8VT7: Tubulin beta-3 chain

Structure of the gamma tubulin ring complex nucleated microtubule protofilament. Determined by electron microscopy at 2.66 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 2.66 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,590
Mol. weight: 206.57 kDa
Ligands: MG, GTP, GDP
Released: 27 Mar 2024

Explore 8VT7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VT7 contains 105 α-helices and 72 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
α-helix	10-28	19
β-strand	30	1	9
β-strand	35	1	10
β-strand	36	1	9
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-54	4	10
β-strand	58-61	4	10
β-strand	63-67	5	8
α-helix	70-77	8
α-helix	87-89	3
β-strand	90-92	3	8
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-125	18
β-strand	129-138	10	8
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-169	7	8
α-helix	170-172	3
α-helix	181-195	15
β-strand	198-202	5	8
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
β-strand	246	1	11
α-helix	250-257	8
β-strand	265-266	2	8
β-strand	267-270	4	11
α-helix	276-278	3
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	11
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	11
β-strand	349-354	6	11
α-helix	357-358	2
β-strand	363-371	9	11
α-helix	374-389	16
α-helix	396-399	4
α-helix	405-427	23

Chain B: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	12
α-helix	10-28	19
β-strand	35	1	13
α-helix	48-51	4
β-strand	53-55	3	14
β-strand	60	1	13
β-strand	61-63	3	14
β-strand	65-69	5	12
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	12
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	132-140	9	12
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	12
α-helix	172-174	3
α-helix	183-194	12
β-strand	200-204	5	12
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	12
α-helix	252-259	8
β-strand	262	1	15
β-strand	265	1	15
β-strand	269-272	4	12
α-helix	278-281	4
α-helix	288-296	9
α-helix	298-300	3
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	359-363	5
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	383-401	19
α-helix	405-409	5
α-helix	415-436	22

Chain F: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	10-28	19
β-strand	30	1	2
β-strand	35	1	3
β-strand	36	1	2
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-54	4	3
β-strand	58-61	4	3
β-strand	63-67	5	1
α-helix	70-77	8
α-helix	87-89	3
β-strand	90-92	3	1
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-126	19
β-strand	129-138	10	1
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	1
α-helix	171-172	2
α-helix	181-195	15
β-strand	198-200	3	1
β-strand	202-203	2	1
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
β-strand	246	1	4
α-helix	250-257	8
β-strand	265-266	2	1
β-strand	267-270	4	4
α-helix	276-278	3
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-318	9	4
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	4
β-strand	349-354	6	4
α-helix	357-358	2
β-strand	364-371	8	4
α-helix	374-391	18
α-helix	395-401	7
α-helix	405-427	23

Chain J: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	5
α-helix	10-28	19
α-helix	48-50	3
β-strand	53-55	3	6
β-strand	61-63	3	6
β-strand	65-69	5	5
α-helix	73-79	7
α-helix	82-85	4
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	131-140	10	5
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	5
α-helix	172-174	3
α-helix	183-194	12
β-strand	200-204	5	5
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	5
α-helix	252-258	7
β-strand	262	1	7
β-strand	265	1	7
β-strand	269	1	5
β-strand	272	1	5
α-helix	278-281	4
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	5
α-helix	325-337	13
β-strand	343	1	5
β-strand	351-355	5	5
α-helix	359-363	5
α-helix	369-370	2
β-strand	373-381	9	5
α-helix	383-399	17
α-helix	405-409	5
α-helix	415-436	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta-3 chain	A, F	protein	456	Homo sapiens	Q13509 (AlphaFold model)
Tubulin alpha-1B chain	B, J	protein	457	Homo sapiens	P68363 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>8VT7_1 Tubulin beta-3 chain (chains A, F)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDEEESEAQGPKENLYFQ

Sequence of entity 2 (B, J), FASTA

>8VT7_2 Tubulin alpha-1B chain (chains B, J)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIHHHHHHGGGDDSFNTFFS
ETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEI
IDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPA
PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQI
VSSITASLRFDGALNVDLTDFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNA
CFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVG
INYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGME
EGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Ligands and cofactors

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

Primary citation

Structure of the gamma-tubulin ring complex-capped microtubule. Aher, A., Urnavicius, L., Xue, A. et al. Nat Struct Mol Biol (2024) 31:1124-1133. DOI 10.1038/s41594-024-01264-z · PubMed

Other PDB entries of the same protein (UniProt Q13509 (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
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
9WD9 2.26 Å, GMPCPP-stabilized human alpha1A/beta3 S239C microtubule
9WD7 2.34 Å, GMPCPP-stabilizsd human alpha1A/beta3 microtubule
9WDA 2.35 Å, Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 microtubule
9WDB 2.39 Å, Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 S239C microtubule
22AK 2.41 Å, GDP human alpha1A/beta3 microtubule
22AJ 2.48 Å, GDP human alpha1A/beta3 S239C microtubule
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
6WSL 3.1 Å, Cryo-EM structure of VASH1-SVBP bound to microtubules
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
7M18 3.38 Å, HeLa-tubulin in complex with cryptophycin 1

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