8V2J: Alpha1B and betaI/IVb microtubule

Structure of alpha1B and betaI/IVb microtubule bound to GDP. Determined by electron microscopy at 2.9 Å resolution. Released 27 Nov 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,580
Mol. weight: 201.83 kDa
Ligands: GDP, GTP, MG
Released: 27 Nov 2024

Explore 8V2J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V2J contains 97 α-helices and 69 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	12
α-helix	10-28	19
α-helix	45-52	8
β-strand	53-55	3	13
β-strand	61-63	3	13
β-strand	65-69	5	12
α-helix	73-80	8
β-strand	93-94	2	12
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-128	19
β-strand	131-140	10	12
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-171	7	12
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	12
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	12
α-helix	249-251	3
α-helix	252-259	8
β-strand	269	1	12
β-strand	272-273	2	12
α-helix	278-281	4
α-helix	288-295	8
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-337	13
β-strand	343	1	12
β-strand	351-356	6	12
α-helix	358-360	3
α-helix	362-363	2
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	384-399	16
α-helix	405-410	6
α-helix	415-435	21
α-helix	438-439	2

Chain B: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
β-strand	30	1	2
β-strand	35	1	3
β-strand	36	1	2
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-53	3	4
α-helix	55-57	3
β-strand	58	1	3
β-strand	59-61	3	4
β-strand	63-67	5	1
α-helix	71-78	8
β-strand	90-92	3	1
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-126	19
β-strand	130-138	9	1
α-helix	142-158	17
β-strand	164-170	7	1
α-helix	181-195	15
β-strand	198-203	6	1
α-helix	204-210	7
α-helix	211-215	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	5
α-helix	250-257	8
β-strand	265-266	2	1
β-strand	267-271	5	5
α-helix	278-281	4
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	5
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	5
β-strand	349-354	6	5
α-helix	357	1
β-strand	363-371	9	5
α-helix	374-391	18
α-helix	395-400	6
α-helix	405-427	23

Chain D: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-28	19
α-helix	45-52	8
β-strand	53-55	3	15
β-strand	61-63	3	15
β-strand	65-69	5	14
α-helix	73-80	8
α-helix	82-84	3
β-strand	92-94	3	14
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
β-strand	132-140	9	14
α-helix	144-160	17
β-strand	165-171	7	14
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	14
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	14
α-helix	252-259	8
β-strand	269	1	14
β-strand	272-273	2	14
α-helix	278-281	4
α-helix	288-296	9
α-helix	307-309	3
β-strand	312-321	10	14
α-helix	325-337	13
β-strand	343	1	14
β-strand	351-356	6	14
α-helix	358-360	3
α-helix	362-363	2
α-helix	369-370	2
β-strand	373-381	9	14
α-helix	384-400	17
α-helix	405-410	6
α-helix	415-435	21
α-helix	438-439	2

Chain E: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	35	1	8
β-strand	36	1	7
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-53	3	9
β-strand	58	1	8
β-strand	59-61	3	9
β-strand	63-67	5	6
α-helix	71-78	8
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-126	18
β-strand	130-138	9	6
α-helix	142-158	17
β-strand	164-170	7	6
α-helix	181-195	15
β-strand	198-203	6	6
α-helix	204-210	7
α-helix	211-215	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	10
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	10
α-helix	278-281	4
α-helix	286-294	9
β-strand	310	1	11
β-strand	313-319	7	10
α-helix	325-336	12
α-helix	338-340	3
β-strand	341	1	11
β-strand	349-354	6	10
β-strand	363-369	7	10
α-helix	374-391	18
α-helix	395-400	6
α-helix	405-427	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta chain	B, E	protein	444	Homo sapiens	P07437 (AlphaFold model)
Tubulin alpha-1B chain	A, D	protein	451	Homo sapiens	P68363 (AlphaFold model)

Sequence of entity 1 (B, E), FASTA

>8V2J_1 Tubulin beta chain (chains B, E)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Sequence of entity 2 (A, D), FASTA

>8V2J_2 Tubulin alpha-1B chain (chains A, D)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Cryo-EM structures of human alpha 1B/ beta I+ beta IVb microtubules shed light on isoform specific assembly. Zehr, E.A., Roll-Mecak, A. bioRxiv (2023). DOI 10.1101/2023.12.01.569594

Other PDB entries of the same protein (UniProt P07437 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QNZ 2.2 Å, Orthorhombic form of IgG1 Fab fragment (in complex with antigenic tubulin peptide)…
3QO0 2.3 Å, Monoclinic form of IgG1 Fab fragment (in complex with antigenic peptide) sharing same Fv…
8BPO 2.8 Å, Structure of rabbit 80S ribosome translating beta-tubulin in complex with…
7TTT 2.9 Å, The beta-tubulin folding intermediate III
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
7TRG 3.0 Å, The beta-tubulin folding intermediate I
7X0S 3.1 Å, Human TRiC-tubulin-S3
9BP6 3.1 Å, Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9HQ4 3.28 Å, TTLL11 bound to microtubule
7TTN 3.3 Å, The beta-tubulin folding intermediate II
6I2I 3.6 Å, Refined 13pf Hela Cell Tubulin microtubule (EML4-NTD decorated)

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