3i6l

Newly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402

Method: X-RAY DIFFRACTION Dmax: 74.6 Å Quality: EXCELLENT

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 D; UniProt 25–298 Fragment:alpha 1-3 regions, UNP residues 25-298 Beta-2-microglobulin × 1 (P61769) Nucleoprotein peptide × 1 (P59595) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.9;277 K;0.2M Ammonium sulfate, 0.1M Tris pH 8.9, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.284

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 46 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 D; PDBConstruct 1–274; 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 E; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Nucleoprotein peptide × 1 (P59595) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.9;277 K;0.2M Ammonium sulfate, 0.1M Tris pH 8.9, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.284

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 E; PDBConstruct 2–100; UniProt 21–119

Nucleoprotein peptide

OrganismNot specified

UniProt P59595

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 F; UniProt 346–354 Fragment:UNP residue 346-354 HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.9;277 K;0.2M Ammonium sulfate, 0.1M Tris pH 8.9, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.284

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.

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCAP_CVHSA
Isoform
PDB entities 3
Chains and sequence ranges Author chain F; PDBConstruct 1–9; UniProt 346–354

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 3i6l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3i6l
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3i6l
Deposition date deposition_date2009-07-07
Structure title titleNewly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402
Keywords keywords;HLA-A*2402, SARS-CoV, nucleocapsid protein, Disulfide bond, Glycoprotein, Host-virus interaction, Immune response, Membrane, MHC I, Transmembrane, Disease mutation, Glycation, Immunoglobulin domain, Pyrrolidone carboxylic acid, Secreted, Golgi apparatus, Phosphoprotein, Ribonucleoprotein, RNA-binding, Viral nucleoprotein, 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_guinier24.07
Radius of gyration Rg (electron density) rg_electron22.92
Forward intensity I(0) i035986400.00
Molecular weight molecular_weight44449.0 kDa
Excluded volume excluded_volume54817 ų
Envelope volume envelope_volume67646 ų
Hydration-shell volume shell_volume24661 ų
Envelope diameter envelope_diameter76.9
Shell Rg shell_rg29.80
Envelope Rg envelope_rg23.08
Shape Rg shape_rg22.89
Total Rg total_rg23.80
Total atoms total_atoms3136
Residues n_residues383
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 dmax74.6
Rg (real space) rg_real24.00
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real3.5990e+07
I(0) uncertainty (real space) i0_real_error4.6660e+05
Rg (reciprocal space) rg_reciprocal24.02
I(0) (reciprocal space) i0_reciprocal35990000.0000
Solution quality estimate total_estimate0.9104
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9802000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.970

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_idd3i6le1
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_idd3i6le2
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_id3i6lD01
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_id3i6lD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3i6lE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)