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6wsl

Cryo-EM structure of VASH1-SVBP bound to microtubules

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tubulin alpha-1A chain

Homo sapiens

UniProt Q71U36

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Tubulin beta-3 chain × 2 （Q13509） Tubulinyl-Tyr carboxypeptidase 1 × 2 （Q7L8A9） Small vasohibin-binding protein × 2 （Q8N300） GUANOSINE-5'-TRIPHOSPHATE × 2 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
22aj 22ak 5jco 6wsl 7un1 7ung 8j07 8sh7 9ox7 9wd7 9wd9 9wda

13 assemblies; showing the first 12

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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Tubulin alpha-1A chain × 2 （Q71U36） Tubulinyl-Tyr carboxypeptidase 1 × 2 （Q7L8A9） Small vasohibin-binding protein × 2 （Q8N300） GUANOSINE-5'-TRIPHOSPHATE × 2 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
22aj 22ak 5ij0 5ij9 5jco 6e7b 6s8l 6wsl 7lxb 7m18 7m20 7pjf

29 assemblies; showing the first 12

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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Tubulin alpha-1A chain × 2 （Q71U36） Tubulin beta-3 chain × 2 （Q13509） Small vasohibin-binding protein × 2 （Q8N300） GUANOSINE-5'-TRIPHOSPHATE × 2 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6j4u 6j7b 6j8f 6j8n 6j8n 6j8o 6j91 6j9h 6j9h 6k81 6lpg 6nvq

17 assemblies; showing the first 12

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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Tubulin alpha-1A chain × 2 （Q71U36） Tubulin beta-3 chain × 2 （Q13509） Tubulinyl-Tyr carboxypeptidase 1 × 2 （Q7L8A9） GUANOSINE-5'-TRIPHOSPHATE × 2 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6j4o 6j4p 6j4q 6j4q 6j4q 6j4q 6j4s 6j4u 6j4v 6j7b 6j8f 6j8n

32 assemblies; showing the first 12

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.

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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
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6wsl__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6wsl__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6wsl__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）44.86 Å
Rg (electron density)44.56 Å
Total Rg44.74 Å
Atom count18204
Residues2278
Excluded volume322370 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6wsl__assembly_1__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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6. 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
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7. Citations (1)