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

Method: ELECTRON MICROSCOPY D_max: 170.3 Å Quality: REASONABLE

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

Tubulin alpha-1B chain

OrganismNot specified

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-2B chain × 4 （Q9BVA1） Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） Small vasohibin-binding protein × 1 （Q8N300） GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 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.

Other PDB	Difference from Current Entry 7ZCW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2E4H Solution structure of cytoskeletal protein in complex with tubulin tail Deposited 2006-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 416–451（36 aa） Fragment：C-tail, residues 416-451	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；303 K；Pressure ambient NMR sample composition 0.9mM U-15N,13C CLIP: Nonlabel tubulin; 30mM BisTris buffer K; 1mM DTT; 100% D2O \| 100% D2O NMR sample composition 0.9mM U-15N CLIP: Nonlabel tubulin; 30mM BisTris buffer K; 1mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9mM U-15N,13C tubulin: Nonlabel CLIP; 30mM BisTris buffer K; 1mM DTT; 100% D2O \| 100% D2O NMR sample composition 0.9mM U-15N tubulin: Nonlabel CLIP; 30mM BisTris buffer K; 1mM DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5IJ0 Cryo EM density of microtubule assembled from human TUBB3 Deposited 2016-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–437（437 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
5IJ9 Cryo EM density of microtubule assembled from human TUBB3-D417H mutant Deposited 2016-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–437（437 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
5N5N Cryo-EM structure of tsA201 cell alpha1B and betaI and betaIVb microtubules Deposited 2017-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 1–437（437 aa） Chain H 1–437（437 aa） Chain I 1–437（437 aa） Chain J 1–437（437 aa） Chain K 1–437（437 aa） Chain L 1–437（437 aa）	Not recorded	G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 6 MG MAGNESIUM ION × 12 GTP GUANOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；BRB80 with GMPCPP (80mM PIPES, 2mM MgCl2, 1mM EGTA, 1mM DTT, 1mM GMPCPP) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6E7B 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubules Deposited 2018-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–437（437 aa）	Not recorded	MG MAGNESIUM ION × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6E7C 14-pf 3-start GMPCPP-human alpha1B/beta2B microtubules Deposited 2018-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–437（437 aa）	Not recorded	MG MAGNESIUM ION × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
6I2I Refined 13pf Hela Cell Tubulin microtubule (EML4-NTD decorated) Deposited 2018-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 TA1 TAXOL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；25mM PIPES, 1.5mM MgCl2, 1mM EGTA, 1mM DTT, 30mM NaCl,1mM GMPCPP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6J4V Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 431–451（21 aa）	Mutation：E450C	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.2；293 K；For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up crystallization trials. The resulting V2c-SVBP S58C-maTail complex was crystallized in 1.4 M sodium/potassium phosphate, pH 8.2.	Resolution 2.10 Å R-free 0.200
6QUS HsCKK (human CAMSAP1) decorated 13pf taxol-GDP microtubule Deposited 2019-02-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain O 1–451（451 aa） Chain X 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；BRB20 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6QUY NgCKK (N.Gruberi CKK) decorated 13pf taxol-GDP microtubule Deposited 2019-02-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；BRB20 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6QVE NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule Deposited 2019-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；BRB20 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6QVJ HsCKK (human CAMSAP1) decorated 14pf taxol-GDP microtubule Deposited 2019-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain O 1–451（451 aa） Chain X 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；BRB20 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6S8L Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes Deposited 2019-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 PN6 (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100 mM Bis-TrisMethane, pH 5.5, supplemented with 200 mM ammonium sulfate and 25% PEG3350	Resolution 1.80 Å R-free 0.266
7LXB HeLa-tubulin in complex with cryptophycin 52 Deposited 2021-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain G 1–451（451 aa） Chain I 1–451（451 aa） Chain K 1–451（451 aa） Chain M 1–451（451 aa） Chain O 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 8 YGY Cryptophycin 52 × 8 GDP GUANOSINE-5'-DIPHOSPHATE × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
7M18 HeLa-tubulin in complex with cryptophycin 1 Deposited 2021-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain G 1–451（451 aa） Chain I 1–451（451 aa） Chain K 1–451（451 aa） Chain M 1–451（451 aa） Chain O 1–451（451 aa）	Not recorded	YNP Cryptophycin 1 × 8 GDP GUANOSINE-5'-DIPHOSPHATE × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
7M20 18-mer HeLa-tubulin rings in complex with Cryptophycin 1 Deposited 2021-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain G 1–451（451 aa） Chain I 1–451（451 aa） Chain K 1–451（451 aa） Chain M 1–451（451 aa） Chain O 1–451（451 aa） Chain Q 1–451（451 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 9 YNP Cryptophycin 1 × 9 GTP GUANOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
7PJF Inhibiting parasite proliferation using a rationally designed anti-tubulin agent Deposited 2021-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；100 mM Bis-TrisMethane, pH 5.5, supplemented with 200 mM ammonium sulfate and 25% PEG3350	Resolution 1.86 Å R-free 0.218
7SJ7 Undecorated 13pf wildtype microtubule from recombinant human tubulin Deposited 2021-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain J 1–451（451 aa） Chain K 1–451（451 aa） Chain L 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 2 mM GTP, pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7SJ8 13pf wildtype microtubule from recombinant human tubulin decorated with kinesin Deposited 2021-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain J 1–451（451 aa） Chain K 1–451（451 aa） Chain L 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 2 mM GTP, pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30 second adsorption time onto grid. blot force 15, 4 second blot time, 37 degrees, and 100 percent humidity. 0.5 second drain time.	Resolution 3.60 Å
7SJ9 13pf E254A microtubule from recombinant human tubulin decorated with EB3 Deposited 2021-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain J 1–451（451 aa） Chain K 1–451（451 aa） Chain L 1–451（451 aa）	Mutation：E254A Mutation：E254A Mutation：E254A Mutation：E254A Mutation：E254A Mutation：E254A	GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 2 mM GTP, pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7SJA Undecorated 13pf E254N microtubule from recombinant human tubulin Deposited 2021-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain J 1–451（451 aa） Chain K 1–451（451 aa） Chain L 1–451（451 aa）	Mutation：E254N Mutation：E254N Mutation：E254N Mutation：E254N Mutation：E254N Mutation：E254N	GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；80 mM PIPES, 1 mM EGTA, 5 mM MgCl2, 2 mM GTP, pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
7Z6S MATCAP bound to a human 14 protofilament microtubule Deposited 2022-03-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: Hexameric	Chain A 1–451（451 aa） Chain K 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8T42 Model of TTLL6 MTBH1-2 bound to microtubule Deposited 2023-06-08	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–451（451 aa） Chain F 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；The sample was blotted with Whatman #5 blotting paper on both sides of the grid for 3 s with a blot offset of -1 using a Vitrobot Mark IV (Thermo Fisher Scientific) with a chamber set to 30C at 100% humidity and subsequently plunged into liquid ethane.	Resolution 3.60 Å
8U3Z Model of TTLL6 bound to microtubule from composite map Deposited 2023-09-08	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–451（451 aa） Chain F 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 5 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8V2J Structure of alpha1B and betaI/IVb microtubule bound to GDP Deposited 2023-11-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–451（451 aa） Chain D 1–451（451 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；5 ul of microtubules were applied to glow-discharged cryo-EM grid and allowed to absorb for 30 sec.	Resolution 2.90 Å
8VA2 Symmetry expanded map of 2 gamma-tubulins bound to 2 alpha tubulins in gamma tubulin ring complex capped microtubule end. Deposited 2023-12-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain a 1–451（451 aa） Chain b 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
8VRJ Rigid body fitted model for gamma tubulin ring complex capped microtubule Deposited 2024-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric	Chain 1 1–451（451 aa） Chain O 1–451（451 aa） Chain P 1–451（451 aa） Chain Q 1–451（451 aa） Chain R 1–451（451 aa） Chain S 1–451（451 aa） Chain T 1–451（451 aa） Chain U 1–451（451 aa） Chain V 1–451（451 aa） Chain W 1–451（451 aa） Chain X 1–451（451 aa） Chain Y 1–451（451 aa） Chain Z 1–451（451 aa）	Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D Mutation：E254D	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
8VRK Rigid body fitted model for refined density map of gamma tubulin ring complex capped microtubule Deposited 2024-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric	Chain 1 1–451（451 aa） Chain O 1–451（451 aa） Chain P 1–451（451 aa） Chain Q 1–451（451 aa） Chain R 1–451（451 aa） Chain S 1–451（451 aa） Chain T 1–451（451 aa） Chain U 1–451（451 aa） Chain V 1–451（451 aa） Chain W 1–451（451 aa） Chain X 1–451（451 aa） Chain Y 1–451（451 aa） Chain Z 1–451（451 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.50 Å
8VT7 Structure of the gamma tubulin ring complex nucleated microtubule protofilament. Deposited 2024-01-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–451（451 aa） Chain J 1–451（451 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å
9BP6 Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP Deposited 2024-05-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–451（451 aa） Chain I 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Double-cycled GMPCPP microtubules were diluted to 2.5uM in Brb80 buffer. 5 ul of microtubules were applied to glow-discharged cryo-EM grid and allowed to absorb for 30 sec.	Resolution 3.10 Å
9CMM Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP Deposited 2024-07-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain E 1–451（451 aa） Chain I 1–451（451 aa）	Not recorded	G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4 MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Double-cycled GMPCPP microtubules were diluted to 2.5uM in Brb80 buffer. 5 ul of microtubules were applied to glow-discharged cryo-EM grid and allowed to absorb for 30 sec.	Resolution 3.10 Å
9COC Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP Deposited 2024-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa） Chain D 1–451（451 aa） Chain I 1–451（451 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；5 ul of microtubules were applied to glow-discharged electron microscopy grids and allowed to absorb for 30 sec.	Resolution 2.90 Å
9F3B Undecorated 13pf E254Q microtubule from recombinant human tubulin Deposited 2024-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–42（42 aa） Chain A 47–441（395 aa） Chain C 1–42（42 aa） Chain C 47–441（395 aa） Chain E 1–42（42 aa） Chain E 47–441（395 aa） Chain G 1–42（42 aa） Chain G 47–441（395 aa） Chain I 1–42（42 aa） Chain I 47–441（395 aa） Chain K 1–42（42 aa） Chain K 47–441（395 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9F3H Undecorated 13pf mosaic 20%E254Q - 80% E254QN microtubule from recombinant human tubulin Deposited 2024-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 47–441（395 aa） Chain C 47–441（395 aa） Chain E 47–441（395 aa） Chain G 47–441（395 aa） Chain I 47–441（395 aa） Chain K 47–441（395 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9F3R 13pf E254Q microtubule from recombinant human tubulin decorated with EB3 Deposited 2024-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain A 1–42（42 aa） Chain A 47–441（395 aa） Chain C 1–42（42 aa） Chain C 47–441（395 aa） Chain E 1–42（42 aa） Chain E 47–441（395 aa） Chain G 1–42（42 aa） Chain G 47–441（395 aa） Chain I 1–42（42 aa） Chain I 47–441（395 aa） Chain K 1–42（42 aa） Chain K 47–441（395 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9F3S 13pf mosaic 20%E254Q - 80% E254N microtubule from recombinant human tubulin decorated with EB3 Deposited 2024-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain A 1–42（42 aa） Chain A 47–441（395 aa） Chain C 1–42（42 aa） Chain C 47–441（395 aa） Chain E 1–42（42 aa） Chain E 47–441（395 aa） Chain G 1–42（42 aa） Chain G 47–441（395 aa） Chain I 1–42（42 aa） Chain I 47–441（395 aa） Chain K 1–42（42 aa） Chain K 47–441（395 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9HQ4 TTLL11 bound to microtubule Deposited 2024-12-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–451（451 aa） Chain C 1–451（451 aa）	Not recorded	G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4 MG MAGNESIUM ION × 4 TA1 TAXOL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7；40 mM Tris-HCl, pH 7.0, 1 mM TCEP, 1 mM MgCl2, 5 % glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
9SMX CM1-activated gTuRC in complex with nascent alpha-E254D mutant microtubules Deposited 2025-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 73 PDB declaration: 73-meric	Chain BA 1–451（451 aa） Chain CA 1–451（451 aa） Chain DA 1–451（451 aa） Chain EA 1–451（451 aa） Chain FA 1–451（451 aa） Chain GA 1–451（451 aa） Chain HA 1–451（451 aa） Chain IA 1–451（451 aa） Chain JA 1–451（451 aa） Chain KA 1–451（451 aa） Chain LA 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å

38 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

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	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 1–445 Chain F； UniProt 1–445 Chain G； UniProt 1–445 Chain H； UniProt 1–445	Not recorded	Tubulin alpha-1B chain × 2 （P68363） Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） Small vasohibin-binding protein × 1 （Q8N300） GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ZCW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6E7C 14-pf 3-start GMPCPP-human alpha1B/beta2B microtubules Deposited 2018-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–426（426 aa）	Not recorded	MG MAGNESIUM ION × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9OX7 In situ microtubule structure in the axon of a human neuron Deposited 2025-06-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–445（445 aa） Chain D 1–445（445 aa） Chain E 1–445（445 aa） Chain F 1–445（445 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å

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

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	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 1–355	Mutation：C158A	Tubulin alpha-1B chain × 2 （P68363） Tubulin beta-2B chain × 4 （Q9BVA1） Small vasohibin-binding protein × 1 （Q8N300） GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ZCW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6J4O Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 46–296（251 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 5 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.2；293 K；1.6 M sodium/potassium phosphate, pH 8.2	Resolution 2.30 Å R-free 0.224
6J4P Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 46–296（251 aa）	Not recorded	BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor epoY at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-epoY was crystallized in 1.0 M lithium chloride, 0.1 M HEPES, pH 7.0, 20% PEG 6000.	Resolution 1.60 Å R-free 0.188
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 46–296（251 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 46–296（251 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 46–296（251 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 46–296（251 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4S Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–355（355 aa）	Not recorded	GOL GLYCEROL × 3 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；293 K；full-length V2-SVBP complex at a concentration of 15 mg/mL was crystallized in 1.8 M sodium/potassium phosphate, pH 6.8	Resolution 2.80 Å R-free 0.227
6J4V Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 46–296（251 aa）	Not recorded	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.2；293 K；For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up crystallization trials. The resulting V2c-SVBP S58C-maTail complex was crystallized in 1.4 M sodium/potassium phosphate, pH 8.2.	Resolution 2.10 Å R-free 0.200
6QBY Crystal structure of VASH 2 in complex with SVBP Deposited 2018-12-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–295（256 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.2M Sodium formate 0.1M Bis-Tris propane pH 6.5 20% PEG3350	Resolution 2.09 Å R-free 0.230
6QBY Crystal structure of VASH 2 in complex with SVBP Deposited 2018-12-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 40–295（256 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.2M Sodium formate 0.1M Bis-Tris propane pH 6.5 20% PEG3350	Resolution 2.09 Å R-free 0.230

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

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	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	Not recorded	Tubulin alpha-1B chain × 2 （P68363） Tubulin beta-2B chain × 4 （Q9BVA1） Tubulinyl-Tyr carboxypeptidase 2 × 1 （Q86V25） GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ZCW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6J4O Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 5 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.2；293 K；1.6 M sodium/potassium phosphate, pH 8.2	Resolution 2.30 Å R-free 0.224
6J4P Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor epoY at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-epoY was crystallized in 1.0 M lithium chloride, 0.1 M HEPES, pH 7.0, 20% PEG 6000.	Resolution 1.60 Å R-free 0.188
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4Q Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–66（66 aa）	Not recorded	TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；V2c-SVBP was mixed with the inhibitor TPCK at a mole ratio of 1:5 and incubated on ice for 30 min. Then, the resulting co-complex of V2c-SVBP-TPCK was crystallized in 1.0 M sodium malonate, pH 7.0.	Resolution 2.70 Å R-free 0.247
6J4S Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	GOL GLYCEROL × 3 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.8；293 K；full-length V2-SVBP complex at a concentration of 15 mg/mL was crystallized in 1.8 M sodium/potassium phosphate, pH 6.8	Resolution 2.80 Å R-free 0.227
6J4U Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；293 K；by introducing three mutations E71S/A72H/K79M into V1c allowed us to solve the V1c-SVBP to high resolution. Well diffracting crystals of the mutant V1c-SVBP complex were obtained in 1.0 M lithium chloride, 0.1 M citric acid, pH 5.0, 20% PEG 6000.	Resolution 2.00 Å R-free 0.204
6J4V Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications Deposited 2019-01-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–66（66 aa）	Mutation：C58S	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.2；293 K；For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up crystallization trials. The resulting V2c-SVBP S58C-maTail complex was crystallized in 1.4 M sodium/potassium phosphate, pH 8.2.	Resolution 2.10 Å R-free 0.200
6J7B Crystal structure of VASH1-SVBP in complex with epoY Deposited 2019-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–52（52 aa）	Not recorded	BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；20%PEG6000, 1M lithium chloride, 0.1M MES pH6.0	Resolution 1.62 Å R-free 0.197
6J8F Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin Deposited 2019-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 3–48（46 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.0, 18% PEG 20000	Resolution 2.28 Å R-free 0.237
6J8N Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 Deposited 2019-01-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000	Resolution 1.95 Å R-free 0.210
6J8N Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 Deposited 2019-01-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000	Resolution 1.95 Å R-free 0.210
6J8O Structure of a hypothetical protease Deposited 2019-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 3–49（47 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M BIS-TRIS pH 6.5, 16% polyethylene glycol 10000	Resolution 1.85 Å R-free 0.195
6J91 Structure of a hypothetical protease Deposited 2019-01-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 3.50 Å R-free 0.258
6J9H Crystal structure of SVBP-VASH1 complex Deposited 2019-01-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 2.31 Å R-free 0.271
6J9H Crystal structure of SVBP-VASH1 complex Deposited 2019-01-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate	Resolution 2.31 Å R-free 0.271
6JZC Structural basis of tubulin detyrosination Deposited 2019-05-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–66（66 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；HEPES, Ammonium sulphate, potassium chloride	Resolution 2.20 Å R-free 0.215
6JZC Structural basis of tubulin detyrosination Deposited 2019-05-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–66（66 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；HEPES, Ammonium sulphate, potassium chloride	Resolution 2.20 Å R-free 0.215
6JZD Crystal structure of peptide-bound VASH2-SVBP complex Deposited 2019-05-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；HEPES, potassium chloride, Ammonium sulphate	Resolution 2.48 Å R-free 0.230
6JZE Crystal structure of VASH2-SVBP complex with the magic triangle I3C Deposited 2019-05-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；BIS-TRIS propane, Sodium formate	Resolution 2.51 Å R-free 0.266
6K81 Crystal structure of human VASH1-SVBP complex Deposited 2019-06-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；Calcium acetate, PEG 3000	Resolution 2.28 Å R-free 0.242
6LPG human VASH1-SVBP complex Deposited 2020-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–66（65 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.16 M ammonium sulfate, 0.08 M Sodium acetate pH4.6, 20%(w/v) PEG4000, 20%(v/v) glycerol	Resolution 2.30 Å R-free 0.236
6NVQ Crystal structure of the VASH1-SVBP complex Deposited 2019-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；19% PEG 3000, 0.1M Tris-HCl, 0.2M calcium chloride	Resolution 2.10 Å R-free 0.214
6OCF The crystal structure of VASH1-SVBP complex Deposited 2019-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–66（49 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M sodium citrate tribasic dihydrate, pH 5.0, and 18% (w/v) PEG20000	Resolution 2.10 Å R-free 0.222
6OCG Crystal structure of VASH1-SVBP complex bound with EpoY Deposited 2019-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 26–51（26 aa）	Not recorded	CL CHLORIDE ION × 1 GOL GLYCEROL × 1 BJL N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；5% (v/v) TacsimateTM, 0.1 M HEPES, pH 7.0, and 10% (w/v) polyethylene glycol monomethyl ether 5,000	Resolution 1.83 Å R-free 0.219
6OCH Crystal structure of VASH1-SVBP complex bound with parthenolide Deposited 2019-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–52（28 aa）	Not recorded	M4Y parthenolide × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, and 25 % (w/v) PEG 3350	Resolution 2.00 Å R-free 0.229
6OCH Crystal structure of VASH1-SVBP complex bound with parthenolide Deposited 2019-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 25–52（28 aa）	Not recorded	M4Y parthenolide × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammonium sulfate, 0.1 M Bis-tris, pH 5.5, and 25 % (w/v) PEG 3350	Resolution 2.00 Å R-free 0.229
6QBY Crystal structure of VASH 2 in complex with SVBP Deposited 2018-12-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.2M Sodium formate 0.1M Bis-Tris propane pH 6.5 20% PEG3350	Resolution 2.09 Å R-free 0.230
6QBY Crystal structure of VASH 2 in complex with SVBP Deposited 2018-12-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–66（66 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；0.2M Sodium formate 0.1M Bis-Tris propane pH 6.5 20% PEG3350	Resolution 2.09 Å R-free 0.230
6WSL Cryo-EM structure of VASH1-SVBP bound to microtubules Deposited 2020-05-01	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–66（66 aa） Chain H 1–66（66 aa）	Not recorded	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

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

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7zcw
Deposition date deposition_date	2022-03-29
Structure title title	Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP
Keywords keywords	Microtubule, Enzyme, Complex, Detyrosination, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	48.78 Å
Radius of gyration Rg (electron density) rg_electron	48.28 Å
Forward intensity I(0) i0	1564120000.00
Molecular weight molecular_weight	321430.0 kDa
Excluded volume excluded_volume	398470 Å³
Envelope volume envelope_volume	536550 Å³
Hydration-shell volume shell_volume	90898 Å³
Envelope diameter envelope_diameter	176.2 Å
Shell Rg shell_rg	53.84 Å
Envelope Rg envelope_rg	47.55 Å
Shape Rg shape_rg	48.29 Å
Total Rg total_rg	48.46 Å
Total atoms total_atoms	44338
Residues n_residues	2837
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	170.3 Å
Rg (real space) rg_real	48.64 Å
Rg uncertainty (real space) rg_real_error	1.63 Å
I(0) (real space) i0_real	1.5640e+09
I(0) uncertainty (real space) i0_real_error	3.0950e+07
Rg (reciprocal space) rg_reciprocal	48.78 Å
I(0) (reciprocal space) i0_reciprocal	1564000000.0000
Solution quality estimate total_estimate	0.6572
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.9 Å
Skewness Skewness skewness	0.256
Kurtosis Kurtosis kurtosis	-0.307
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	244500000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 0.087; Positv: 1.000; Valcen: 1.000; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Tubulin alpha-1B chain
Molecular weight formula_weight	50204.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	44390

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 Entity 2 polymer

Description description	Tubulin beta-2B chain
Molecular weight formula_weight	49907.8 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,G,H

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA

Entity 3 Entity 3 polymer

Description description	Tubulinyl-Tyr carboxypeptidase 2
Molecular weight formula_weight	40488.9 kDa
EC 编号 ec_number	3.4.17.17
Mutation mutation	C158A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTGSAADTHRCPHPKGAKGTRSRSSHARPVSLATSGGSEEEDKDGGVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKALEAVILGIYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTLSDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKILKPASAHSPTQVRSRGKSLSPRRRQASPPRRLGRREKSPALPEKKVADLSTLNEVGYQIRI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Small vasohibin-binding protein
Molecular weight formula_weight	8780.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQMQPPGEKHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Molecular weight formula_weight	521.2 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	7zcwA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	7zcwA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	7zcwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	7zcwB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	7zcwB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	7zcwE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	7zcwE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	7zcwF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	7zcwF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	7zcwF03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	7zcwG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	7zcwG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	7zcwG03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	7zcwH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	7zcwH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	7zcwH03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	96922

fit	/app/data/saxs_computation/zc/7zcw/7zcw.fit
pddf	/app/data/pr_computation/zc/7zcw/7zcw.pr.out
profile	/app/data/saxs_computation/zc/7zcw/7zcw.dat

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

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

Tubulin alpha-1B chain

State in the Current Structure

Other States of the Same Protein in the Database

Tubulin beta-2B chain

State in the Current Structure

Other States of the Same Protein in the Database

Tubulinyl-Tyr carboxypeptidase 2

State in the Current Structure

Other States of the Same Protein in the Database

Small vasohibin-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)