3mbe

TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)

Method: X-RAY DIFFRACTION Dmax: 167.1 Å Quality: GOOD

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

MHC CLASS II H2-IAg7 ALPHA CHAIN

Mus musculus

UniProt P04228

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 24–205 Not recorded MHC CLASS II H2-IAg7 BETA CHAIN × 1 (Q31135) PEPTIDE HEL 11-27 × 1 (P00698) TCR 21.3 alpha chain × 1 TCR 21.3 beta chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.89 Å R-free 0.281
2 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 24–205 Not recorded MHC CLASS II H2-IAg7 BETA CHAIN × 1 (Q31135) PEPTIDE HEL 11-27 × 1 (P00698) TCR 21.3 alpha chain × 1 TCR 21.3 beta chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.89 Å R-free 0.281

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.

14 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HA2D_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–182; UniProt 24–205 Author chain E; PDBConstruct 1–182; UniProt 24–205

MHC CLASS II H2-IAg7 BETA CHAIN

Mus musculus

UniProt Q31135

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 28–214 Not recorded MHC CLASS II H2-IAg7 ALPHA CHAIN × 1 (P04228) PEPTIDE HEL 11-27 × 1 (P00698) TCR 21.3 alpha chain × 1 TCR 21.3 beta chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.89 Å R-free 0.281
2 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 28–214 Not recorded MHC CLASS II H2-IAg7 ALPHA CHAIN × 1 (P04228) PEPTIDE HEL 11-27 × 1 (P00698) TCR 21.3 alpha chain × 1 TCR 21.3 beta chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.89 Å R-free 0.281

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 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q31135_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 7–193; UniProt 28–214 Author chain F; PDBConstruct 7–193; UniProt 28–214

PEPTIDE HEL 11-27

OrganismNot specified

UniProt P00698

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 28–45 Not recorded MHC CLASS II H2-IAg7 ALPHA CHAIN × 1 (P04228) MHC CLASS II H2-IAg7 BETA CHAIN × 1 (Q31135) TCR 21.3 alpha chain × 1 TCR 21.3 beta chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.89 Å R-free 0.281
2 Other combination Heteromer Protein × 5 其他Polymer 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain Q; UniProt 28–45 Not recorded MHC CLASS II H2-IAg7 ALPHA CHAIN × 1 (P04228) MHC CLASS II H2-IAg7 BETA CHAIN × 1 (Q31135) TCR 21.3 alpha chain × 1 TCR 21.3 beta chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;295 K;20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.89 Å R-free 0.281

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.

1320 other PDB entries and 1449 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 3
Chains and sequence ranges Author chain P; PDBConstruct 1–18; UniProt 28–45 Author chain Q; PDBConstruct 1–18; UniProt 28–45

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 3mbe

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3mbe
Deposition date deposition_date2010-03-25
Structure title titleTCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
Keywords keywordsT cell receptor, Histocompatability antigen, MHC class II, I-Ag7, 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_guinier50.32
Radius of gyration Rg (electron density) rg_electron50.07
Forward intensity I(0) i0514154000.00
Molecular weight molecular_weight184580.0 kDa
Excluded volume excluded_volume229260 ų
Envelope volume envelope_volume356860 ų
Hydration-shell volume shell_volume60079 ų
Envelope diameter envelope_diameter176.2
Shell Rg shell_rg54.04
Envelope Rg envelope_rg48.00
Shape Rg shape_rg50.07
Total Rg total_rg50.24
Total atoms total_atoms13028
Residues n_residues1602
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 dmax167.1
Rg (real space) rg_real50.35
Rg uncertainty (real space) rg_real_error1.55
I(0) (real space) i0_real5.1420e+08
I(0) uncertainty (real space) i0_real_error9.7030e+06
Rg (reciprocal space) rg_reciprocal50.27
I(0) (reciprocal space) i0_reciprocal514100000.0000
Solution quality estimate total_estimate0.8503
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.1
Skewness Skewness skewness0.231
Kurtosis Kurtosis kurtosis-0.454
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23490000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.687

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3mbed1
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_idd3mbed2
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_idd3mbef1
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_idd3mbef2
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_idd3mbef3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (16 domains)

Domain ID domain_id3mbeA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id3mbeA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id3mbeB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeE01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id3mbeE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeF01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id3mbeF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3mbeH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)