1akj

COMPLEX OF THE HUMAN MHC CLASS I GLYCOPROTEIN HLA-A2 AND THE T CELL CORECEPTOR CD8

Method: X-RAY DIFFRACTION Dmax: 82.0 Å Quality: EXCELLENT

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

MHC CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–300 Fragment:EXTRACELLULAR DOMAIN BETA 2-MICROGLOBULIN × 1 (P61769) HIV REVERSE TRANSCRIPTASE EPITOPE × 1 T-CELL CORECEPTOR CD8 × 2 (P01732) X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;PROTEIN WAS CRYSTALLIZED FROM 12% PEG 20000, 100 MM MES, PH 6.5 Resolution 2.65 Å R-free 0.276

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 465 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 1–276; UniProt 25–300

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Fragment:EXTRACELLULAR DOMAIN MHC CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN) × 1 (P01892) HIV REVERSE TRANSCRIPTASE EPITOPE × 1 T-CELL CORECEPTOR CD8 × 2 (P01732) X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;PROTEIN WAS CRYSTALLIZED FROM 12% PEG 20000, 100 MM MES, PH 6.5 Resolution 2.65 Å R-free 0.276

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 B; PDBConstruct 1–99; UniProt 21–119

T-CELL CORECEPTOR CD8

Homo sapiens

UniProt P01732

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 22–141 Chain E; UniProt 22–141 Fragment:EXTRACELLULAR IGSF DOMAIN, RESIDUES 1 - 120, ALPHA CHAIN MHC CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN) × 1 (P01892) BETA 2-MICROGLOBULIN × 1 (P61769) HIV REVERSE TRANSCRIPTASE EPITOPE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;PROTEIN WAS CRYSTALLIZED FROM 12% PEG 20000, 100 MM MES, PH 6.5 Resolution 2.65 Å R-free 0.276

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.

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD8A_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–120; UniProt 22–141 Author chain E; PDBConstruct 1–120; UniProt 22–141

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 1akj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1akj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1akj
Deposition date deposition_date1997-05-21
Structure title titleCOMPLEX OF THE HUMAN MHC CLASS I GLYCOPROTEIN HLA-A2 AND THE T CELL CORECEPTOR CD8
Keywords keywordsT-CELL, GLYCOPROTEIN, COMPLEX, IMMUNOLOGY, COMPLEX (MHC I-PEPTIDE-CD8), COMPLEX (MHC I-PEPTIDE-CD8) complex; COMPLEX (MHC I/PEPTIDE/CD8)
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.87
Radius of gyration Rg (electron density) rg_electron25.66
Forward intensity I(0) i083435100.00
Molecular weight molecular_weight70151.0 kDa
Excluded volume excluded_volume87166 ų
Envelope volume envelope_volume108770 ų
Hydration-shell volume shell_volume34352 ų
Envelope diameter envelope_diameter84.6
Shell Rg shell_rg33.70
Envelope Rg envelope_rg25.54
Shape Rg shape_rg25.65
Total Rg total_rg26.54
Total atoms total_atoms4957
Residues n_residues611
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 dmax82.0
Rg (real space) rg_real26.69
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real8.3440e+07
I(0) uncertainty (real space) i0_real_error1.0740e+06
Rg (reciprocal space) rg_reciprocal26.75
I(0) (reciprocal space) i0_reciprocal83440000.0000
Solution quality estimate total_estimate0.9071
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.8
Skewness Skewness skewness0.101
Kurtosis Kurtosis kurtosis-0.531
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16420000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.976

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1akja1
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_idd1akja2
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_idd1akjb_
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_idd1akjd_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1akje_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id1akjA01
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_id1akjA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1akjB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1akjD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1akjE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)