28OP: Human inner kinetochore CCAN and CENP-C

Structure of the human inner kinetochore CCAN and CENP-C bound to DNA. Determined by electron microscopy at 2.7 Å resolution. Released 20 May 2026.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Homo sapiens, Trichoplusia ni
Chains: 18
Atoms: 27,973
Mol. weight: 720.3 kDa
Released: 20 May 2026

Explore 28OP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

28OP contains 148 α-helices and 79 β-strands across 16 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 C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	262-273	12
β-strand	303-305	3	15

Chain H: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	38-65	28
α-helix	76-118	43
α-helix	125-188	64
α-helix	193-222	30
α-helix	227-229	3
α-helix	231-237	7

Chain I: 44 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	62-75	14
α-helix	83-101	19
β-strand	104	1	10
α-helix	106-118	13
α-helix	123-131	9
β-strand	135	1	10
α-helix	138	1
β-strand	139	1	11
α-helix	140	1
α-helix	141-153	13
α-helix	158-170	13
β-strand	175	1	11
α-helix	179-183	5
α-helix	185-189	5
α-helix	198-208	11
α-helix	216-229	14
β-strand	230	1	9
α-helix	233-245	13
β-strand	250-251	2	12
α-helix	270-281	12
α-helix	311-313	3
α-helix	315	1
α-helix	317	1
α-helix	341-343	3
α-helix	347-353	7
α-helix	358-360	3
α-helix	363-368	6
α-helix	370-377	8
α-helix	382-399	18
α-helix	408-410	3
α-helix	412-426	15
α-helix	433-442	10
α-helix	452-460	9
α-helix	462-464	3
α-helix	467-470	4
α-helix	471-475	5
α-helix	476-482	7
α-helix	487-512	26
α-helix	526-550	25
α-helix	555-569	15
α-helix	572-575	4
α-helix	582-584	3
α-helix	585-592	8
α-helix	597-624	28
α-helix	634-652	19
α-helix	665-671	7
α-helix	689-699	11
α-helix	708-710	3
α-helix	714-725	12
α-helix	729-738	10

Chain K: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	20-42	23
β-strand	49	1	3
α-helix	55-75	21
α-helix	83-85	3
α-helix	86-148	63
α-helix	155-187	33
α-helix	189-191	3
α-helix	209-211	3
α-helix	212-225	14
β-strand	232-233	2	13
α-helix	240-248	9
β-strand	252-254	3	13
β-strand	261-264	4	13

Chain L: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	26-37	12
β-strand	47-48	2	14
α-helix	49-50	2
α-helix	54-56	3
α-helix	61-67	7
β-strand	72-77	6	15
α-helix	78-79	2
β-strand	80-81	2	16
α-helix	88-104	17
β-strand	109-110	2	12
β-strand	117-124	8	15
β-strand	128	1	17
α-helix	134-135	2
β-strand	136-143	8	15
β-strand	155-163	9	15
β-strand	164	1	17
α-helix	168-171	4
β-strand	178-179	2	16
β-strand	183-187	5	15
α-helix	190-204	15
β-strand	208-210	3	15
α-helix	215-227	13
β-strand	237-245	9	15
β-strand	248-256	9	15
α-helix	258-268	11
β-strand	274-275	2	14
α-helix	277-295	19
β-strand	297	1	18
β-strand	303-308	6	15
β-strand	312-315	4	15
β-strand	319-322	4	15
α-helix	325-327	3
α-helix	328-343	16

Chain M: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	15-21	7	2
α-helix	25-37	13
β-strand	43-49	7	2
α-helix	54-56	3
β-strand	65-71	7	2
α-helix	75-84	10
β-strand	88	1	1
β-strand	89	1	3
α-helix	90-93	4
β-strand	97-102	6	2
α-helix	107-109	3
α-helix	114-123	10
β-strand	128-130	3	2
α-helix	136-154	19
α-helix	162-168	7

Chain N: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	18-28	11
α-helix	33-38	6
α-helix	45-58	14
α-helix	63-75	13
α-helix	78-80	3
β-strand	83-89	7	19
α-helix	101-113	13
β-strand	119-125	7	19
β-strand	130-137	8	19
β-strand	150-155	6	19
β-strand	160-164	5	19
α-helix	167-170	4
α-helix	172-183	12
β-strand	187-195	9	19
α-helix	198-205	8
β-strand	237-239	3	2
α-helix	242-256	15
α-helix	260-263	4
β-strand	264-273	10	15
α-helix	290	1
β-strand	291-302	12	15
α-helix	306-308	3
β-strand	315	1	18
α-helix	321-324	4
α-helix	326-329	4
β-strand	333-338	6	15

Chain O: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-28	12
α-helix	90-108	19
α-helix	109-111	3
β-strand	113	1	20
β-strand	117	1	20
β-strand	121-130	10	20
β-strand	133-143	11	20
α-helix	148	1
β-strand	149-153	5	20
α-helix	161-168	8
α-helix	173-200	28
β-strand	205	1	21
β-strand	210-211	2	21
β-strand	217-224	8	21
β-strand	231-238	8	21
β-strand	249-254	6	21
α-helix	262-277	16
α-helix	280-286	7

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere protein M	M	protein	180	Homo sapiens	Q9NSP4 (AlphaFold model)
Centromere protein S	S	protein	138	Homo sapiens	Q8N2Z9 (AlphaFold model)
Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T	T	protein	777	Homo sapiens	P16455 (AlphaFold model), Q96BT3 (AlphaFold model)
Centromere protein U	U	protein	211	Homo sapiens	Q71F23
DNA (59-mer)	V	DNA	212	Homo sapiens
Centromere protein W	W	protein	88	Homo sapiens	Q5EE01
Centromere protein X	X	protein	81	Homo sapiens	A8MT69
DNA (61-mer)	Y	DNA	212	Homo sapiens
Centromere protein H	H	protein	247	Homo sapiens	Q9H3R5
Centromere protein I	I	protein	762	Homo sapiens	Q92674
Centromere protein K	K	protein	269	Homo sapiens	Q9BS16
Centromere protein L	L	protein	348	Homo sapiens	Q8N0S6

6 more molecules are not listed.

Sequence of entity 1 (M), FASTA

>28OP_1 Centromere protein M (chains M)
MSVLRPLDKLPGLNTATILLVGTEDALLQQLADSMLKEDCASELKVHLAKSLPLPSSVNR
PRIDLIVFVVNLHSKYSLQNTEESLRHVDASFFLGKVCFLATGAGRESHCSIHRHTVVKL
AHTYQSPLLYCDLEVEGFRATMAQRLVRVLQICAGHVPGVSALNLLSLLRSSEGPSLEDL

Sequence of entity 2 (S), FASTA

>28OP_2 Centromere protein S (chains S)
MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCEN
FAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDKSEEIAQINLERKAQKKKKSED
GSKNSRQPAEAGVVESEN

Sequence of entity 3 (T), FASTA

>28OP_3 Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T (chains T)
MSYYHHHHHHDYDIPTTENLYFQGMDKDCEMKRTTLDSPLGKLELSGCEQGLHRIIFLGK
GTSAADAVEVPAPAAVLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTR
QVLWKLLKVVKFGEVISYSHLAALAGNPAATAAVKTALSGNPVPILIPCHRVVQGDLDVG
GYEGGLAVKEWLLAHEGHRLGKPGLGSDLEVLFQGPMADHNPDSDSTPRTLLRRVLDTAD
PRTPRRPRSARAGARRALLETASPRKLSGQTRTIARGRSHGARSVGRSAHIQASGHLEEQ
TPRTLLKNILLTAPESSILMPESVVKPVPAPQAVQPSRQESSCGSLELQLPELEPPTTLA
PGLLAPGRRKQRLRLSVFQQGVDQGLSLSQEPQGNADASSLTRSLNLTFATPLQPQSVQR
PGLARRPPARRAVDVGAFLRDLRDTSLAPPNIVLEDTQPFSQPMVGSPNVYHSLPCTPHT
GAEDAEQAAGRKTQSSGPGLQKNSPGKPAQFLAGEAEEVNAFALGFLSTSSGVSGEDEVE
PLHDGVEEAEKKMEEEGVSVSEMEATGAQGPSRVEEAEGHTEVTEAEGSQGTAEADGPGA
SSGDEDASGRAASPESASSTPESLQARRHHQFLEPAPAPGAAVLSSEPAEPLLVRHPPRP
RTTGPRPRQDPHKAGLSHYVKLFSFYAKMPMERKALEMVEKCLDKYFQHLCDDLEVFAAH
AGRKTVKPEDLELLMRRQGLVTDQVSLHVLVERHLPLEYRQLLIPCAYSGNSVFPAQ

Sequence of entity 4 (U), FASTA

>28OP_4 Centromere protein U (chains U)
MKTSDIKELNIVLPEFEKTHLEHQQRIESKVCKAAIATFYVNVKEQFIKMLKESQMLTNL
KRKNAKMISDIEKKRQRMIEVQDELLRLEPQLKQLQTKYDELKERKSSLRNAAYFLSNLK
QLYQDYSDVQAQEPNVKETYDSSSLPALLFKARTLLGAESHLRNINHQLEKLLDQGENLY
FQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 5 (V), FASTA

>28OP_5 DNA (59-MER) (chains V)
CATACTCTTTTTGTAGTATCTGCAAGTGGACATTCGGAGCACTTTGTGGCCTTCGTTGGA
AACGGGAATATGTTCACATAAAAACTAGACAATTGGTCGTAGACAGCTCTAGCACCGCTT
AAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTC
CTTGTAGTATCTGGAATTGGACATTTGGAGAT

Sequence of entity 6 (W), FASTA

>28OP_6 Centromere protein W (chains W)
MALSTIVSQRKQIKRKAPRGFLKRVFKRKKPQLRLEKSGDLLVHLNCLLFVHRLAEESRT
NACASKCRVINKEHVLAAAKVILKKSRG

Sequence of entity 7 (X), FASTA

>28OP_7 Centromere protein X (chains X)
MEGAGAGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAE
DALRVDVDQLEKVLPQLLLDF

Sequence of entity 8 (Y), FASTA

>28OP_8 DNA (61-MER) (chains Y)
ATCTCCAAATGTCCAATTCCAGATACTACAAGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGTCTAGTTTTTATGTGAACATATTCCCGTTTCCAACGAAGGCCACAAAGTGCTCCGAA
TGTCCACTTGCAGATACTACAAAAAGAGTATG

Sequence of entity 9 (H), FASTA

>28OP_9 Centromere protein H (chains H)
MEEQPQMQDADEPADSGGEGRAGGPPQVAGAQAACSEDRMTLLLRLRAQTKQQLLEYKSM
VDASEEKTPEQIMQEKQIEAKIEDLENEIEEVKVAFEIKKLALDRMRLSTALKKNLEKIS
RQSSVLMDNMKHLLELNKLIMKSQQESWDLEEKLLDIRKKRLQLKQASESKLLEIQTEKN
KQKIDLDSMENSERIKIIRQNLQMEIKITTVIQHVFQNLILGSKVNWAEDPALKEIVLQL
EKNVDMM

Sequence of entity 10 (I), FASTA

>28OP_10 Centromere protein I (chains I)
MSPQKRVKNVQAQNRTSQGSSSFQTTLSAWKVKQDPSNSKNISKHGQNNPVGDYEHADDQ
AEEDALQMAVGYFEKGPIKASQNKDKTLEKHLKTVENVAWKNGLASEEIDILLNIALSGK
FGNAVNTRILKCMIPATVISEDSVVKAVSWLCVGKCSGSTKVLFYRWLVAMFDFIDRKEQ
INLLYGFFFASLQDDALCPYVCHLLYLLTKKENVKPFRVRKLLDLQAKMGMQPHLQALLS
LYKFFAPALISVSLPVRKKIYFKNSENLWKTALLAVKQRNRGPSPEPLKLMLGPANVRPL
KRKWNSLSVIPVLNSSSYTKECGKKEMSLSDCLNRSGSFPLEQLQSFPQLLQNIHCLELP
SQMGSVLNNSLLLHYINCVRDEPVLLRFYYWLSQTLQEECIWYKVNNYEHGKEFTNFLDT
IIRAECFLQEGFYSCEAFLYKSLPLWDGLCCRSQFLQLVSWIPFSSFSEVKPLLFDHLAQ
LFFTSTIYFKCSVLQSLKELLQNWLLWLSMDIHMKPVTNSPLETTLGGSMNSVSKLIHYV
GWLSTTAMRLESNNTFLLHFILDFYEKVCDIYINYNLPLVVLFPPGIFYSALLSLDTSIL
NQLCFIMHRYRKNLTAAKKNELVQKTKSEFNFSSKTYQEFNHYLTSMVGCLWTSKPFGKG
IYIDPEILEKTGVAEYKNSLNVVHHPSFLSYAVSFLLQESPEERTVNVSSIRGKKWSWYL
DYLFSQGLQGLKLFIRSSVHHSSIPRAEGINCNNQYENLYFQ

Sequence of entity 11 (K), FASTA

>28OP_11 Centromere protein K (chains K)
MNQEDLDPDSTTDVGDVTNTEEELIRECEEMWKDMEECQNKLSLIGTETLTDSNAQLSLL
IMQVKCLTAELSQWQKKTPETIPLTEDVLITLGKEEFQKLRQDLEMVLSTKESKNEKLKE
DLEREQRWLDEQQQIMESLNVLHSELKNKVETFSESRIFNELKTKMLNIKEYKEKLLSTL
GEFLEDHFPLPDRSVKKKKKNIQESSVNLITLHEMLEILINRLFDVPHDPYVKISDSFWP
PYVELLLRNGIALRHPEDPTRIRLEAFHQ

Sequence of entity 12 (L), FASTA

>28OP_12 Centromere protein L (chains L)
GPLGMDSYSAPESTPSASSRPEDYFIGATPLQKRLESVRKQSSFILTPPRRKIPQCSQLQ
EDVDPQKVAFLLHKQWTLYSLTPLYKFSYSNLKEYSRLLNAFIVAEKQKGLAVEVGEDFN
IKVIFSTLLGMKGTQRDPEAFLVQIVSKSQLPSENREGKVLWTGWFCCVFGDSLLETVSE
DFTCLPLFLANGAESNTAIIGTWFQKTFDCYFSPLAINAFNLSWMAAMWTACKMDHYVAT
TEFLWSVPCSPQSLDISFAIHPEDAKALWDSVHKTPGEVTQEEVDLFMDCLYSHFHRHFK
IHLSATRLVRVSTSVASAHTDGKIKILCHKYLIGVLAYLTELAIFQIE

Primary citation

Models for the architecture of the human inner kinetochore on centromeric alpha-satellite CENP-A nucleosome arrays. Yu, C., Muir, K.W., Yang, J. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-72856-0 · PubMed

Other PDB entries of the same protein (UniProt Q9NSP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4P0T 1.49 Å, Crystal structure of human centromere protein M
4WAU 2.2 Å, Crystal structure of CENP-M solved by native-SAD phasing
7R5S 2.83 Å, Structure of the human CCAN bound to alpha satellite DNA
7PKN 3.2 Å, Structure of the human CCAN deltaCT complex
7XHO 3.29 Å, Structure of human inner kinetochore CCAN complex
9TAW 3.54 Å, Structure of the human inner kinetochore CCAN bound to DNA
7XHN 3.71 Å, Structure of human inner kinetochore CCAN-DNA complex
9TAX 4.5 Å, Structure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome
7R5V 4.55 Å, Structure of the human CCAN CENP-A alpha-satellite complex
7QOO 4.6 Å, Structure of the human inner kinetochore CCAN complex
7YYH 8.9 Å, Structure of the human CCANdeltaT CENP-A alpha-satellite complex
7YWX 12.0 Å, Structure of the human CCAN CENP-A alpha-satellite complex

Browse structure collections

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