3bh9

Crystal Structure of RTY Phosphopeptide Bound to Human Class I MHC HLA-A2

Method: X-RAY DIFFRACTION Dmax: 74.2 Å Quality: EXCELLENT

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:Alpha-1, Alpha-2, Alpha-3 Beta-2-microglobulin × 1 (P61769) decameric peptide from Protein POF1B × 1 (Q8WVV4) NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;21% PEG 3350, 0.1M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 25–299 Fragment:Alpha-1, Alpha-2, Alpha-3 Beta-2-microglobulin × 2 (P61769) decameric peptide from Protein POF1B × 2 (Q8WVV4) NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;21% PEG 3350, 0.1M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.229

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

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) decameric peptide from Protein POF1B × 1 (Q8WVV4) NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;21% PEG 3350, 0.1M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 2 (P01892) decameric peptide from Protein POF1B × 2 (Q8WVV4) NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;21% PEG 3350, 0.1M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.229

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

decameric peptide from Protein POF1B

OrganismNot specified

UniProt Q8WVV4

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 C; UniProt 53–62 Fragment:UNP residues 53-62 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;21% PEG 3350, 0.1M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 53–62 Fragment:UNP residues 53-62 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class I histocompatibility antigen, A-2 alpha chain × 2 (P01892) Beta-2-microglobulin × 2 (P61769) NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;21% PEG 3350, 0.1M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.70 Å R-free 0.229

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name POF1B_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 53–62

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 3bh9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bh9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bh9
Deposition date deposition_date2007-11-28
Structure title titleCrystal Structure of RTY Phosphopeptide Bound to Human Class I MHC HLA-A2
Keywords keywords;PHOSPHOSERINE, PHOSPHOPEPTIDE, MHC, HLA-A2, ANCHOR RESIDUE, TUMOR ANTIGEN, GLYCOPROTEIN, HOST-VIRUS INTERACTION, IMMUNE RESPONSE, MHC I, POLYMORPHISM, TRANSMEMBRANE, UBL CONJUGATION, IMMUNOGLOBULIN DOMAIN, PHOSPHOPROTEIN, 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_guinier24.17
Radius of gyration Rg (electron density) rg_electron22.96
Forward intensity I(0) i037057800.00
Molecular weight molecular_weight45044.0 kDa
Excluded volume excluded_volume55476 ų
Envelope volume envelope_volume68248 ų
Hydration-shell volume shell_volume24827 ų
Envelope diameter envelope_diameter77.7
Shell Rg shell_rg29.93
Envelope Rg envelope_rg23.05
Shape Rg shape_rg22.94
Total Rg total_rg23.84
Total atoms total_atoms3177
Residues n_residues384
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 dmax74.2
Rg (real space) rg_real24.09
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real3.7060e+07
I(0) uncertainty (real space) i0_real_error5.3910e+05
Rg (reciprocal space) rg_reciprocal24.11
I(0) (reciprocal space) i0_reciprocal37060000.0000
Solution quality estimate total_estimate0.9133
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.2
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.504
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9643000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3bh9a1
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_idd3bh9a2
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_idd3bh9b2
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_idd3bh9b3
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_id3bh9A01
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_id3bh9A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bh9B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)