2x4s

Crystal structure of MHC CLass I HLA-A2.1 bound to a peptide representing the epitope of the H5N1 (Avian Flu) Nucleoprotein

Method: X-RAY DIFFRACTION Dmax: 101.1 Å Quality: GOOD

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

HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1

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:RESIDUES 25 - 299 BETA-2-MICROGLOBULIN × 1 (P61769) H5N1 INFLUENZA A NUCLEOPROTEIN × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.55 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–299 Fragment:RESIDUES 25 - 299 BETA-2-MICROGLOBULIN × 1 (P61769) H5N1 INFLUENZA A NUCLEOPROTEIN × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.55 Å R-free 0.247

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 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1 × 1 (P01892) H5N1 INFLUENZA A NUCLEOPROTEIN × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.55 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1 × 1 (P01892) H5N1 INFLUENZA A NUCLEOPROTEIN × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 2.55 Å R-free 0.247

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

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 2x4s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2x4s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2x4s
Deposition date deposition_date2010-02-02
Structure title titleCrystal structure of MHC CLass I HLA-A2.1 bound to a peptide representing the epitope of the H5N1 (Avian Flu) Nucleoprotein
Keywords keywordsPHOTOCLEAVABLE PEPTIDE, GLYCOPROTEIN, IMMUNE SYSTEM, IMMUNOGLOBULIN DOMAIN, MATRIX (M1); IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.46
Radius of gyration Rg (electron density) rg_electron31.59
Forward intensity I(0) i0139891000.00
Molecular weight molecular_weight89978.0 kDa
Excluded volume excluded_volume110600 ų
Envelope volume envelope_volume143650 ų
Hydration-shell volume shell_volume38018 ų
Envelope diameter envelope_diameter108.1
Shell Rg shell_rg38.50
Envelope Rg envelope_rg31.26
Shape Rg shape_rg31.57
Total Rg total_rg32.23
Total atoms total_atoms6334
Residues n_residues764
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 dmax101.1
Rg (real space) rg_real32.39
Rg uncertainty (real space) rg_real_error0.79
I(0) (real space) i0_real1.3990e+08
I(0) uncertainty (real space) i0_real_error2.2440e+06
Rg (reciprocal space) rg_reciprocal32.43
I(0) (reciprocal space) i0_reciprocal139900000.0000
Solution quality estimate total_estimate0.8375
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.2
Skewness Skewness skewness0.210
Kurtosis Kurtosis kurtosis-0.586
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17660000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.965; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2x4sb1
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_idd2x4sb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2x4se1
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_idd2x4se2
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_id2x4sA01
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_id2x4sA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2x4sB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2x4sD01
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_id2x4sD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2x4sE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)