5ij9

Cryo EM density of microtubule assembled from human TUBB3-D417H mutant

Method: ELECTRON MICROSCOPY D_max: 98.7 Å Quality: GOOD

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

Tubulin alpha-1B chain

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–437	Not recorded	Tubulin beta-3 chain × 1 （Q13509） 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

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 5IJ9	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 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 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
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 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 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 ligand/ion Different experimental conditions Different structure-quality metrics	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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	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 construct Different mutation/modification 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 construct Different mutation/modification 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 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 construct Different mutation/modification 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 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 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 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 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 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 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；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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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
7ZCW Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP Deposited 2022-03-29	Different construct Different mutation/modification Different oligomeric state 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 E 1–451（451 aa）	Not recorded	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
8T42 Model of TTLL6 MTBH1-2 bound to microtubule Deposited 2023-06-08	Different construct Different mutation/modification 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 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 construct Different mutation/modification 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 oligomeric state 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 oligomeric state 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 Different structure-quality metrics	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 construct Different mutation/modification 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 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 1–437； UniProt 1–437

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–426	Mutation：D417H	Tubulin alpha-1B chain × 1 （P68363） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5IJ9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
22AJ GDP human alpha1A/beta3 S239C microtubule Deposited 2026-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–450（450 aa）	Mutation：S239C	MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.48 Å
22AK GDP human alpha1A/beta3 microtubule Deposited 2026-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–450（450 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.41 Å
5IJ0 Cryo EM density of microtubule assembled from human TUBB3 Deposited 2016-03-01	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–426（426 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
5JCO Structure and dynamics of single-isoform recombinant neuronal human tubulin Deposited 2016-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 1–426（426 aa） Chain D 1–426（426 aa） Chain I 1–426（426 aa） Chain J 1–426（426 aa） Chain K 1–426（426 aa） Chain L 1–426（426 aa）	Not recorded	G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 6 MG MAGNESIUM ION × 12 GTP GUANOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6E7B 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubules Deposited 2018-07-25	Different mutation/modification 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 3.50 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 B 1–450（450 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
6WSL Cryo-EM structure of VASH1-SVBP bound to microtubules Deposited 2020-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–450（450 aa） Chain F 1–450（450 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
7LXB HeLa-tubulin in complex with cryptophycin 52 Deposited 2021-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain H 1–450（450 aa） Chain J 1–450（450 aa） Chain L 1–450（450 aa） Chain N 1–450（450 aa） Chain P 1–450（450 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain H 1–450（450 aa） Chain J 1–450（450 aa） Chain L 1–450（450 aa） Chain N 1–450（450 aa） Chain P 1–450（450 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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain H 1–450（450 aa） Chain J 1–450（450 aa） Chain L 1–450（450 aa） Chain N 1–450（450 aa） Chain P 1–450（450 aa） Chain R 1–450（450 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 B 1–450（450 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 B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain G 1–450（450 aa） Chain H 1–450（450 aa） Chain I 1–450（450 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 Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain G 1–450（450 aa） Chain H 1–450（450 aa） Chain I 1–450（450 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 B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain G 1–450（450 aa） Chain H 1–450（450 aa） Chain I 1–450（450 aa）	Not recorded	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 B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain G 1–450（450 aa） Chain H 1–450（450 aa） Chain I 1–450（450 aa）	Not recorded	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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: Hexameric	Chain B 1–450（450 aa） Chain H 1–450（450 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
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 2 1–450（450 aa） Chain o 1–450（450 aa） Chain p 1–450（450 aa） Chain q 1–450（450 aa） Chain r 1–450（450 aa） Chain s 1–450（450 aa） Chain t 1–450（450 aa） Chain u 1–450（450 aa） Chain v 1–450（450 aa） Chain w 1–450（450 aa） Chain x 1–450（450 aa） Chain y 1–450（450 aa） Chain z 1–450（450 aa）	Not recorded	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 2 1–450（450 aa） Chain o 1–450（450 aa） Chain p 1–450（450 aa） Chain q 1–450（450 aa） Chain r 1–450（450 aa） Chain s 1–450（450 aa） Chain t 1–450（450 aa） Chain u 1–450（450 aa） Chain v 1–450（450 aa） Chain w 1–450（450 aa） Chain x 1–450（450 aa） Chain y 1–450（450 aa） Chain z 1–450（450 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 construct Different mutation/modification 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 1–450（450 aa） Chain F 1–450（450 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
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 Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain N 1–450（450 aa） Chain P 1–450（450 aa） Chain R 1–450（450 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 B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain N 1–450（450 aa） Chain P 1–450（450 aa） Chain R 1–450（450 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 B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain N 1–450（450 aa） Chain P 1–450（450 aa） Chain R 1–450（450 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 B 1–450（450 aa） Chain D 1–450（450 aa） Chain F 1–450（450 aa） Chain N 1–450（450 aa） Chain P 1–450（450 aa） Chain R 1–450（450 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
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 structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 73 PDB declaration: 73-meric	Chain BB 1–450（450 aa） Chain CB 1–450（450 aa） Chain DB 1–450（450 aa） Chain EB 1–450（450 aa） Chain FB 1–450（450 aa） Chain GB 1–450（450 aa） Chain HB 1–450（450 aa） Chain IB 1–450（450 aa） Chain JB 1–450（450 aa） Chain KB 1–450（450 aa） Chain LB 1–450（450 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
9WD7 GMPCPP-stabilizsd human alpha1A/beta3 microtubule Deposited 2025-08-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain b 1–450（450 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.34 Å
9WD9 GMPCPP-stabilized human alpha1A/beta3 S239C microtubule Deposited 2025-08-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain b 1–450（450 aa）	Mutation：S239C	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.26 Å
9WDA Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 microtubule Deposited 2025-08-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain b 1–450（450 aa）	Not recorded	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 TA1 TAXOL × 1 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å
9WDB Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 S239C microtubule Deposited 2025-08-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain b 1–450（450 aa）	Mutation：S239c	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 TA1 TAXOL × 1 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.39 Å

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 1–426； UniProt 1–426

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ij9
Deposition date deposition_date	2016-03-01
Structure title title	Cryo EM density of microtubule assembled from human TUBB3-D417H mutant
Keywords keywords	human, microtubules, mutant tubulin, hydrolysis, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	29.87 Å
Radius of gyration Rg (electron density) rg_electron	29.19 Å
Forward intensity I(0) i0	154981000.00
Molecular weight molecular_weight	96665.0 kDa
Excluded volume excluded_volume	119810 Å³
Envelope volume envelope_volume	142090 Å³
Hydration-shell volume shell_volume	40132 Å³
Envelope diameter envelope_diameter	106.6 Å
Shell Rg shell_rg	37.06 Å
Envelope Rg envelope_rg	29.42 Å
Shape Rg shape_rg	29.20 Å
Total Rg total_rg	29.80 Å
Total atoms total_atoms	13309
Residues n_residues	856
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	98.7 Å
Rg (real space) rg_real	29.89 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.5500e+08
I(0) uncertainty (real space) i0_real_error	2.0110e+06
Rg (reciprocal space) rg_reciprocal	29.89 Å
I(0) (reciprocal space) i0_reciprocal	155000000.0000
Solution quality estimate total_estimate	0.8778
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.281
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	53790000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.915

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Tubulin alpha-1B chain
Molecular weight formula_weight	48665.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	13309

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Tubulin beta-3 chain
Molecular weight formula_weight	47833.0 kDa
Mutation mutation	D417H
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNHLVSEYQQYQ

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	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5ij9A01
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	5ij9A02
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	5ij9A03
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	5ij9B01
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	5ij9B02
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	5ij9B03
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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Resolution resolution	3.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	26959

fit	/app/data/saxs_computation/ij/5ij9/5ij9.fit
pddf	/app/data/pr_computation/ij/5ij9/5ij9.pr.out
profile	/app/data/saxs_computation/ij/5ij9/5ij9.dat

Cryo EM density of microtubule assembled from human TUBB3-D417H mutant

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-3 chain

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)