4e5x

Crystal structure of a complex between the human adenovirus type 2 E3-19K protein and MHC class I molecule HLA-A2/Tax

Method: X-RAY DIFFRACTION Dmax: 125.4 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-2 alpha chain

Homo sapiens

UniProt P01892

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 25–299 Fragment:heavy chain Beta-2-microglobulin × 1 (P61769) Protein Tax-1 × 1 (P0C213) Early E3 18.5 kDa glycoprotein × 1 (P68979) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 25–299 Fragment:heavy chain Beta-2-microglobulin × 1 (P61769) Protein Tax-1 × 1 (P0C213) Early E3 18.5 kDa glycoprotein × 1 (P68979) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241

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.

271 other PDB entries and 464 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A02_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–275; UniProt 25–299 Author chain D; PDBConstruct 1–275; UniProt 25–299

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Fragment:Beta 2-microglobulin HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Protein Tax-1 × 1 (P0C213) Early E3 18.5 kDa glycoprotein × 1 (P68979) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 21–119 Fragment:Beta 2-microglobulin HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Protein Tax-1 × 1 (P0C213) Early E3 18.5 kDa glycoprotein × 1 (P68979) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241

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

Protein Tax-1

OrganismNot specified

UniProt P0C213

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 11–19 Fragment:Tax peptide HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Early E3 18.5 kDa glycoprotein × 1 (P68979) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 11–19 Fragment:Tax peptide HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Early E3 18.5 kDa glycoprotein × 1 (P68979) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241

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 TAX_HTL1F
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 11–19 Author chain F; PDBConstruct 1–9; UniProt 11–19

Early E3 18.5 kDa glycoprotein

Human adenovirus 6

UniProt P68979

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 18–117 Fragment:Ad2 e3-19K HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Protein Tax-1 × 1 (P0C213) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain H; UniProt 18–117 Fragment:Ad2 e3-19K HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Protein Tax-1 × 1 (P0C213) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;290 K;0.8M succinic acid pH7.0 0.1M calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.95 Å R-free 0.241

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name E3GL_ADE06
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–100; UniProt 18–117 Author chain H; PDBConstruct 1–100; UniProt 18–117

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 4e5x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4e5x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4e5x
Deposition date deposition_date2012-03-14
Structure title titleCrystal structure of a complex between the human adenovirus type 2 E3-19K protein and MHC class I molecule HLA-A2/Tax
Keywords keywords;Ad2 E3-19K-HLA-A2 complex, unique tertiary structure, Adenovirus E3-19K, Immune evasion function, MHC class I molecule, Endoplasmic reticulum, IMMUNE SYSTEM-TRANSCRIPTION complex ;; IMMUNE SYSTEM/TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.97
Radius of gyration Rg (electron density) rg_electron37.81
Forward intensity I(0) i0202028000.00
Molecular weight molecular_weight112900.0 kDa
Excluded volume excluded_volume140130 ų
Envelope volume envelope_volume191310 ų
Hydration-shell volume shell_volume43450 ų
Envelope diameter envelope_diameter125.0
Shell Rg shell_rg42.11
Envelope Rg envelope_rg37.63
Shape Rg shape_rg37.78
Total Rg total_rg38.19
Total atoms total_atoms7967
Residues n_residues964
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 dmax125.4
Rg (real space) rg_real38.08
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real2.0200e+08
I(0) uncertainty (real space) i0_real_error3.4330e+06
Rg (reciprocal space) rg_reciprocal38.02
I(0) (reciprocal space) i0_reciprocal202000000.0000
Solution quality estimate total_estimate0.8936
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.8
Skewness Skewness skewness0.323
Kurtosis Kurtosis kurtosis-0.630
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17520000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.938

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4e5xA01
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_id4e5xA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4e5xB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4e5xD01
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_id4e5xD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4e5xE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4e5xG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3530
Domain ID domain_id4e5xH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3530

8. Citations (1)

9. Files and Curves (10)