5syg

Cryo-EM reconstruction of zampanolide-bound microtubule

Method: ELECTRON MICROSCOPY Dmax: 98.5 Å Quality: GOOD

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

Tubulin alpha chain

OrganismNot specified

UniProt B6A7R0

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 × 52 PDB declaration: 130-meric(130) Count mismatch; review required Chain A; UniProt 1–437 Not recorded Tubulin beta chain × 26 (P02554) GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 GDP GUANOSINE-5'-DIPHOSPHATE × 26 ZPN (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;Blot for 4 seconds, blot force 10, before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.50 Å
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: pentameric(5) Count mismatch; review required Chain A; UniProt 1–437 Not recorded Tubulin beta chain × 1 (P02554) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZPN (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;Blot for 4 seconds, blot force 10, before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.50 Å
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: pentameric(5) Count mismatch; review required Chain A; UniProt 1–437 Not recorded Tubulin beta chain × 1 (P02554) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZPN (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;Blot for 4 seconds, blot force 10, before plunging into liquid ethane (FEI VITROBOT MARK IV). 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 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B6A7R0_PIG
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–437; UniProt 1–437

Tubulin beta chain

OrganismNot specified

UniProt P02554

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 × 52 PDB declaration: 130-meric(130) Count mismatch; review required Chain B; UniProt 1–426 Not recorded Tubulin alpha chain × 26 (B6A7R0) GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 GDP GUANOSINE-5'-DIPHOSPHATE × 26 ZPN (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;Blot for 4 seconds, blot force 10, before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.50 Å
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: pentameric(5) Count mismatch; review required Chain B; UniProt 1–426 Not recorded Tubulin alpha chain × 1 (B6A7R0) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZPN (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;Blot for 4 seconds, blot force 10, before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.50 Å
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: pentameric(5) Count mismatch; review required Chain B; UniProt 1–426 Not recorded Tubulin alpha chain × 1 (B6A7R0) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZPN (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8 cryo-EM vitrification conditions:Cryogen ETHANE;Blot for 4 seconds, blot force 10, before plunging into liquid ethane (FEI VITROBOT MARK IV). 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.

137 other PDB entries and 157 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB_PIG
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–426; UniProt 1–426

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 5syg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5syg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5syg
Deposition date deposition_date2016-08-11
Structure title titleCryo-EM reconstruction of zampanolide-bound microtubule
Keywords keywordszampanolide, microtubule, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier29.66
Radius of gyration Rg (electron density) rg_electron28.98
Forward intensity I(0) i0154616000.00
Molecular weight molecular_weight96790.0 kDa
Excluded volume excluded_volume120060 ų
Envelope volume envelope_volume141340 ų
Hydration-shell volume shell_volume40064 ų
Envelope diameter envelope_diameter105.6
Shell Rg shell_rg36.90
Envelope Rg envelope_rg29.30
Shape Rg shape_rg28.99
Total Rg total_rg29.61
Total atoms total_atoms6792
Residues n_residues852
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 dmax98.5
Rg (real space) rg_real29.67
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.5460e+08
I(0) uncertainty (real space) i0_real_error2.2190e+06
Rg (reciprocal space) rg_reciprocal29.67
I(0) (reciprocal space) i0_reciprocal154600000.0000
Solution quality estimate total_estimate0.8768
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.411
Kurtosis Kurtosis kurtosis-0.268
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45900000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.935

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id5sygA01
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_id5sygA02
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_id5sygA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5sygB01
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_id5sygB02
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_id5sygB03
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)