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7zcw

Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP

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

Tubulin alpha-1B chain

OrganismNot specified

UniProt P68363

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-2B chain × 4 （Q9BVA1） Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） Small vasohibin-binding protein × 1 （Q8N300） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4 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
2e4h 5ij0 5ij9 5n5n 6e7b 6e7c 6i2i 6j4v 6qus 6quy 6qve 6qvj

39 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TBA1B_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-2B chain

OrganismNot specified

UniProt Q9BVA1

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-1B chain × 2 （P68363） Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） Small vasohibin-binding protein × 1 （Q8N300） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4 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
6e7c 7zcw 9ox7

3 assemblies

View Construct and Data Evidence
UniProt name TBB2B_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–445； UniProt 1–445 Author chain F； PDBConstruct 1–445； UniProt 1–445 Author chain G； PDBConstruct 1–445； UniProt 1–445 Author chain H； PDBConstruct 1–445； UniProt 1–445

Tubulinyl-Tyr carboxypeptidase 2

Homo sapiens

UniProt Q86V25

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-1B chain × 2 （P68363） Tubulin beta-2B chain × 4 （Q9BVA1） Small vasohibin-binding protein × 1 （Q8N300） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4 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 6j4v 6qby 6qby 7zcw

11 assemblies

View Construct and Data Evidence
UniProt name VASH2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–355； UniProt 1–355

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-1B chain × 2 （P68363） Tubulin beta-2B chain × 4 （Q9BVA1） Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 6 PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4 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

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_id7zcw
Deposition date deposition_date2022-03-29
Structure title titleCryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP
Keywords keywordsMicrotubule, Enzyme, Complex, Detyrosination, 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.

7zcw__assembly_1__model_1

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

Download this curve (.dat)

7zcw__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

7zcw__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）48.78 Å
Rg (electron density)48.28 Å
Total Rg48.46 Å
Atom count44338
Residues2837
Excluded volume398470 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7zcw__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 (7)

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id7zcwA01
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_id7zcwA02
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_id7zcwB01
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_id7zcwB02
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_id7zcwB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id7zcwE01
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_id7zcwE02
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_id7zcwF01
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_id7zcwF02
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_id7zcwF03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id7zcwG01
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_id7zcwG02
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_id7zcwG03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id7zcwH01
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_id7zcwH02
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_id7zcwH03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
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7. Citations (1)