7PKN: Human CCAN deltaCT complex

Structure of the human CCAN deltaCT complex. Determined by electron microscopy at 3.2 Å resolution. Released 27 Apr 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 11
Atoms: 18,616
Mol. weight: 410.98 kDa
Released: 27 Apr 2022

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

Secondary structure: helices and β-sheets

7PKN contains 107 α-helices and 55 β-strands across 11 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 H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	36-64	29
α-helix	79-114	36
α-helix	126-181	56

Chain I: 25 helices, 0 β-strands

Element	Residues	Length
α-helix	311-313	3
α-helix	347-352	6
α-helix	358-360	3
α-helix	363-368	6
α-helix	370-376	7
α-helix	382-398	17
α-helix	412-426	15
α-helix	427-429	3
α-helix	433-442	10
α-helix	452-460	9
α-helix	467-470	4
α-helix	471-475	5
α-helix	476-482	7
α-helix	487-511	25
α-helix	526-550	25
α-helix	555-568	14
α-helix	571-574	4
α-helix	585-592	8
α-helix	597-624	28
α-helix	634-648	15
α-helix	649-653	5
α-helix	665-671	7
α-helix	689-697	9
α-helix	720-726	7
α-helix	729-739	11

Chain K: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	20-42	23
β-strand	49	1	1
α-helix	56-76	21
α-helix	87-148	62

Chain L: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	27-36	10
α-helix	43-46	4
β-strand	47-48	2	2
α-helix	49-50	2
α-helix	54-56	3
α-helix	61-67	7
β-strand	72-77	6	3
α-helix	78-79	2
β-strand	80-81	2	4
α-helix	89-102	14
β-strand	117-123	7	3
α-helix	134-136	3
β-strand	137-143	7	3
β-strand	155-163	9	3
α-helix	168-171	4
β-strand	178-179	2	4
β-strand	183-188	6	3
α-helix	190-204	15
β-strand	208-210	3	3
α-helix	215-227	13
β-strand	237-242	6	3
β-strand	251-256	6	3
α-helix	258-268	11
β-strand	274-275	2	2
α-helix	277-295	19
β-strand	297	1	5
α-helix	299-301	3
β-strand	303-308	6	3
β-strand	312-315	4	3
β-strand	319-322	4	3
α-helix	328-343	16

Chain M: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	6
β-strand	15-21	7	7
α-helix	25-35	11
β-strand	43-49	7	7
α-helix	54-56	3
β-strand	65-71	7	7
α-helix	75-84	10
α-helix	85-87	3
β-strand	88	1	6
β-strand	89	1	1
α-helix	90-93	4
β-strand	97-102	6	7
α-helix	114-123	10
β-strand	128-131	4	7
α-helix	136-153	18
α-helix	162-168	7

Chain N: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	21-28	8
α-helix	33-35	3
α-helix	45-58	14
α-helix	63-77	15
β-strand	83-89	7	8
α-helix	94-97	4
α-helix	101-115	15
β-strand	120-126	7	8
β-strand	130-136	7	8
β-strand	139	1	9
β-strand	142	1	9
α-helix	143-145	3
β-strand	149-155	7	8
β-strand	160-164	5	8
α-helix	168-170	3
α-helix	172-182	11
β-strand	187-195	9	8
α-helix	198-205	8
β-strand	237-239	3	7
α-helix	242-256	15
α-helix	260-263	4
β-strand	264-273	10	3
α-helix	274-275	2
β-strand	291-302	12	3
α-helix	306-308	3
α-helix	309-312	4
β-strand	315	1	5
α-helix	319-320	2
α-helix	326-329	4
β-strand	333-337	5	3

Chain O: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	17-26	10
α-helix	90-109	20
β-strand	113-117	5	10
β-strand	122-130	9	10
β-strand	133-142	10	10
α-helix	148	1
β-strand	150-153	4	10
α-helix	161-168	8
α-helix	173-199	27
β-strand	205	1	11
α-helix	208-209	2
β-strand	210-211	2	11
β-strand	217-224	8	11
β-strand	231-238	8	11
β-strand	249-253	5	11
α-helix	262-277	16
α-helix	280-287	8

Chain P: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	54-74	21
β-strand	77-87	11	12
β-strand	99-111	13	12
β-strand	114-126	13	12
β-strand	131-141	11	12
α-helix	148-160	13
α-helix	164-190	27
β-strand	195	1	13
β-strand	205-210	6	13
β-strand	213-226	14	13
β-strand	232-241	10	13
α-helix	244-249	6
α-helix	258-269	12
α-helix	272-282	11

3 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 H	H	protein	247	Homo sapiens	Q9H3R5 (AlphaFold model)
Centromere protein I	I	protein	756	Homo sapiens	Q92674 (AlphaFold model)
Centromere protein K	K	protein	269	Homo sapiens	Q9BS16 (AlphaFold model)
Centromere protein L	L	protein	344	Homo sapiens	Q8N0S6 (AlphaFold model)
Centromere protein M	M	protein	180	Homo sapiens	Q9NSP4
Centromere protein N	N	protein	339	Homo sapiens	Q96H22
Centromere protein O	O	protein	300	Homo sapiens	Q9BU64
Centromere protein P	P	protein	288	Homo sapiens	Q6IPU0
Centromere protein Q	Q	protein	268	Homo sapiens	Q7L2Z9
Centromere protein U	U	protein	418	Homo sapiens	Q71F23
Centromere protein R	R	protein	177	Homo sapiens	Q13352

Sequence of entity 1 (H), FASTA

>7PKN_1 Centromere protein H (chains H)
MEEQPQMQDADEPADSGGEGRAGGPPQVAGAQAACSEDRMTLLLRLRAQTKQQLLEYKSM
VDASEEKTPEQIMQEKQIEAKIEDLENEIEEVKVAFEIKKLALDRMRLSTALKKNLEKIS
RQSSVLMDNMKHLLELNKLIMKSQQESWDLEEKLLDIRKKRLQLKQASESKLLEIQTEKN
KQKIDLDSMENSERIKIIRQNLQMEIKITTVIQHVFQNLILGSKVNWAEDPALKEIVLQL
EKNVDMM

Sequence of entity 2 (I), FASTA

>7PKN_2 Centromere protein I (chains I)
MSPQKRVKNVQAQNRTSQGSSSFQTTLSAWKVKQDPSNSKNISKHGQNNPVGDYEHADDQ
AEEDALQMAVGYFEKGPIKASQNKDKTLEKHLKTVENVAWKNGLASEEIDILLNIALSGK
FGNAVNTRILKCMIPATVISEDSVVKAVSWLCVGKCSGSTKVLFYRWLVAMFDFIDRKEQ
INLLYGFFFASLQDDALCPYVCHLLYLLTKKENVKPFRVRKLLDLQAKMGMQPHLQALLS
LYKFFAPALISVSLPVRKKIYFKNSENLWKTALLAVKQRNRGPSPEPLKLMLGPANVRPL
KRKWNSLSVIPVLNSSSYTKECGKKEMSLSDCLNRSGSFPLEQLQSFPQLLQNIHCLELP
SQMGSVLNNSLLLHYINCVRDEPVLLRFYYWLSQTLQEECIWYKVNNYEHGKEFTNFLDT
IIRAECFLQEGFYSCEAFLYKSLPLWDGLCCRSQFLQLVSWIPFSSFSEVKPLLFDHLAQ
LFFTSTIYFKCSVLQSLKELLQNWLLWLSMDIHMKPVTNSPLETTLGGSMNSVSKLIHYV
GWLSTTAMRLESNNTFLLHFILDFYEKVCDIYINYNLPLVVLFPPGIFYSALLSLDTSIL
NQLCFIMHRYRKNLTAAKKNELVQKTKSEFNFSSKTYQEFNHYLTSMVGCLWTSKPFGKG
IYIDPEILEKTGVAEYKNSLNVVHHPSFLSYAVSFLLQESPEERTVNVSSIRGKKWSWYL
DYLFSQGLQGLKLFIRSSVHHSSIPRAEGINCNNQY

Sequence of entity 3 (K), FASTA

>7PKN_3 Centromere protein K (chains K)
MNQEDLDPDSTTDVGDVTNTEEELIRECEEMWKDMEECQNKLSLIGTETLTDSNAQLSLL
IMQVKCLTAELSQWQKKTPETIPLTEDVLITLGKEEFQKLRQDLEMVLSTKESKNEKLKE
DLEREQRWLDEQQQIMESLNVLHSELKNKVETFSESRIFNELKTKMLNIKEYKEKLLSTL
GEFLEDHFPLPDRSVKKKKKNIQESSVNLITLHEMLEILINRLFDVPHDPYVKISDSFWP
PYVELLLRNGIALRHPEDPTRIRLEAFHQ

Sequence of entity 4 (L), FASTA

>7PKN_4 Centromere protein L (chains L)
MDSYSAPESTPSASSRPEDYFIGATPLQKRLESVRKQSSFILTPPRRKIPQCSQLQEDVD
PQKVAFLLHKQWTLYSLTPLYKFSYSNLKEYSRLLNAFIVAEKQKGLAVEVGEDFNIKVI
FSTLLGMKGTQRDPEAFLVQIVSKSQLPSENREGKVLWTGWFCCVFGDSLLETVSEDFTC
LPLFLANGAESNTAIIGTWFQKTFDCYFSPLAINAFNLSWMAAMWTACKMDHYVATTEFL
WSVPCSPQSLDISFAIHPEDAKALWDSVHKTPGEVTQEEVDLFMDCLYSHFHRHFKIHLS
ATRLVRVSTSVASAHTDGKIKILCHKYLIGVLAYLTELAIFQIE

Sequence of entity 5 (M), FASTA

>7PKN_5 Centromere protein M (chains M)
MSVLRPLDKLPGLNTATILLVGTEDALLQQLADSMLKEDCASELKVHLAKSLPLPSSVNR
PRIDLIVFVVNLHSKYSLQNTEESLRHVDASFFLGKVCFLATGAGRESHCSIHRHTVVKL
AHTYQSPLLYCDLEVEGFRATMAQRLVRVLQICAGHVPGVSALNLLSLLRSSEGPSLEDL

Sequence of entity 6 (N), FASTA

>7PKN_6 Centromere protein N (chains N)
MDETVAEFIKRTILKIPMNELTTILKAWDFLSENQLQTVNFRQRKESVVQHLIHLCEEKR
ASISDAALLDIIYMQFHQHQKVWEVFQMSKGPGEDVDLFDMKQFKNSFKKILQRALKNVT
VSFRETEENAVWIRIAWGTQYTKPNQYKPTYVVYYSQTPYAFTSSSMLRRNTPLLGQALT
IASKHHQIVKMDLRSRYLDSLKAIVFKQYNQTFETHNSTTPLQERSLGLDINMDSRIIHE
NIVEKERVQRITQETFGDYPQPQLEFAQYKLETKFKSGLNGSILAEREEPLRCLIKFSSP
HLLEALKSLAPAGIADAPLSPLLTCIPNKRMNYFKIRDK

Sequence of entity 7 (O), FASTA

>7PKN_7 Centromere protein O (chains O)
MEQANPLRPDGESKGGVLAHLERLETQVSRSRKQSEELQSVQAQEGALGTKIHKLRRLRD
ELRAVVRHRRASVKACIANVEPNQTVEINEQEALEEKLENVKAILQAYHFTGLSGKLTSR
GVCVCISTAFEGNLLDSYFVDLVIQKPLRIHHHSVPVFIPLEEIAAKYLQTNIQHFLFSL
CEYLNAYSGRKYQADRLQSDFAALLTGPLQRNPLCNLLSFTYKLDPGGQSFPFCARLLYK
DLTATLPTDVTVTCQGVEVLSTSWEEQRASHETLFCTKPLHQVFASFTRKGEKLDMSLVS

Sequence of entity 8 (P), FASTA

>7PKN_8 Centromere protein P (chains P)
MDAELAEVRALQAEIAALRRACEDPPAPWEEKSRVQKSFQAIHQFNLEGWKSSKDLKNQL
GHLESELSFLSTLTGINIRNHSKQTEDLTSTEMTEKSIRKVLQRHRLSGNCHMVTFQLEF
QILEIQNKERLSSAVTDLNIIMEPTECSELSEFVSRAEERKDLFMFFRSLHFFVEWFEYR
KRTFKHLKEKYPDAVYLSEGPSSCSMGIRSASRPGFELVIVWRIQIDEDGKVFPKLDLLT
KVPQRALELDKNRAIETAPLSFRTLVGLLGIEAALESLIKSLCAEENN

Sequence of entity 9 (Q), FASTA

>7PKN_9 Centromere protein Q (chains Q)
MSGKANASKKNAQQLKRNPKRKKDNEEVVLSENKVRNTVKKNKNHLKDLSSEGQTKHTNL
KHGKTAASKRKTWQPLSKSTRDHLQTMMESVIMTILSNSIKEKEEIQYHLNFLKKRLLQQ
CETLKVPPKKMEDLTNVSSLLNMERARDKANEEGLALLQEEIDKMVETTELMTGNIQSLK
NKIQILASEVEEEEERVKQMHQINSSGVLSLPELSQKTLKAPTLQKEILALIPNQNALLK
DLDILHNSSQMKSMSTFIEEAYKKLDAS

Sequence of entity 10 (U), FASTA

>7PKN_10 Centromere protein U (chains U)
MAPRGRRRPRPHRSEGARRSKNTLERTHSMKDKAGQKCKPIDVFDFPDNSDVSSIGRLGE
NEKDEETYETFDPPLHSTAIYADEEEFSKHCGLSLSSTPPGKEAKRSSDTSGNEASEIES
VKISAKKPGRKLRPISDDSESIEESDTRRKVKSAEKISTQRHEVIRTTASSELSEKPAES
VTSKKTGPLSAQPSVEKENLAIESQSKTQKKGKISHDKRKKSRSKAIGSDTSDIVHIWCP
EGMKTSDIKELNIVLPEFEKTHLEHQQRIESKVCKAAIATFYVNVKEQFIKMLKESQMLT
NLKRKNAKMISDIEKKRQRMIEVQDELLRLEPQLKQLQTKYDELKERKSSLRNAAYFLSN
LKQLYQDYSDVQAQEPNVKETYDSSSLPALLFKARTLLGAESHLRNINHQLEKLLDQG

Sequence of entity 11 (R), FASTA

>7PKN_11 Centromere protein R (chains R)
MPVKRSLKLDGLLEENSFDPSKITRKKSVITYSPTTGTCQMSLFASPTSSEEQKHRNGLS
NEKRKKLNHPSLTESKESTTKDNDEFMMLLSKVEKLSEEIMEIMQNLSSIQALEGSRELE
NLIGISCASHFLKREMQKTKELMTKVNKQKLFEKSTGLPHKASRHLDSYEFLKAILN

Primary citation

Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome. Yatskevich, S., Muir, K.W., Bellini, D. et al. Science (2022) 376:844-852. DOI 10.1126/science.abn3810 · PubMed

Other PDB entries of the same protein (UniProt Q9H3R5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7PB4 2.49 Å, Cenp-HIK 3-protein complex
28OP 2.7 Å, Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
7R5S 2.83 Å, Structure of the human CCAN bound to alpha satellite DNA
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
9TAY 15.5 Å, Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome

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