7Z0F: Cpap:s-TUBULIN:IIH5 alpharep complex

Cpap:s-TUBULIN:IIH5 alpharep complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 13 Apr 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Ovis aries, synthetic construct, Homo sapiens
Chains: 4
Atoms: 8,066
Mol. weight: 129.35 kDa
Ligands: GTP, MG, GDP
Released: 13 Apr 2022

Explore 7Z0F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z0F contains 64 α-helices and 39 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: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	48-51	4
β-strand	53-55	3	3
β-strand	60	1	2
β-strand	61-63	3	3
β-strand	65-69	5	1
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
β-strand	134-140	7	1
α-helix	144-160	17
β-strand	165-172	8	1
α-helix	183-194	12
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
β-strand	312-321	10	4
α-helix	325-336	12
β-strand	343	1	4
α-helix	350-351	2
β-strand	352-356	5	4
α-helix	359-360	2
β-strand	368	1	5
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	416-435	20

Chain B: 24 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	49-51	3
β-strand	53-55	3	9
β-strand	60	1	8
β-strand	61-63	3	9
β-strand	65-69	5	6
α-helix	73-79	7
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-128	19
β-strand	132-140	9	6
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	6
α-helix	183-197	15
β-strand	200-205	6	6
α-helix	206-214	9
β-strand	223	1	10
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-273	5	11
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	11
α-helix	307-309	3
β-strand	312-321	10	11
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	11
β-strand	351-356	6	11
β-strand	373-381	9	11
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22

Chain C: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	16-22	7
α-helix	28-40	13
α-helix	44-46	3
α-helix	47-52	6
α-helix	53-55	3
α-helix	59-72	14
α-helix	75-77	3
α-helix	78-84	7
α-helix	90-103	14
α-helix	106-108	3
α-helix	109-114	6
α-helix	115-117	3
α-helix	121-134	14
α-helix	137-149	13
α-helix	153-164	12

Chain P: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	326	1	10
α-helix	340-352	13
α-helix	376-377	2
α-helix	380-384	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A	protein	451	Ovis aries	A0A836D7T3 (AlphaFold model)
Tubulin beta chain	B	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
IIH5 alpharep	C	protein	170	synthetic construct
Centromere protein J	P	protein	79	Homo sapiens	Q9HC77 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7Z0F_1 Tubulin alpha chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>7Z0F_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (C), FASTA

>7Z0F_3 IIH5 ALPHAREP (chains C)
MRGSHHHHHHTDPEKVEMYIKNLQDDSPPVRFNAAVALGKIGDERAVEPLIKALKDEDWQ
VRKTAAYALGKIGDERAVEPLIKALKDEDRYVRSRAALALGKIGDERAVEPLIKALKDED
EYVRLSAASALGKIGGERVRAAMEKLAETGTGFARKVAVNYLETHKSLIS

Sequence of entity 4 (P), FASTA

>7Z0F_4 Centromere protein J (chains P)
MVNIEERPIKAAIGERKQTFEDYLEEQIQLEEQELKQKQLKEAEGPLPIKAKPKQPFLKR
GEGLARFTNAKSKFQKGKE

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural convergence for tubulin binding of CPAP and vinca domain microtubule inhibitors. Campanacci, V., Urvoas, A., Ammar Khodja, L. et al. Proc Natl Acad Sci U S A (2022) 119:e2120098119-e2120098119. DOI 10.1073/pnas.2120098119 · PubMed

Other PDB entries of the same protein (UniProt A0A836D7T3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TH4 2.12 Å, Tubulin-inhibitor complex
4LNU 2.19 Å, Nucleotide-free kinesin motor domain in complex with tubulin and a DARPin
7Q1F 2.35 Å, CPAP:TUBULIN:IE5 alpharep complex
8CGZ 2.53 Å, tubulin-AB8939 complex
7Q1E 2.7 Å, CPAP:TUBULIN:IIH5 alpharep complex
7Z0G 3.49 Å, CPAP:TUBULIN:IE5 alpharep complex P1 space group

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