6wsl

Cryo-EM structure of VASH1-SVBP bound to microtubules

Method: ELECTRON MICROSCOPY Dmax: 149.3 Å Quality: GOOD

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

Tubulin alpha-1A chain

Homo sapiens

UniProt Q71U36

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–451 Chain E; UniProt 1–451 Not recorded Tubulin beta-3 chain × 2 (Q13509) Tubulinyl-Tyr carboxypeptidase 1 × 2 (Q7L8A9) Small vasohibin-binding protein × 2 (Q8N300) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–451; UniProt 1–451 Author chain E; PDBConstruct 1–451; UniProt 1–451

Tubulin beta-3 chain

Homo sapiens

UniProt Q13509

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 1–450 Chain F; UniProt 1–450 Not recorded Tubulin alpha-1A chain × 2 (Q71U36) Tubulinyl-Tyr carboxypeptidase 1 × 2 (Q7L8A9) Small vasohibin-binding protein × 2 (Q8N300) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 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.

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–450; UniProt 1–450 Author chain F; PDBConstruct 1–450; UniProt 1–450

Tubulinyl-Tyr carboxypeptidase 1

Homo sapiens

UniProt Q7L8A9

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain C; UniProt 52–310 Chain G; UniProt 52–310 Not recorded Tubulin alpha-1A chain × 2 (Q71U36) Tubulin beta-3 chain × 2 (Q13509) Small vasohibin-binding protein × 2 (Q8N300) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 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.

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VASH1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–259; UniProt 52–310 Author chain G; PDBConstruct 1–259; UniProt 52–310

Small vasohibin-binding protein

Homo sapiens

UniProt Q8N300

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain D; UniProt 1–66 Chain H; UniProt 1–66 Not recorded Tubulin alpha-1A chain × 2 (Q71U36) Tubulin beta-3 chain × 2 (Q13509) Tubulinyl-Tyr carboxypeptidase 1 × 2 (Q7L8A9) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 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.

23 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SVBP_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–66; UniProt 1–66 Author chain H; PDBConstruct 1–66; UniProt 1–66

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 6wsl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6wsl
Deposition date deposition_date2020-05-01
Structure title titleCryo-EM structure of VASH1-SVBP bound to microtubules
Keywords keywordsMicrotubule, Posttranslational modification, Detyrosination, Vasohibin, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.86
Radius of gyration Rg (electron density) rg_electron44.56
Forward intensity I(0) i01013800000.00
Molecular weight molecular_weight259130.0 kDa
Excluded volume excluded_volume322370 ų
Envelope volume envelope_volume434540 ų
Hydration-shell volume shell_volume79731 ų
Envelope diameter envelope_diameter156.5
Shell Rg shell_rg50.39
Envelope Rg envelope_rg44.35
Shape Rg shape_rg44.59
Total Rg total_rg44.74
Total atoms total_atoms18204
Residues n_residues2278
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 dmax149.3
Rg (real space) rg_real44.83
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real1.0140e+09
I(0) uncertainty (real space) i0_real_error1.9120e+07
Rg (reciprocal space) rg_reciprocal44.86
I(0) (reciprocal space) i0_reciprocal1014000000.0000
Solution quality estimate total_estimate0.8647
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary59.7
Skewness Skewness skewness0.362
Kurtosis Kurtosis kurtosis-0.141
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha210700000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.731

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6wsla1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6wsla2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd6wslb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6wslb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd6wsle1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6wsle2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd6wslf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd6wslf2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain

8. Citations (1)

9. Files and Curves (10)