9BP6: Alpha1B and betaI/IVb microtubule

Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP. Determined by electron microscopy at 3.1 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,631
Mol. weight: 202.03 kDa
Ligands: G2P, MG, GTP
Released: 12 Jun 2024

Explore 9BP6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BP6 contains 97 α-helices and 64 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	1
α-helix	10-28	19
α-helix	44-46	3
α-helix	48-51	4
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	72-80	9
α-helix	82-84	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	135-140	6	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	166-172	7	1
α-helix	183-196	14
β-strand	200-205	6	1
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
β-strand	248	1	3
α-helix	252-259	8
β-strand	269-273	5	3
α-helix	278-283	6
α-helix	288-295	8
α-helix	298-300	3
β-strand	312-321	10	3
α-helix	325-337	13
β-strand	343	1	3
β-strand	351-356	6	3
α-helix	362-363	2
α-helix	369-370	2
β-strand	373-381	9	3
α-helix	384-400	17
α-helix	405-410	6
α-helix	415-435	21
α-helix	438-439	2

Chain B: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	4
α-helix	10-27	18
β-strand	30	1	5
β-strand	36	1	5
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-53	3	6
α-helix	55-57	3
β-strand	59-61	3	6
β-strand	63-67	5	4
α-helix	71-77	7
α-helix	87-89	3
β-strand	90-92	3	4
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-126	19
β-strand	130-138	9	4
α-helix	143-158	16
β-strand	163-170	8	4
α-helix	181-194	14
β-strand	198-203	6	4
α-helix	204-213	10
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	7
α-helix	250-257	8
β-strand	265-266	2	4
β-strand	267-271	5	7
α-helix	278-281	4
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-318	9	7
α-helix	323-336	14
β-strand	341	1	7
β-strand	349-354	6	7
β-strand	364-371	8	7
α-helix	372-374	3
α-helix	375-389	15
α-helix	392-395	4
α-helix	396-399	4
α-helix	405-427	23

Chain I: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	8
α-helix	10-28	19
α-helix	45-52	8
β-strand	53-55	3	9
β-strand	61-63	3	9
β-strand	65-69	5	8
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	8
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	132-140	9	8
α-helix	144-160	17
β-strand	167-172	6	8
α-helix	183-197	15
β-strand	200-205	6	8
α-helix	206-217	12
α-helix	224-243	20
β-strand	248	1	8
α-helix	252-259	8
β-strand	269-273	5	8
β-strand	277	1	10
α-helix	278-281	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	312-321	10	8
α-helix	325-337	13
β-strand	343	1	8
β-strand	351-356	6	8
α-helix	359-361	3
β-strand	368	1	10
α-helix	369-370	2
β-strand	373-381	9	8
α-helix	384-399	16
α-helix	405-410	6
α-helix	416-435	20

Chain Q: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	10-28	19
β-strand	30	1	12
β-strand	36	1	12
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-53	3	13
β-strand	59-61	3	13
β-strand	63-67	5	11
α-helix	70-77	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	11
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-125	17
β-strand	130-138	9	11
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-169	7	11
α-helix	181-194	14
β-strand	198-202	5	11
α-helix	204-213	10
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	14
α-helix	250-257	8
β-strand	265-266	2	11
β-strand	267-271	5	14
α-helix	276-281	6
α-helix	286-294	9
α-helix	296-298	3
β-strand	310-319	10	14
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	14
β-strand	349-354	6	14
β-strand	363-371	9	14
α-helix	372-374	3
α-helix	375-390	16
α-helix	395-401	7
α-helix	405-427	23

Molecules and chains

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

Sequence of entity 1 (A, I), FASTA

>9BP6_1 Tubulin alpha-1B chain (chains A, I)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, Q), FASTA

>9BP6_2 Tubulin beta chain (chains B, Q)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Ligands and cofactors

ID	Name	Formula	Copies
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	2
MG	Magnesium ion	Mg	4
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Cryo-EM structures of human alpha1B/betaI+betaIVb 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 P68363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8L 1.8 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
6J8O 1.85 Å, Structure of a hypothetical protease
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
8VT7 2.66 Å, Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
8V2J 2.9 Å, Structure of alpha1B and betaI/IVb microtubule bound to GDP
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
9HQ4 3.28 Å, TTLL11 bound to microtubule
7M18 3.38 Å, HeLa-tubulin in complex with cryptophycin 1

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