6tdr

Crystal structure of the disulfide engineered HLA-A0201 molecule devoid of peptide (annealed)

Method: X-RAY DIFFRACTION Dmax: 105.6 Å Quality: EXCELLENT

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

MHC class I antigen

Homo sapiens

UniProt F6IQS1

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–299 Not recorded Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.1 M HEPES pH 7.5, 20% PEG 10 000, 8% ethylene glycol Resolution 1.75 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 24–299 Not recorded Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.1 M HEPES pH 7.5, 20% PEG 10 000, 8% ethylene glycol Resolution 1.75 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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F6IQS1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 24–299 Author chain C; PDBConstruct 1–276; UniProt 24–299

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded MHC class I antigen × 1 (F6IQS1) EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.1 M HEPES pH 7.5, 20% PEG 10 000, 8% ethylene glycol Resolution 1.75 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 21–119 Not recorded MHC class I antigen × 1 (F6IQS1) EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;0.1 M HEPES pH 7.5, 20% PEG 10 000, 8% ethylene glycol Resolution 1.75 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 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 D; 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 6tdr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6tdr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6tdr
Deposition date deposition_date2019-11-10
Structure title titleCrystal structure of the disulfide engineered HLA-A0201 molecule devoid of peptide (annealed)
Keywords keywordsMHC Class I molecule, 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_guinier32.48
Radius of gyration Rg (electron density) rg_electron31.61
Forward intensity I(0) i0131605000.00
Molecular weight molecular_weight87686.0 kDa
Excluded volume excluded_volume108060 ų
Envelope volume envelope_volume142100 ų
Hydration-shell volume shell_volume37750 ų
Envelope diameter envelope_diameter112.7
Shell Rg shell_rg38.48
Envelope Rg envelope_rg31.24
Shape Rg shape_rg31.58
Total Rg total_rg32.25
Total atoms total_atoms6184
Residues n_residues750
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 dmax105.6
Rg (real space) rg_real32.43
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real1.3160e+08
I(0) uncertainty (real space) i0_real_error2.2260e+06
Rg (reciprocal space) rg_reciprocal32.46
I(0) (reciprocal space) i0_reciprocal131600000.0000
Solution quality estimate total_estimate0.9004
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.8
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.516
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14960000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6tdra1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd6tdra2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6tdrb1
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_idd6tdrb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6tdrc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd6tdrc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6tdrd1
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_idd6tdrd2
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_id6tdrA01
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_id6tdrA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6tdrB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6tdrC01
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_id6tdrC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6tdrD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)