6at6

Crystal structure of the KFJ5 TCR

Method: X-RAY DIFFRACTION Dmax: 75.9 Å Quality: EXCELLENT

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

T-cell receptor beta variable 28, Human nkt tcr beta chain chimera

Homo sapiens

UniProt A0A5B6

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 20–113 Not recorded T-cell receptor alpha variable 4, T-cell receptor, sp3.4 alpha chain chimera × 1 (A0A0B4J268,K7N5N2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris-HCl pH 8.5 and 25 % PEG3350 Resolution 1.42 Å R-free 0.218

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 A0A5B6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 3–96; UniProt 20–113

T-cell receptor beta variable 28, Human nkt tcr beta chain chimera

Homo sapiens

UniProt K7N5M4

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 120–249 Not recorded T-cell receptor alpha variable 4, T-cell receptor, sp3.4 alpha chain chimera × 1 (A0A0B4J268,K7N5N2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris-HCl pH 8.5 and 25 % PEG3350 Resolution 1.42 Å R-free 0.218

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.

23 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K7N5M4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 116–245; UniProt 120–249

T-cell receptor alpha variable 4, T-cell receptor, sp3.4 alpha chain chimera

Homo sapiens

UniProt A0A0B4J268

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 18–108 Not recorded T-cell receptor beta variable 28, Human nkt tcr beta chain chimera × 1 (A0A5B6,K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris-HCl pH 8.5 and 25 % PEG3350 Resolution 1.42 Å R-free 0.218

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0B4J268_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 3–93; UniProt 18–108

T-cell receptor alpha variable 4, T-cell receptor, sp3.4 alpha chain chimera

Homo sapiens

UniProt K7N5N2

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 115–207 Not recorded T-cell receptor beta variable 28, Human nkt tcr beta chain chimera × 1 (A0A5B6,K7N5M4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;0.1 M Tris-HCl pH 8.5 and 25 % PEG3350 Resolution 1.42 Å R-free 0.218

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.

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

View Construct and Data Evidence
UniProt name K7N5N2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 116–208; UniProt 115–207

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 6at6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6at6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6at6
Deposition date deposition_date2017-08-28
Structure title titleCrystal structure of the KFJ5 TCR
Keywords keywordsImmunogolbulin, 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_guinier25.11
Radius of gyration Rg (electron density) rg_electron24.04
Forward intensity I(0) i041706500.00
Molecular weight molecular_weight48847.0 kDa
Excluded volume excluded_volume60642 ų
Envelope volume envelope_volume75419 ų
Hydration-shell volume shell_volume26153 ų
Envelope diameter envelope_diameter77.1
Shell Rg shell_rg31.14
Envelope Rg envelope_rg23.83
Shape Rg shape_rg24.03
Total Rg total_rg24.91
Total atoms total_atoms3440
Residues n_residues430
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 dmax75.9
Rg (real space) rg_real25.03
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real4.1710e+07
I(0) uncertainty (real space) i0_real_error5.9050e+05
Rg (reciprocal space) rg_reciprocal25.06
I(0) (reciprocal space) i0_reciprocal41710000.0000
Solution quality estimate total_estimate0.9168
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.1
Skewness Skewness skewness0.171
Kurtosis Kurtosis kurtosis-0.616
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9117000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6at6a1
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_idd6at6a2
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_idd6at6b1
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_idd6at6b2
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 (3 domains)

Domain ID domain_id6at6A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6at6B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6at6B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)