3mrj

Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide V5M variant

Method: X-RAY DIFFRACTION Dmax: 75.2 Å Quality: EXCELLENT

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–300 Fragment:HLA-A*0201 alpha chain, UNP resiude 25-300 Mutation:A245V Beta-2-microglobulin × 1 (P61769) 9-meric peptide from Serine protease/NTPase/helicase NS3 × 1 (Q03463) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;13% PEG 6000, 0.1M NaCitrate, 0.05M NaCl, 2.84mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.87 Å R-free 0.230

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 465 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 1–276; UniProt 25–300

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 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) 9-meric peptide from Serine protease/NTPase/helicase NS3 × 1 (Q03463) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;13% PEG 6000, 0.1M NaCitrate, 0.05M NaCl, 2.84mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.87 Å R-free 0.230

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

9-meric peptide from Serine protease/NTPase/helicase NS3

OrganismNot specified

UniProt Q03463

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 P; UniProt 1073–1081 Fragment:NS3 protein fragment, UNP residues 1073-1081 Mutation:V5M HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;13% PEG 6000, 0.1M NaCitrate, 0.05M NaCl, 2.84mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.87 Å R-free 0.230

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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HCVJ1
Isoform
PDB entities 3
Chains and sequence ranges Author chain P; PDBConstruct 1–9; UniProt 1073–1081

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 3mrj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3mrj
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3mrj
Deposition date deposition_date2010-04-29
Structure title titleCrystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide V5M variant
Keywords keywordsMHC class I, HLA, IMMUNE SYSTEM, IMMUNE RESPONSE, NONAPEPTIDE, VIRAL PEPTIDE, HEPATITIS C VIRUS, NS3 PROTEIN; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.25
Radius of gyration Rg (electron density) rg_electron23.05
Forward intensity I(0) i036341000.00
Molecular weight molecular_weight44699.0 kDa
Excluded volume excluded_volume55084 ų
Envelope volume envelope_volume67965 ų
Hydration-shell volume shell_volume24610 ų
Envelope diameter envelope_diameter78.7
Shell Rg shell_rg29.92
Envelope Rg envelope_rg23.17
Shape Rg shape_rg23.03
Total Rg total_rg23.91
Total atoms total_atoms3154
Residues n_residues384
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 dmax75.2
Rg (real space) rg_real24.18
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real3.6340e+07
I(0) uncertainty (real space) i0_real_error4.9070e+05
Rg (reciprocal space) rg_reciprocal24.20
I(0) (reciprocal space) i0_reciprocal36340000.0000
Solution quality estimate total_estimate0.9105
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.8
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.482
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8822000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.967

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3mrjb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3mrjb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id3mrjA01
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_id3mrjA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mrjB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)