4f7t

Crystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009 H1N1 PB1 (498-505)

Method: X-RAY DIFFRACTION Dmax: 107.3 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-24 alpha chain

Homo sapiens

UniProt P05534

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 25–298 Fragment:unp residues 25-298 Beta-2-microglobulin × 1 (P61769) RNA-directed RNA polymerase catalytic subunit × 1 (Q9YXL6) X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;293 K;0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.227
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–298 Fragment:unp residues 25-298 Beta-2-microglobulin × 1 (P61769) RNA-directed RNA polymerase catalytic subunit × 1 (Q9YXL6) X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;293 K;0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.227

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.

28 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A24_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–275; UniProt 25–298 Author chain D; PDBConstruct 2–275; UniProt 25–298

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 Fragment:unp residues 21-119 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) RNA-directed RNA polymerase catalytic subunit × 1 (Q9YXL6) X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;293 K;0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.227
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Fragment:unp residues 21-119 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) RNA-directed RNA polymerase catalytic subunit × 1 (Q9YXL6) X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;293 K;0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.227

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 2–100; UniProt 21–119 Author chain E; PDBConstruct 2–100; UniProt 21–119

RNA-directed RNA polymerase catalytic subunit

OrganismNot specified

UniProt Q9YXL6

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 C; UniProt 498–505 Fragment:unp residues 498-505 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;293 K;0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.227
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 498–505 Fragment:unp residues 498-505 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;293 K;0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.70 Å R-free 0.227

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9YXL6_9INFA
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–8; UniProt 498–505 Author chain F; PDBConstruct 1–8; UniProt 498–505

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 4f7t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4f7t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4f7t
Deposition date deposition_date2012-05-16
Structure title titleCrystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009 H1N1 PB1 (498-505)
Keywords keywordsHLA-A*2402, 2009H1N1, HLA-A3 supertype, cross-allele 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_guinier32.49
Radius of gyration Rg (electron density) rg_electron31.78
Forward intensity I(0) i0134196000.00
Molecular weight molecular_weight88404.0 kDa
Excluded volume excluded_volume108930 ų
Envelope volume envelope_volume142770 ų
Hydration-shell volume shell_volume38389 ų
Envelope diameter envelope_diameter108.8
Shell Rg shell_rg37.97
Envelope Rg envelope_rg31.20
Shape Rg shape_rg31.77
Total Rg total_rg32.33
Total atoms total_atoms6242
Residues n_residues762
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 dmax107.3
Rg (real space) rg_real32.52
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real1.3420e+08
I(0) uncertainty (real space) i0_real_error2.2180e+06
Rg (reciprocal space) rg_reciprocal32.51
I(0) (reciprocal space) i0_reciprocal134200000.0000
Solution quality estimate total_estimate0.8850
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.2
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.358
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15050000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.824

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4f7tA01
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_id4f7tA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4f7tB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4f7tD01
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_id4f7tD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4f7tE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)