9N9F: SAH domain of human INCENP

Cryo-EM structure of the SAH domain of human INCENP bound to the paclitaxel-stabilized microtubule. Determined by electron microscopy at 2.91 Å resolution. Released 4 Feb 2026.

Method: Electron microscopy
Resolution: 2.91 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 4
Atoms: 10,723
Mol. weight: 261.26 kDa
Ligands: GTP, ZN, MG, GDP
Released: 4 Feb 2026

Explore 9N9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N9F contains 79 α-helices and 49 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: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	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	72-79	8
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-140	9	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	206-215	10
α-helix	224-243	20
β-strand	248	1	4
α-helix	252-259	8
β-strand	269-273	5	4
α-helix	278-283	6
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-336	12
β-strand	343	1	4
β-strand	351-356	6	4
α-helix	358-363	6
α-helix	369-370	2
β-strand	373-381	9	4
α-helix	384-399	16
α-helix	405-410	6
α-helix	416-434	19

Chain B: 28 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	36	1	6
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	7
β-strand	60-63	4	7
β-strand	65-69	5	5
α-helix	72-80	9
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-128	19
β-strand	131-140	10	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	167-172	6	5
α-helix	173	1
α-helix	175-177	3
α-helix	183-197	15
β-strand	200-205	6	5
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
β-strand	248	1	8
α-helix	252-259	8
β-strand	267-268	2	5
β-strand	269-273	5	8
α-helix	278-280	3
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-320	9	8
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	8
β-strand	351-356	6	8
α-helix	359-360	2
β-strand	374-381	8	8
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-434	20

Chain C: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
α-helix	10-28	19
β-strand	35	1	10
α-helix	48-51	4
β-strand	53-55	3	11
β-strand	60	1	10
β-strand	61-63	3	11
β-strand	65-69	5	9
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	132-140	9	9
α-helix	144-160	17
β-strand	166-171	6	9
α-helix	172-174	3
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-204	5	9
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
β-strand	248	1	12
α-helix	252-259	8
β-strand	269-273	5	12
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	12
α-helix	325-337	13
β-strand	343	1	12
β-strand	351-356	6	12
α-helix	358-363	6
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	384-401	18
α-helix	405-409	5
α-helix	416-436	21

Chain S: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	535-585	51

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B	protein	445	Sus scrofa	P02554 (AlphaFold model)
Inner centromere protein	S	protein	941	Homo sapiens	Q9NQS7 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9N9F_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>9N9F_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (S), FASTA

>9N9F_3 Inner centromere protein (chains S)
MGTTAPGPIHLLELCDQKLMEFLCNMDNKDLVWLEEIQEEAERMFTREFSKEPELMPKTP
SQKNRRKKRRISYVQDENRDPIRRRLSRRKSRSSQLSSRRLRSKDSVEKLATVVGENGSV
LRRVTRAAAAAAAATMALAAPSSPTPESPTMLTKKPEDNHTQCQLVPVVEIGISERQNAE
QHVTQLMSTEPLPRTLSPTPASATAPTSQGIPTSDEESTPKKSKARILESITVSSLMATP
QDPKGQGVGTGRSASKLRIAQVSPGPRDSPAFPDSPWRERVLAPILPDNFSTPTGSRTDS
QSVRHSPIAPSSPSPQVLAQKYSLVAKQESVVRRASRRLAKKTAEEPAASGRIICHSYLE
RLLNVEVPQKVGSEQKEPPEEAEPVAAAEPEVPENNGNNSWPHNDTEIANSTPNPKPAAS
SPETPSAGQQEAKTDQADGPREPPQSARRKRSYKQAVSELDEEQHLEDEELQPPRSKTPS
SPCPASKVVRPLRTFLHTVQRNQMLMTPTSAPRSVMKSFIKRNTPLRMDPKCSFVEKERQ
RLENLRRKEEAEQLRRQKVEEDKRRRLEEVKLKREERLRKVLQARERVEQMKEEKKKQIE
QKFAQIDEKTEKAKEERLAEEKAKKKAAAKKMEEVEARRKQEEDARRLRWLQQEEEERRH
QELLQKKKEEEQERLRKAAEAKRLAEQREQERREQERREQERREQERREQERREQERQLA
EQERRREQERLQAERELQEREKALRLQKEQLQRELEEKKKKEEQQRLAERQLQEEQEKKA
KEAAGASKALNVTVDVQSPACTSYQMTPQGHRAPPKINPDNYGMDLNSDDSTDDEAHPRK
PIPTWARGTPLSQAIIHQYYHPPNLLELFGTILPLDLEDIFKKSKPRYHKRTSSAVWNSP
PLQGARVPSSLAYSLKKHPSRLEEELRRRLTESNSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	3
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
TA1	Taxol	C47 H51 N O14	1

Primary citation

Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule. Funabiki, H., Niu, Y. Sci Adv (2026).

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

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