7phr

Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I

Method: ELECTRON MICROSCOPY Dmax: 177.0 Å Quality: GOOD

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

T-cell surface glycoprotein CD3 gamma chain

Homo sapiens

UniProt P09693

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain C; UniProt 23–144 Not recorded T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 (P04234,P42212) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) Tumor-associated antigentic peptide gp100 × 1 (P40967) T-cell surface glycoprotein CD3 zeta chain × 2 (P20963) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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.

37 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD3G_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–122; UniProt 23–144

T-cell surface glycoprotein CD3 delta chain, green fluorescent protein

Aequorea victoria

UniProt P04234

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain D; UniProt 22–132 Not recorded T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) Tumor-associated antigentic peptide gp100 × 1 (P40967) T-cell surface glycoprotein CD3 zeta chain × 2 (P20963) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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.

30 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD3D_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–111; UniProt 22–132

T-cell surface glycoprotein CD3 delta chain, green fluorescent protein

Aequorea victoria

UniProt P42212

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain D; UniProt 1–238 Not recorded T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) Tumor-associated antigentic peptide gp100 × 1 (P40967) T-cell surface glycoprotein CD3 zeta chain × 2 (P20963) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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.

568 other PDB entries and 744 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GFP_AEQVI
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 118–356; UniProt 1–238

T-cell surface glycoprotein CD3 epsilon chain

Homo sapiens

UniProt P07766

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain E; UniProt 23–158 Chain e; UniProt 23–158 Not recorded T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 (P04234,P42212) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) Tumor-associated antigentic peptide gp100 × 1 (P40967) T-cell surface glycoprotein CD3 zeta chain × 2 (P20963) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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.

42 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD3E_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–136; UniProt 23–158 Author chain e; PDBConstruct 1–136; UniProt 23–158

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain H; UniProt 25–304 Not recorded T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 (P04234,P42212) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) Beta-2-microglobulin × 1 (P61769) Tumor-associated antigentic peptide gp100 × 1 (P40967) T-cell surface glycoprotein CD3 zeta chain × 2 (P20963) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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.

53 other PDB entries and 78 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAA_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain H; PDBConstruct 13–292; UniProt 25–304

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 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain L; UniProt 20–119 Not recorded T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 (P04234,P42212) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Tumor-associated antigentic peptide gp100 × 1 (P40967) T-cell surface glycoprotein CD3 zeta chain × 2 (P20963) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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 7
Chains and sequence ranges Author chain L; PDBConstruct 2–101; UniProt 20–119

Tumor-associated antigentic peptide gp100

OrganismNot specified

UniProt P40967

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain P; UniProt 280–288 Mutation:A9V T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 (P04234,P42212) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) T-cell surface glycoprotein CD3 zeta chain × 2 (P20963) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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.

15 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PMEL_HUMAN
Isoform
PDB entities 8
Chains and sequence ranges Author chain P; PDBConstruct 1–9; UniProt 280–288

T-cell surface glycoprotein CD3 zeta chain

Homo sapiens

UniProt P20963

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 11 PDB declaration: undecameric(11) Consistent with protein copy count Chain Z; UniProt 22–57 Chain z; UniProt 22–57 Not recorded T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 (P04234,P42212) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) Tumor-associated antigentic peptide gp100 × 1 (P40967) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.08 Å

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.

36 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD3Z_HUMAN
Isoform
PDB entities 9
Chains and sequence ranges Author chain Z; PDBConstruct 1–36; UniProt 22–57 Author chain z; PDBConstruct 1–36; UniProt 22–57

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 7phr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7phr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7phr
Deposition date deposition_date2021-08-18
Structure title titleStructure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
Keywords keywordsT-cell receptor, TCR, Major Histocompatibility Complex, MHC, Antigen, Adaptive Immunity, Cancer, Complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier46.05
Radius of gyration Rg (electron density) rg_electron47.61
Forward intensity I(0) i0401551000.00
Molecular weight molecular_weight163440.0 kDa
Excluded volume excluded_volume204090 ų
Envelope volume envelope_volume289360 ų
Hydration-shell volume shell_volume55671 ų
Envelope diameter envelope_diameter186.9
Shell Rg shell_rg45.50
Envelope Rg envelope_rg48.28
Shape Rg shape_rg47.62
Total Rg total_rg47.50
Total atoms total_atoms11511
Residues n_residues1443
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 dmax177.0
Rg (real space) rg_real46.90
Rg uncertainty (real space) rg_real_error3.00
I(0) (real space) i0_real4.0160e+08
I(0) uncertainty (real space) i0_real_error8.6410e+06
Rg (reciprocal space) rg_reciprocal46.06
I(0) (reciprocal space) i0_reciprocal401100000.0000
Solution quality estimate total_estimate0.7569
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.9
Skewness Skewness skewness0.781
Kurtosis Kurtosis kurtosis0.331
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29050000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.468; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.738; Smooth: 0.697

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7phrH01
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_id7phrH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)