8VA2: Symmetry expanded map of 2 gamma-tubulins

Symmetry expanded map of 2 gamma-tubulins bound to 2 alpha tubulins in gamma tubulin ring complex capped microtubule end. Determined by electron microscopy at 4.5 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 4.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,430
Mol. weight: 204.06 kDa
Ligands: GDP, MG, GTP
Released: 27 Mar 2024

Explore 8VA2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VA2 contains 83 α-helices and 58 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: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	1
α-helix	10-27	18
α-helix	48-50	3
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-68	4	1
α-helix	72-79	8
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	134-138	5	1
α-helix	144-160	17
β-strand	165-169	5	1
α-helix	183-197	15
β-strand	201	1	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
α-helix	279-282	4
α-helix	288-296	9
α-helix	298-300	3
β-strand	314	1	4
β-strand	317-320	4	3
α-helix	325-337	13
β-strand	353-356	4	3
α-helix	359-360	2
α-helix	369-370	2
β-strand	375-377	3	3
β-strand	380	1	4
α-helix	383-401	19
α-helix	406-409	4
α-helix	415-435	21

Chain b: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	5
α-helix	10-28	19
α-helix	49-51	3
β-strand	53-55	3	6
β-strand	61-63	3	6
β-strand	65-66	2	5
α-helix	72-80	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	134-138	5	5
α-helix	144-160	17
β-strand	165-169	5	5
α-helix	172-174	3
α-helix	183-194	12
β-strand	200-201	2	5
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
α-helix	252-258	7
β-strand	269-270	2	7
α-helix	278-281	4
α-helix	288-296	9
β-strand	314-317	4	7
β-strand	320-321	2	8
α-helix	325-337	13
β-strand	351-352	2	7
α-helix	358-360	3
α-helix	362-363	2
β-strand	373-374	2	8
β-strand	377-380	4	7
α-helix	383-401	19
α-helix	406-409	4
α-helix	415-436	22

Chain g: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	9
α-helix	11-28	18
β-strand	31	1	10
β-strand	37	1	10
β-strand	52-54	3	11
β-strand	60-62	3	11
β-strand	64-66	3	9
α-helix	72-77	6
α-helix	83-85	3
α-helix	104-113	10
α-helix	115-127	13
β-strand	134-140	7	9
α-helix	144-158	15
β-strand	165-171	7	9
β-strand	172	1	12
α-helix	173-174	2
α-helix	178-179	2
α-helix	184-197	14
β-strand	201-202	2	9
β-strand	206	1	12
α-helix	207-216	10
α-helix	225-244	20
α-helix	253-258	6
β-strand	270-273	4	13
α-helix	290-296	7
β-strand	317-319	3	14
β-strand	321-324	4	13
α-helix	330-343	14
β-strand	357-360	4	13
β-strand	376-379	4	13
β-strand	380-381	2	14
α-helix	382-384	3
α-helix	385-399	15
α-helix	408-410	3
α-helix	419-438	20

Chain h: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	15
α-helix	11-28	18
β-strand	31	1	16
β-strand	37	1	16
α-helix	40-43	4
α-helix	48-50	3
β-strand	54	1	17
β-strand	60	1	17
β-strand	66-67	2	15
α-helix	71-78	8
α-helix	83-85	3
α-helix	88-90	3
β-strand	91	1	15
α-helix	104-128	25
β-strand	134-138	5	15
α-helix	144-160	17
β-strand	165-172	8	15
α-helix	173-174	2
α-helix	184-198	15
β-strand	201-206	6	15
α-helix	207-218	12
α-helix	224-244	21
α-helix	253-258	6
α-helix	264-266	3
β-strand	270	1	18
β-strand	273	1	18
α-helix	281-284	4
α-helix	290-298	9
α-helix	300-302	3
β-strand	317-325	9	18
α-helix	330-343	14
β-strand	357-361	5	18
β-strand	374-381	8	18
α-helix	382-384	3
α-helix	385-401	17
α-helix	406-409	4
α-helix	412-415	4
α-helix	419-439	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	a, b	protein	457	Homo sapiens	P68363 (AlphaFold model)
Tubulin gamma-1 chain	g, h	protein	441	Homo sapiens	P23258 (AlphaFold model)

Sequence of entity 1 (a, b), FASTA

>8VA2_1 Tubulin alpha-1B chain (chains a, b)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIHHHHHHGGGDDSFNTFFS
ETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEI
IDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPA
PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQI
VSSITASLRFDGALNVDLTDFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNA
CFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVG
INYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGME
EGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (g, h), FASTA

>8VA2_2 Tubulin gamma-1 chain (chains g, h)
MPREIITLQLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHY
IPRAVLLDLEPRVIHSILNSPYAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFD
IIDREADGSDSLEGFVLCHSIAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQDEMSD
VVVQPYNSLLTLKRLTQNADCVVVLDNTALNRIATDRLHIQNPSFSQINQLVSTIMSAST
TTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTDQSVASVRKTTVLDVMRRLLQP
KNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANFIPWGPASIQVAL
SRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNFDE
MDTSREIVQQLIDEYHAATRP

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	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 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
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
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
9HQ4 3.28 Å, TTLL11 bound to microtubule

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