8ou0

bovine sperm endpiece singlet microtubules (one tubulin dimer and associated microtubule inner proteins)

Method: ELECTRON MICROSCOPY Dmax: 102.5 Å Quality: EXCELLENT

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

Tubulin beta-4B chain

OrganismNot specified

UniProt Q3MHM5

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–445 Not recorded Stabilizer of axonemal microtubules 1 × 1 (A0A3S5ZPV0) Sperm acrosome associated 9 × 1 (A0A3Q1MYU9) Tubulin alpha-3 chain × 1 (Q32KN8) GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.3 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.50 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.

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

View Construct and Data Evidence
UniProt name TBB4B_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–445; UniProt 1–445

Stabilizer of axonemal microtubules 1

OrganismNot specified

UniProt A0A3S5ZPV0

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 1–477 Not recorded Tubulin beta-4B chain × 1 (Q3MHM5) Sperm acrosome associated 9 × 1 (A0A3Q1MYU9) Tubulin alpha-3 chain × 1 (Q32KN8) GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.3 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.50 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A3S5ZPV0_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–477; UniProt 1–477

Sperm acrosome associated 9

OrganismNot specified

UniProt A0A3Q1MYU9

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–224 Not recorded Tubulin beta-4B chain × 1 (Q3MHM5) Stabilizer of axonemal microtubules 1 × 1 (A0A3S5ZPV0) Tubulin alpha-3 chain × 1 (Q32KN8) GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.3 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.50 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 A0A3Q1MYU9_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–224; UniProt 1–224

Tubulin alpha-3 chain

OrganismNot specified

UniProt Q32KN8

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–450 Not recorded Tubulin beta-4B chain × 1 (Q3MHM5) Stabilizer of axonemal microtubules 1 × 1 (A0A3S5ZPV0) Sperm acrosome associated 9 × 1 (A0A3Q1MYU9) GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.3 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.50 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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA3_BOVIN
Isoform
PDB entities 4
Chains and sequence ranges Author chain A; PDBConstruct 1–450; UniProt 1–450

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 8ou0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ou0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ou0
Deposition date deposition_date2023-04-21
Structure title titlebovine sperm endpiece singlet microtubules (one tubulin dimer and associated microtubule inner proteins)
Keywords keywordsmicrotubule, microtubule inner protein, sperm, cilia, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier32.72
Radius of gyration Rg (electron density) rg_electron31.96
Forward intensity I(0) i0220979000.00
Molecular weight molecular_weight115980.0 kDa
Excluded volume excluded_volume143850 ų
Envelope volume envelope_volume186920 ų
Hydration-shell volume shell_volume47936 ų
Envelope diameter envelope_diameter109.6
Shell Rg shell_rg39.63
Envelope Rg envelope_rg31.96
Shape Rg shape_rg31.96
Total Rg total_rg32.55
Total atoms total_atoms8139
Residues n_residues1027
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 dmax102.5
Rg (real space) rg_real32.60
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real2.2100e+08
I(0) uncertainty (real space) i0_real_error3.5250e+06
Rg (reciprocal space) rg_reciprocal32.65
I(0) (reciprocal space) i0_reciprocal221000000.0000
Solution quality estimate total_estimate0.9008
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.5
Skewness Skewness skewness0.238
Kurtosis Kurtosis kurtosis-0.507
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha53650000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.901

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id8ou0A01
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_id8ou0A02
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_id8ou0B01
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_id8ou0B02
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_id8ou0B03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin

8. Citations (1)

9. Files and Curves (10)