2uwe

Large CDR3a loop alteration as a function of MHC mutation

Method: X-RAY DIFFRACTION Dmax: 149.8 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–299 Fragment:ECTO-DOMAIN, RESIDUES 25-299 Mutation:YES BETA-2-MICROGLOBULIN × 1 (P61769) UNCHARACTERIZED PROTEIN C15ORF24 × 1 (Q9NPA0) AHIII TCR ALPHA CHAIN × 1 AHIII TCR BETA CHAIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.8;14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8 Resolution 2.40 Å R-free 0.290
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 25–299 Fragment:ECTO-DOMAIN, RESIDUES 25-299 Mutation:YES BETA-2-MICROGLOBULIN × 1 (P61769) UNCHARACTERIZED PROTEIN C15ORF24 × 1 (Q9NPA0) AHIII TCR ALPHA CHAIN × 1 AHIII TCR BETA CHAIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.8;14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8 Resolution 2.40 Å R-free 0.290

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 H; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Fragment:RESIDUES 21-119 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN × 1 (P01892) UNCHARACTERIZED PROTEIN C15ORF24 × 1 (Q9NPA0) AHIII TCR ALPHA CHAIN × 1 AHIII TCR BETA CHAIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.8;14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8 Resolution 2.40 Å R-free 0.290
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 21–119 Fragment:RESIDUES 21-119 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN × 1 (P01892) UNCHARACTERIZED PROTEIN C15ORF24 × 1 (Q9NPA0) AHIII TCR ALPHA CHAIN × 1 AHIII TCR BETA CHAIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.8;14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8 Resolution 2.40 Å R-free 0.290

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 I; PDBConstruct 2–100; UniProt 21–119

UNCHARACTERIZED PROTEIN C15ORF24

OrganismNot specified

UniProt Q9NPA0

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 4–12 Fragment:RESIDUES 4-12 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN × 1 (P01892) BETA-2-MICROGLOBULIN × 1 (P61769) AHIII TCR ALPHA CHAIN × 1 AHIII TCR BETA CHAIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.8;14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8 Resolution 2.40 Å R-free 0.290
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain J; UniProt 4–12 Fragment:RESIDUES 4-12 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN × 1 (P01892) BETA-2-MICROGLOBULIN × 1 (P61769) AHIII TCR ALPHA CHAIN × 1 AHIII TCR BETA CHAIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.8;14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8 Resolution 2.40 Å R-free 0.290

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.

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

View Construct and Data Evidence
UniProt name CO024_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 4–12 Author chain J; PDBConstruct 1–9; UniProt 4–12

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 2uwe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2uwe
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2uwe
Deposition date deposition_date2007-03-20
Structure title titleLarge CDR3a loop alteration as a function of MHC mutation
Keywords keywords;HOST-VIRUS INTERACTION, PYRROLIDONE CARBOXYLIC ACID, GLYCOPROTEIN, TRANSMEMBRANE, IMMUNE SYSTEM, MHC I, MEMBRANE, RECEPTOR, CLASS I MHC, HYPOTHETICAL PROTEIN, IMMUNOGLOBULIN DOMAIN, IMMUNOGLOBULIN, IMMUNE RESPONSE, TCR-PMHC COMPLEX, T CELL SIGNALING, DISEASE MUTATION ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.70
Radius of gyration Rg (electron density) rg_electron43.28
Forward intensity I(0) i0535573000.00
Molecular weight molecular_weight186080.0 kDa
Excluded volume excluded_volume230740 ų
Envelope volume envelope_volume327600 ų
Hydration-shell volume shell_volume63231 ų
Envelope diameter envelope_diameter151.9
Shell Rg shell_rg48.05
Envelope Rg envelope_rg42.74
Shape Rg shape_rg43.23
Total Rg total_rg43.65
Total atoms total_atoms13140
Residues n_residues1628
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 dmax149.8
Rg (real space) rg_real43.77
Rg uncertainty (real space) rg_real_error1.60
I(0) (real space) i0_real5.3560e+08
I(0) uncertainty (real space) i0_real_error1.0640e+07
Rg (reciprocal space) rg_reciprocal43.70
I(0) (reciprocal space) i0_reciprocal535500000.0000
Solution quality estimate total_estimate0.8749
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.9
Skewness Skewness skewness0.380
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha55480000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.848

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd2uwea1
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_idd2uwea2
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_idd2uweb2
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_idd2uweb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2uwee1
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_idd2uwee2
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_idd2uwef1
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_idd2uwef2
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_idd2uweh1
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_idd2uweh2
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_idd2uwei2
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_idd2uwei3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2uwel1
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_idd2uwel2
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_idd2uwem1
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_idd2uwem2
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_id2uweA01
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_id2uweA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweH01
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_id2uweH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweM01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uweM02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)