7tub

The beta-tubulin folding intermediate IV

Method: ELECTRON MICROSCOPY Dmax: 173.2 Å Quality: GOOD

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

Tubulin beta chain

Homo sapiens

UniProt P07437

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain A; UniProt 1–444 Not recorded T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–444; UniProt 1–444

T-complex protein 1 subunit theta

Homo sapiens

UniProt P50990

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain B; UniProt 1–547 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPQ_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–547; UniProt 1–547

T-complex protein 1 subunit eta

Homo sapiens

UniProt Q99832

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain C; UniProt 1–543 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

63 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPH_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–553; UniProt 1–543

T-complex protein 1 subunit epsilon

Homo sapiens

UniProt P48643

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain D; UniProt 1–541 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

68 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPE_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–541; UniProt 1–541

T-complex protein 1 subunit beta

Homo sapiens

UniProt P78371

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain E; UniProt 1–535 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPB_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–535; UniProt 1–535

T-complex protein 1 subunit delta

Homo sapiens

UniProt P50991

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain F; UniProt 1–539 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

65 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPD_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain F; PDBConstruct 1–539; UniProt 1–539

T-complex protein 1 subunit alpha

Homo sapiens

UniProt P17987

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain G; UniProt 1–556 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPA_HUMAN
Isoform
PDB entities 7
Chains and sequence ranges Author chain G; PDBConstruct 1–556; UniProt 1–556

T-complex protein 1 subunit gamma

Homo sapiens

UniProt P49368

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain H; UniProt 1–545 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit zeta × 1 (P40227) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

65 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPG_HUMAN
Isoform
PDB entities 8
Chains and sequence ranges Author chain H; PDBConstruct 1–545; UniProt 1–545

T-complex protein 1 subunit zeta

Homo sapiens

UniProt P40227

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain I; UniProt 1–531 Not recorded Tubulin beta chain × 1 (P07437) T-complex protein 1 subunit theta × 1 (P50990) T-complex protein 1 subunit eta × 1 (Q99832) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPZ_HUMAN
Isoform
PDB entities 9
Chains and sequence ranges Author chain I; PDBConstruct 1–531; UniProt 1–531

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 7tub

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7tub
Deposition date deposition_date2022-02-02
Structure title titleThe beta-tubulin folding intermediate IV
Keywords keywordsHuman chaperonin TRiC with beta-tubulin folding intermediate IV, CHAPERONE; CHAPERONE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier56.39
Radius of gyration Rg (electron density) rg_electron55.78
Forward intensity I(0) i03763980000.00
Molecular weight molecular_weight512980.0 kDa
Excluded volume excluded_volume641970 ų
Envelope volume envelope_volume958160 ų
Hydration-shell volume shell_volume137530 ų
Envelope diameter envelope_diameter175.6
Shell Rg shell_rg64.48
Envelope Rg envelope_rg53.42
Shape Rg shape_rg55.78
Total Rg total_rg55.99
Total atoms total_atoms35869
Residues n_residues4650
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 dmax173.2
Rg (real space) rg_real56.08
Rg uncertainty (real space) rg_real_error1.13
I(0) (real space) i0_real3.7640e+09
I(0) uncertainty (real space) i0_real_error6.9960e+07
Rg (reciprocal space) rg_reciprocal56.63
I(0) (reciprocal space) i0_reciprocal3767000000.0000
Solution quality estimate total_estimate0.8812
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary68.0
Skewness Skewness skewness0.057
Kurtosis Kurtosis kurtosis-0.669
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha371300000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.630

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (13)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id7tubA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id7tubA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id7tubB01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology7 — GroEL
Homologous superfamily homologous superfamily10 — GroEL
Domain ID domain_id7tubC01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology7 — GroEL
Homologous superfamily homologous superfamily10 — GroEL
Domain ID domain_id7tubD01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology7 — GroEL
Homologous superfamily homologous superfamily10 — GroEL
Domain ID domain_id7tubE01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology7 — GroEL
Homologous superfamily homologous superfamily10 — GroEL
Domain ID domain_id7tubG01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology7 — GroEL
Homologous superfamily homologous superfamily10 — GroEL

8. Citations (1)

9. Files and Curves (10)