2x4n

Crystal structure of MHC CLass I HLA-A2.1 bound to residual fragments of a photocleavable peptide that is cleaved upon UV-light treatment

Method: X-RAY DIFFRACTION Dmax: 116.7 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:RESIDUES 25-299 BETA-2-MICROGLOBULIN × 1 (P61769) HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;100 MM MES PH 5.5, 20% PEG 1500. CRYSTALS WERE FROZEN IN 100 MM MES, 30% PEG 1500, 10% GLYCEROL Resolution 2.34 Å R-free 0.274
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) HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE × 1 GOL GLYCEROL × 7 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;100 MM MES PH 5.5, 20% PEG 1500. CRYSTALS WERE FROZEN IN 100 MM MES, 30% PEG 1500, 10% GLYCEROL Resolution 2.34 Å R-free 0.274

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) HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;100 MM MES PH 5.5, 20% PEG 1500. CRYSTALS WERE FROZEN IN 100 MM MES, 30% PEG 1500, 10% GLYCEROL Resolution 2.34 Å R-free 0.274
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) HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE × 1 GOL GLYCEROL × 7 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;100 MM MES PH 5.5, 20% PEG 1500. CRYSTALS WERE FROZEN IN 100 MM MES, 30% PEG 1500, 10% GLYCEROL Resolution 2.34 Å R-free 0.274

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 2x4n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2x4n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2x4n
Deposition date deposition_date2010-02-02
Structure title titleCrystal structure of MHC CLass I HLA-A2.1 bound to residual fragments of a photocleavable peptide that is cleaved upon UV-light treatment
Keywords keywords;GLYCOPROTEIN, IMMUNE SYSTEM, TRANSMEMBRANE, DISEASE MUTATION, IMMUNOGLOBULIN DOMAIN, PHOSPHOPROTEIN, IMMUNE RESPONSE, HOST-VIRUS INTERACTION, PYRROLIDONE CARBOXYLIC ACID, GLYCATION, AMYLOIDOSIS ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.85
Radius of gyration Rg (electron density) rg_electron33.29
Forward intensity I(0) i0136550000.00
Molecular weight molecular_weight89754.0 kDa
Excluded volume excluded_volume110730 ų
Envelope volume envelope_volume146090 ų
Hydration-shell volume shell_volume37955 ų
Envelope diameter envelope_diameter125.1
Shell Rg shell_rg38.24
Envelope Rg envelope_rg33.26
Shape Rg shape_rg33.27
Total Rg total_rg33.75
Total atoms total_atoms6326
Residues n_residues759
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 dmax116.7
Rg (real space) rg_real34.00
Rg uncertainty (real space) rg_real_error1.00
I(0) (real space) i0_real1.3650e+08
I(0) uncertainty (real space) i0_real_error2.1940e+06
Rg (reciprocal space) rg_reciprocal33.91
I(0) (reciprocal space) i0_reciprocal136500000.0000
Solution quality estimate total_estimate0.8627
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.2
Skewness Skewness skewness0.497
Kurtosis Kurtosis kurtosis-0.131
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15340000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.878

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_idd2x4nb1
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_idd2x4nb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2x4ne1
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_idd2x4ne2
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_id2x4nA01
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_id2x4nA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2x4nB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2x4nD01
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_id2x4nD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2x4nE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)