3i6g

Newly identified epitope Mn2 from SARS-CoV M protein complexed withHLA-A*0201

Method: X-RAY DIFFRACTION Dmax: 128.2 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) Membrane protein × 1 (P59596) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;0.1M Ammonium acetate, 0.1M BIS-TRIS, pH6.0, 13-17% Polyethylene glycol 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) Membrane protein × 1 (P59596) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;0.1M Ammonium acetate, 0.1M BIS-TRIS, pH6.0, 13-17% Polyethylene glycol 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.246

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 × 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) Membrane protein × 1 (P59596) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;0.1M Ammonium acetate, 0.1M BIS-TRIS, pH6.0, 13-17% Polyethylene glycol 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Membrane protein × 1 (P59596) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;0.1M Ammonium acetate, 0.1M BIS-TRIS, pH6.0, 13-17% Polyethylene glycol 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.246

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

Membrane protein

OrganismNot specified

UniProt P59596

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 88–96 Fragment:UNP residues 88-96 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;277 K;0.1M Ammonium acetate, 0.1M BIS-TRIS, pH6.0, 13-17% Polyethylene glycol 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 88–96 Fragment:UNP residues 88-96 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;277 K;0.1M Ammonium acetate, 0.1M BIS-TRIS, pH6.0, 13-17% Polyethylene glycol 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.246

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 VME1_CVHSA
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 88–96 Author chain F; PDBConstruct 1–9; UniProt 88–96

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 3i6g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3i6g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3i6g
Deposition date deposition_date2009-07-07
Structure title titleNewly identified epitope Mn2 from SARS-CoV M protein complexed withHLA-A*0201
Keywords keywords;HLA-A2, SARS-CoV, membrane glycoprotein, Disulfide bond, Glycoprotein, Host-virus interaction, Immune response, Membrane, MHC I, Phosphoprotein, Transmembrane, Disease mutation, Glycation, Immunoglobulin domain, Pyrrolidone carboxylic acid, Secreted, Envelope protein, Golgi apparatus, Viral matrix protein, Virion, 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_guinier36.38
Radius of gyration Rg (electron density) rg_electron36.26
Forward intensity I(0) i0133178000.00
Molecular weight molecular_weight89554.0 kDa
Excluded volume excluded_volume110550 ų
Envelope volume envelope_volume146110 ų
Hydration-shell volume shell_volume36310 ų
Envelope diameter envelope_diameter134.3
Shell Rg shell_rg38.76
Envelope Rg envelope_rg36.51
Shape Rg shape_rg36.22
Total Rg total_rg36.54
Total atoms total_atoms6326
Residues n_residues768
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 dmax128.2
Rg (real space) rg_real36.81
Rg uncertainty (real space) rg_real_error1.64
I(0) (real space) i0_real1.3320e+08
I(0) uncertainty (real space) i0_real_error2.5750e+06
Rg (reciprocal space) rg_reciprocal36.55
I(0) (reciprocal space) i0_reciprocal133100000.0000
Solution quality estimate total_estimate0.7991
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.8
Skewness Skewness skewness0.583
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13380000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.657; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.588; Smooth: 0.830

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3i6gb1
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_idd3i6gb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3i6ge1
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_idd3i6ge2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id3i6gA01
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_id3i6gA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3i6gB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3i6gD01
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_id3i6gD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3i6gE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)