

Method: X-RAY DIFFRACTION Dmax: 100.3 Å Quality: EXCELLENT

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

MHC class I antigen

Homo sapiens

UniProt Q861F7

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded Beta-2-microglobulin × 1 (P61769) Interleukin-27 receptor subunit alpha × 1 (Q6UWB1) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;273 K;0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine), 0.1M of Na-HEPES and MOPS buffer at pH 7.5, 20% W/V Glycerol and 10% W/V PEG 4000 Resolution 1.67 Å R-free 0.208
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–278 Not recorded Beta-2-microglobulin × 1 (P61769) Interleukin-27 receptor subunit alpha × 1 (Q6UWB1) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;273 K;0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine), 0.1M of Na-HEPES and MOPS buffer at pH 7.5, 20% W/V Glycerol and 10% W/V PEG 4000 Resolution 1.67 Å R-free 0.208

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.

31 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q861F7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–278; UniProt 1–278 Author chain C; PDBConstruct 1–278; UniProt 1–278

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded MHC class I antigen × 1 (Q861F7) Interleukin-27 receptor subunit alpha × 1 (Q6UWB1) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;273 K;0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine), 0.1M of Na-HEPES and MOPS buffer at pH 7.5, 20% W/V Glycerol and 10% W/V PEG 4000 Resolution 1.67 Å R-free 0.208
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 21–119 Not recorded MHC class I antigen × 1 (Q861F7) Interleukin-27 receptor subunit alpha × 1 (Q6UWB1) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;273 K;0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine), 0.1M of Na-HEPES and MOPS buffer at pH 7.5, 20% W/V Glycerol and 10% W/V PEG 4000 Resolution 1.67 Å R-free 0.208

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 1997 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 1–99; UniProt 21–119 Author chain D; PDBConstruct 1–99; UniProt 21–119

Interleukin-27 receptor subunit alpha

OrganismNot specified

UniProt Q6UWB1

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 617–636 Fragment:residues 617-636 MHC class I antigen × 1 (Q861F7) Beta-2-microglobulin × 1 (P61769) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;273 K;0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine), 0.1M of Na-HEPES and MOPS buffer at pH 7.5, 20% W/V Glycerol and 10% W/V PEG 4000 Resolution 1.67 Å R-free 0.208
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 617–636 Fragment:residues 617-636 MHC class I antigen × 1 (Q861F7) Beta-2-microglobulin × 1 (P61769) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;273 K;0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine), 0.1M of Na-HEPES and MOPS buffer at pH 7.5, 20% W/V Glycerol and 10% W/V PEG 4000 Resolution 1.67 Å R-free 0.208

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name I27RA_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–20; UniProt 617–636 Author chain F; PDBConstruct 1–20; UniProt 617–636

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 7t5m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7t5m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7t5m
Deposition date deposition_date2021-12-12
Structure title titleStructure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex
Keywords keywordsHLA, long epitope, 20mer, T cell recognition, 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_guinier32.66
Radius of gyration Rg (electron density) rg_electron31.71
Forward intensity I(0) i0140444000.00
Molecular weight molecular_weight90950.0 kDa
Excluded volume excluded_volume112330 ų
Envelope volume envelope_volume153530 ų
Hydration-shell volume shell_volume39769 ų
Envelope diameter envelope_diameter106.7
Shell Rg shell_rg39.50
Envelope Rg envelope_rg30.59
Shape Rg shape_rg31.72
Total Rg total_rg32.37
Total atoms total_atoms6427
Residues n_residues783
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 dmax100.3
Rg (real space) rg_real32.49
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real1.4040e+08
I(0) uncertainty (real space) i0_real_error2.1080e+06
Rg (reciprocal space) rg_reciprocal32.57
I(0) (reciprocal space) i0_reciprocal140500000.0000
Solution quality estimate total_estimate0.9098
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.7
Skewness Skewness skewness0.096
Kurtosis Kurtosis kurtosis-0.649
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14810000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.932

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7t5mA01
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_id7t5mA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7t5mC01
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_id7t5mC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)