4hkj

Structure of Cowpox CPXV203 in complex with MHCI (H-2Kb)

Method: X-RAY DIFFRACTION Dmax: 157.8 Å Quality: REASONABLE

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

H-2 class I histocompatibility antigen, K-B alpha chain

Mus musculus

UniProt P01901

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 22–301 Fragment:extracellular domain (UNP residues 22-301) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 22–301 Fragment:extracellular domain (UNP residues 22-301) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 22–301 Fragment:extracellular domain (UNP residues 22-301) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain M; UniProt 22–301 Fragment:extracellular domain (UNP residues 22-301) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253

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.

83 other PDB entries and 137 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HA1B_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–280; UniProt 22–301 Author chain E; PDBConstruct 1–280; UniProt 22–301 Author chain I; PDBConstruct 1–280; UniProt 22–301 Author chain M; PDBConstruct 1–280; UniProt 22–301

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:UNP residues 21-119 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 21–119 Fragment:UNP residues 21-119 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain J; UniProt 21–119 Fragment:UNP residues 21-119 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain N; UniProt 21–119 Fragment:UNP residues 21-119 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Ovalbumin × 1 (P01012) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253

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 1995 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 F; PDBConstruct 2–100; UniProt 21–119 Author chain J; PDBConstruct 2–100; UniProt 21–119 Author chain N; PDBConstruct 2–100; UniProt 21–119

Ovalbumin

OrganismNot specified

UniProt P01012

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 258–265 Fragment:UNP residues 258-265 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 258–265 Fragment:UNP residues 258-265 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain K; UniProt 258–265 Fragment:UNP residues 258-265 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain O; UniProt 258–265 Fragment:UNP residues 258-265 H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) CPXV203 protein × 1 (Q8QMP2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253

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.

10 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OVAL_CHICK
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–8; UniProt 258–265 Author chain G; PDBConstruct 1–8; UniProt 258–265 Author chain K; PDBConstruct 1–8; UniProt 258–265 Author chain O; PDBConstruct 1–8; UniProt 258–265

CPXV203 protein

Cowpox virus

UniProt Q8QMP2

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 D; UniProt 17–221 Fragment:UNP residues 17-221 Non-standard monomer:Yes (specific site not provided by mmCIF) H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain H; UniProt 17–221 Fragment:UNP residues 17-221 Non-standard monomer:Yes (specific site not provided by mmCIF) H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain L; UniProt 17–221 Fragment:UNP residues 17-221 Non-standard monomer:Yes (specific site not provided by mmCIF) H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain P; UniProt 17–221 Fragment:UNP residues 17-221 Non-standard monomer:Yes (specific site not provided by mmCIF) H-2 class I histocompatibility antigen, K-B alpha chain × 1 (P01901) Beta-2-microglobulin × 1 (P61769) Ovalbumin × 1 (P01012) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.55;293 K;10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.253

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 Q8QMP2_COWPX
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 2–206; UniProt 17–221 Author chain H; PDBConstruct 2–206; UniProt 17–221 Author chain L; PDBConstruct 2–206; UniProt 17–221 Author chain P; PDBConstruct 2–206; UniProt 17–221

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 4hkj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4hkj
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4hkj
Deposition date deposition_date2012-10-15
Structure title titleStructure of Cowpox CPXV203 in complex with MHCI (H-2Kb)
Keywords keywords;viral immune evasion proteins, antigen presentation, structural genomics, NIAID, National Institute of Allergy and Infectious Diseases, Center for Structural Genomics of Infectious Diseases, CSGID, inhibitor, intracellular, IMMUNE SYSTEM-VIRAL PROTEIN complex ;; IMMUNE SYSTEM/VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier46.56
Radius of gyration Rg (electron density) rg_electron46.25
Forward intensity I(0) i01075700000.00
Molecular weight molecular_weight264500.0 kDa
Excluded volume excluded_volume327390 ų
Envelope volume envelope_volume461400 ų
Hydration-shell volume shell_volume82354 ų
Envelope diameter envelope_diameter160.8
Shell Rg shell_rg51.24
Envelope Rg envelope_rg45.39
Shape Rg shape_rg46.21
Total Rg total_rg46.59
Total atoms total_atoms18588
Residues n_residues2272
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 dmax157.8
Rg (real space) rg_real46.60
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real1.0760e+09
I(0) uncertainty (real space) i0_real_error1.8890e+07
Rg (reciprocal space) rg_reciprocal46.56
I(0) (reciprocal space) i0_reciprocal1076000000.0000
Solution quality estimate total_estimate0.6488
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.1
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.400
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha149300000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 0.021; Positv: 1.000; Valcen: 0.999; Smooth: 0.878

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id4hkjA01
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_id4hkjA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology240 — Viral Chemokine Inhibitor; Chain A
Homologous superfamily homologous superfamily30
Domain ID domain_id4hkjE01
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_id4hkjE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology240 — Viral Chemokine Inhibitor; Chain A
Homologous superfamily homologous superfamily30
Domain ID domain_id4hkjI01
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_id4hkjI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology240 — Viral Chemokine Inhibitor; Chain A
Homologous superfamily homologous superfamily30
Domain ID domain_id4hkjM01
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_id4hkjM02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjN00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4hkjP00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology240 — Viral Chemokine Inhibitor; Chain A
Homologous superfamily homologous superfamily30

8. Citations (1)

9. Files and Curves (10)