1w72

Crystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3

Method: X-RAY DIFFRACTION Dmax: 207.5 Å Quality: REASONABLE

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

HLA CLASS I HISTOCOMPATIBILITY ANTIGEN

HOMO SAPIENS

UniProt P30443

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 25–298 Fragment:EXTRACELLULAR DOMAIN, RESIDUES 25-298 BETA-2-MICROGLOBULIN × 1 (P61769) MELANOMA-ASSOCIATED ANTIGEN 1 × 1 (P43355) HYB3 HEAVY CHAIN × 1 HYB3 LIGHT CHAIN × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE Resolution 2.15 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 25–298 Fragment:EXTRACELLULAR DOMAIN, RESIDUES 25-298 BETA-2-MICROGLOBULIN × 1 (P61769) MELANOMA-ASSOCIATED ANTIGEN 1 × 1 (P43355) HYB3 HEAVY CHAIN × 1 HYB3 LIGHT CHAIN × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE Resolution 2.15 Å R-free 0.248

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 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A01_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–274; UniProt 25–298 Author chain D; PDBConstruct 1–274; UniProt 25–298

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:RESIDUES 21-119 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN × 1 (P30443) MELANOMA-ASSOCIATED ANTIGEN 1 × 1 (P43355) HYB3 HEAVY CHAIN × 1 HYB3 LIGHT CHAIN × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE Resolution 2.15 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 21–119 Fragment:RESIDUES 21-119 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN × 1 (P30443) MELANOMA-ASSOCIATED ANTIGEN 1 × 1 (P43355) HYB3 HEAVY CHAIN × 1 HYB3 LIGHT CHAIN × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE Resolution 2.15 Å R-free 0.248

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

MELANOMA-ASSOCIATED ANTIGEN 1

OrganismNot specified

UniProt P43355

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 C; UniProt 161–169 Not recorded HLA CLASS I HISTOCOMPATIBILITY ANTIGEN × 1 (P30443) BETA-2-MICROGLOBULIN × 1 (P61769) HYB3 HEAVY CHAIN × 1 HYB3 LIGHT CHAIN × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE Resolution 2.15 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 161–169 Not recorded HLA CLASS I HISTOCOMPATIBILITY ANTIGEN × 1 (P30443) BETA-2-MICROGLOBULIN × 1 (P61769) HYB3 HEAVY CHAIN × 1 HYB3 LIGHT CHAIN × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;MES PH 6.5, NACL 600MM, 19% PEG3350, 80MM DIOXANE Resolution 2.15 Å R-free 0.248

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAG1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 161–169 Author chain F; PDBConstruct 1–9; UniProt 161–169

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 1w72

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1w72
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1w72
Deposition date deposition_date2004-08-27
Structure title titleCrystal structure of HLA-A1:MAGE-A1 in complex with Fab-Hyb3
Keywords keywordsIMMUNE SYSTEM, HLA/FAB FRAGMENT, HUMAN LEUCOCYTE ANTIGEN, PEPTIDE-SPECIFIC FAB, TCR-LIKE BINDING, MHC-I; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier55.81
Radius of gyration Rg (electron density) rg_electron57.74
Forward intensity I(0) i0518531000.00
Molecular weight molecular_weight181810.0 kDa
Excluded volume excluded_volume224540 ų
Envelope volume envelope_volume331740 ų
Hydration-shell volume shell_volume55819 ų
Envelope diameter envelope_diameter219.2
Shell Rg shell_rg47.61
Envelope Rg envelope_rg58.70
Shape Rg shape_rg57.66
Total Rg total_rg57.66
Total atoms total_atoms12818
Residues n_residues1608
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 dmax207.5
Rg (real space) rg_real56.87
Rg uncertainty (real space) rg_real_error3.13
I(0) (real space) i0_real5.1850e+08
I(0) uncertainty (real space) i0_real_error1.2490e+07
Rg (reciprocal space) rg_reciprocal54.94
I(0) (reciprocal space) i0_reciprocal517100000.0000
Solution quality estimate total_estimate0.7050
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.1
Skewness Skewness skewness0.729
Kurtosis Kurtosis kurtosis-0.002
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26850000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.417; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.318; Smooth: 0.592

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd1w72a1
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_idd1w72a2
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_idd1w72b1
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_idd1w72b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1w72d1
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_idd1w72d2
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_idd1w72e1
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_idd1w72e2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1w72h1
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_idd1w72h2
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_idd1w72i1
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_idd1w72i2
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_idd1w72l1
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_idd1w72l2
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_idd1w72m1
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_idd1w72m2
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)

CATH v4.4 (14 domains)

Domain ID domain_id1w72A01
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_id1w72A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72D01
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_id1w72D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72I01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72I02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72M01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1w72M02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (3)

9. Files and Curves (10)