8tw6

TCR in nanodisc ND-II

Method: ELECTRON MICROSCOPY Dmax: 93.9 Å Quality: GOOD

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

T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP

human respiratory syncytial virus

UniProt A0A5P9VSM6

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain X; UniProt 2–239 Chain Y; UniProt 2–239 Not recorded TCR alpha × 1 T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY × 1 (A0A0K0K1A5,P0DTU4,A0A4D6FVK6) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) T-cell surface glycoprotein CD3 delta chain × 1 (P04234) T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A5P9VSM6_HRSV
Isoform
PDB entities 1
Chains and sequence ranges Author chain X; PDBConstruct 175–412; UniProt 2–239 Author chain Y; PDBConstruct 175–412; UniProt 2–239

T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP

human respiratory syncytial virus

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain X; UniProt 1–164 Chain Y; UniProt 1–164 Not recorded TCR alpha × 1 T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY × 1 (A0A0K0K1A5,P0DTU4,A0A4D6FVK6) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) T-cell surface glycoprotein CD3 delta chain × 1 (P04234) T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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 1
Chains and sequence ranges Author chain X; PDBConstruct 1–164; UniProt 1–164 Author chain Y; PDBConstruct 1–164; UniProt 1–164

T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY

Escherichia coli str. K-12 substr. MG1655

UniProt A0A0K0K1A5

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 1–114 Not recorded T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP × 2 (P20963,A0A5P9VSM6) TCR alpha × 1 T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) T-cell surface glycoprotein CD3 delta chain × 1 (P04234) T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

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

View Construct and Data Evidence
UniProt name TVB65_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 1–114; UniProt 1–114

T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY

Escherichia coli str. K-12 substr. MG1655

UniProt A0A4D6FVK6

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 2–236 Not recorded T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP × 2 (P20963,A0A5P9VSM6) TCR alpha × 1 T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) T-cell surface glycoprotein CD3 delta chain × 1 (P04234) T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A4D6FVK6_ECOLI
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 322–556; UniProt 2–236

T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY

Escherichia coli str. K-12 substr. MG1655

UniProt P0DTU4

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 132–315 Not recorded T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP × 2 (P20963,A0A5P9VSM6) TCR alpha × 1 T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) T-cell surface glycoprotein CD3 delta chain × 1 (P04234) T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRBR2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 128–311; UniProt 132–315

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain E; UniProt 1–207 Chain F; UniProt 1–207 Not recorded T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP × 2 (P20963,A0A5P9VSM6) TCR alpha × 1 T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY × 1 (A0A0K0K1A5,P0DTU4,A0A4D6FVK6) T-cell surface glycoprotein CD3 delta chain × 1 (P04234) T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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 4
Chains and sequence ranges Author chain E; PDBConstruct 1–207; UniProt 1–207 Author chain F; PDBConstruct 1–207; UniProt 1–207

T-cell surface glycoprotein CD3 delta chain

Homo sapiens

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain D; UniProt 1–171 Not recorded T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP × 2 (P20963,A0A5P9VSM6) TCR alpha × 1 T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY × 1 (A0A0K0K1A5,P0DTU4,A0A4D6FVK6) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) T-cell surface glycoprotein CD3 gamma chain × 1 (P09693) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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 5
Chains and sequence ranges Author chain D; PDBConstruct 1–171; UniProt 1–171

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 × 8 其他Polymer 1 PDB declaration: octameric(8) Consistent with protein copy count Chain G; UniProt 1–182 Not recorded T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP × 2 (P20963,A0A5P9VSM6) TCR alpha × 1 T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY × 1 (A0A0K0K1A5,P0DTU4,A0A4D6FVK6) T-cell surface glycoprotein CD3 epsilon chain × 2 (P07766) T-cell surface glycoprotein CD3 delta chain × 1 (P04234) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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 6
Chains and sequence ranges Author chain G; PDBConstruct 1–182; UniProt 1–182

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 8tw6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8tw6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8tw6
Deposition date deposition_date2023-08-20
Structure title titleTCR in nanodisc ND-II
Keywords keywordsT-cell receptor, TCR, 1G4, nanodisc, CD3, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier30.27
Radius of gyration Rg (electron density) rg_electron29.35
Forward intensity I(0) i0124350000.00
Molecular weight molecular_weight88721.0 kDa
Excluded volume excluded_volume111490 ų
Envelope volume envelope_volume153770 ų
Hydration-shell volume shell_volume42756 ų
Envelope diameter envelope_diameter100.2
Shell Rg shell_rg37.31
Envelope Rg envelope_rg28.78
Shape Rg shape_rg29.36
Total Rg total_rg30.15
Total atoms total_atoms6242
Residues n_residues821
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 dmax93.9
Rg (real space) rg_real30.04
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real1.2430e+08
I(0) uncertainty (real space) i0_real_error1.6260e+06
Rg (reciprocal space) rg_reciprocal30.14
I(0) (reciprocal space) i0_reciprocal124400000.0000
Solution quality estimate total_estimate0.8935
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.7
Skewness Skewness skewness0.059
Kurtosis Kurtosis kurtosis-0.456
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17120000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.972

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)