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Structure of the human CCAN CENP-A alpha-satellite complex

Electron Microscopy
4.55Å resolution
PDB entry 7r5v coloured by chain, front view.
PDB entry 7r5v coloured by chain, side view.
PDB entry 7r5v coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tridecamer (preferred)
Entry contents: 11 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tridecamer
Accessible surface area: 115090.85 Å2
Buried surface area: 45909.25 Å2
Dissociation area: 895.95 Å2
Dissociation energy (ΔGdiss): -1.51 kcal/mol
Dissociation entropy (TΔSdiss): 21.37 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-121884

Macromolecules

Centromere protein H
Chain: H
Length: 247 amino acids
Theoretical weight: 28.52 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9H3R5 (Residues: 1-247; Coverage: 100%)
Gene names: CENPH, ICEN35
Pfam: Centromere protein H (CENP-H)
InterPro:
Centromere protein H in PDB entry 7r5v, assembly 1, front view.
Centromere protein H in PDB entry 7r5v, assembly 1, side view.
Centromere protein H in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9H3R5  
124720406080100120140160180200220240
 
100200MEEQPQMQDADEPADSGGEGRAGGPPQVAGAQAACSEDRMTLLLRLRAQTKQQLLEYKSMVDASEEKTPEQIMQEKQIEAKIEDLENEIEEVKVAFEIKKLALDRMRLSTALKKNLEKISRQSSVLMDNMKHLLELNKLIMKSQQESWDLEEKLLDIRKKRLQLKQASESKLLEIQTEKNKQKIDLDSMENSERIKIIRQNLQMEIKITTVIQHVFQNLILGSKVNWAEDPALKEIVLQLEKNVDMM
UniProt
Q9H3R5
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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Centromere protein I
Chain: I
Length: 756 amino acids
Theoretical weight: 86.82 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92674 (Residues: 1-756; Coverage: 100%)
Gene names: CENPI, FSHPRH1, ICEN19, LRPR1
Pfam: Mis6
InterPro: Centromere protein I
Centromere protein I in PDB entry 7r5v, assembly 1, front view.
Centromere protein I in PDB entry 7r5v, assembly 1, side view.
Centromere protein I in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q92674  
1756100200300400500600700
 
200400600MSPQKRVKNVQAQNRTSQGSSSFQTTLSAWKVKQDPSNSKNISKHGQNNPVGDYEHADDQAEEDALQMAVGYFEKGPIKASQNKDKTLEKHLKTVENVAWKNGLASEEIDILLNIALSGKFGNAVNTRILKCMIPATVISEDSVVKAVSWLCVGKCSGSTKVLFYRWLVAMFDFIDRKEQINLLYGFFFASLQDDALCPYVCHLLYLLTKKENVKPFRVRKLLDLQAKMGMQPHLQALLSLYKFFAPALISVSLPVRKKIYFKNSENLWKTALLAVKQRNRGPSPEPLKLMLGPANVRPLKRKWNSLSVIPVLNSSSYTKECGKKEMSLSDCLNRSGSFPLEQLQSFPQLLQNIHCLELPSQMGSVLNNSLLLHYINCVRDEPVLLRFYYWLSQTLQEECIWYKVNNYEHGKEFTNFLDTIIRAECFLQEGFYSCEAFLYKSLPLWDGLCCRSQFLQLVSWIPFSSFSEVKPLLFDHLAQLFFTSTIYFKCSVLQSLKELLQNWLLWLSMDIHMKPVTNSPLETTLGGSMNSVSKLIHYVGWLSTTAMRLESNNTFLLHFILDFYEKVCDIYINYNLPLVVLFPPGIFYSALLSLDTSILNQLCFIMHRYRKNLTAAKKNELVQKTKSEFNFSSKTYQEFNHYLTSMVGCLWTSKPFGKGIYIDPEILEKTGVAEYKNSLNVVHHPSFLSYAVSFLLQESPEERTVNVSSIRGKKWSWYLDYLFSQGLQGLKLFIRSSVHHSSIPRAEGINCNNQY
UniProt
Q92674
Chains
Domains
Secondary structure
Flexibility predictions
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Sequence conservation
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Centromere protein K
Chain: K
Length: 269 amino acids
Theoretical weight: 31.7 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BS16 (Residues: 1-269; Coverage: 100%)
Gene names: CENPK, FKSG14, ICEN37
Pfam: Centromere-associated protein K
InterPro: Centromere protein Cenp-K
Centromere protein K in PDB entry 7r5v, assembly 1, front view.
Centromere protein K in PDB entry 7r5v, assembly 1, side view.
Centromere protein K in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9BS16  
126920406080100120140160180200220240260
 
100200MNQEDLDPDSTTDVGDVTNTEEELIRECEEMWKDMEECQNKLSLIGTETLTDSNAQLSLLIMQVKCLTAELSQWQKKTPETIPLTEDVLITLGKEEFQKLRQDLEMVLSTKESKNEKLKEDLEREQRWLDEQQQIMESLNVLHSELKNKVETFSESRIFNELKTKMLNIKEYKEKLLSTLGEFLEDHFPLPDRSVKKKKKNIQESSVNLITLHEMLEILINRLFDVPHDPYVKISDSFWPPYVELLLRNGIALRHPEDPTRIRLEAFHQ
UniProt
Q9BS16
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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Centromere protein L
Chain: L
Length: 344 amino acids
Theoretical weight: 39.04 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8N0S6 (Residues: 1-344; Coverage: 100%)
Gene names: C1orf155, CENPL, ICEN33
Pfam: Kinetochore complex Sim4 subunit Fta1
InterPro: Centromere subunit L
Centromere protein L in PDB entry 7r5v, assembly 1, front view.
Centromere protein L in PDB entry 7r5v, assembly 1, side view.
Centromere protein L in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q8N0S6  
134450100150200250300
 
100200300MDSYSAPESTPSASSRPEDYFIGATPLQKRLESVRKQSSFILTPPRRKIPQCSQLQEDVDPQKVAFLLHKQWTLYSLTPLYKFSYSNLKEYSRLLNAFIVAEKQKGLAVEVGEDFNIKVIFSTLLGMKGTQRDPEAFLVQIVSKSQLPSENREGKVLWTGWFCCVFGDSLLETVSEDFTCLPLFLANGAESNTAIIGTWFQKTFDCYFSPLAINAFNLSWMAAMWTACKMDHYVATTEFLWSVPCSPQSLDISFAIHPEDAKALWDSVHKTPGEVTQEEVDLFMDCLYSHFHRHFKIHLSATRLVRVSTSVASAHTDGKIKILCHKYLIGVLAYLTELAIFQIE
UniProt
Q8N0S6
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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Centromere protein M
Chain: M
Length: 180 amino acids
Theoretical weight: 19.76 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NSP4 (Residues: 1-180; Coverage: 100%)
Gene names: C22orf18, CENPM, ICEN39, PANE1
Pfam: Centromere protein M (CENP-M)
InterPro:
Centromere protein M in PDB entry 7r5v, assembly 1, front view.
Centromere protein M in PDB entry 7r5v, assembly 1, side view.
Centromere protein M in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9NSP4  
118020406080100120140160180
 
50100150MSVLRPLDKLPGLNTATILLVGTEDALLQQLADSMLKEDCASELKVHLAKSLPLPSSVNRPRIDLIVFVVNLHSKYSLQNTEESLRHVDASFFLGKVCFLATGAGRESHCSIHRHTVVKLAHTYQSPLLYCDLEVEGFRATMAQRLVRVLQICAGHVPGVSALNLLSLLRSSEGPSLEDL
UniProt
Q9NSP4
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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Centromere protein N
Chain: N
Length: 339 amino acids
Theoretical weight: 39.61 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96H22 (Residues: 1-339; Coverage: 100%)
Gene names: BM-309, C16orf60, CENPN, ICEN32
Pfam: Kinetochore protein CHL4 like
InterPro: Centromere protein Chl4/mis15/CENP-N
Centromere protein N in PDB entry 7r5v, assembly 1, front view.
Centromere protein N in PDB entry 7r5v, assembly 1, side view.
Centromere protein N in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q96H22  
133950100150200250300
 
100200300MDETVAEFIKRTILKIPMNELTTILKAWDFLSENQLQTVNFRQRKESVVQHLIHLCEEKRASISDAALLDIIYMQFHQHQKVWEVFQMSKGPGEDVDLFDMKQFKNSFKKILQRALKNVTVSFRETEENAVWIRIAWGTQYTKPNQYKPTYVVYYSQTPYAFTSSSMLRRNTPLLGQALTIASKHHQIVKMDLRSRYLDSLKAIVFKQYNQTFETHNSTTPLQERSLGLDINMDSRIIHENIVEKERVQRITQETFGDYPQPQLEFAQYKLETKFKSGLNGSILAEREEPLRCLIKFSSPHLLEALKSLAPAGIADAPLSPLLTCIPNKRMNYFKIRDK
UniProt
Q96H22
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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Centromere protein O
Chain: O
Length: 300 amino acids
Theoretical weight: 33.83 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BU64 (Residues: 1-300; Coverage: 100%)
Gene names: CENPO, ICEN36, MCM21R
Pfam: Cenp-O kinetochore centromere component
InterPro: Centromere protein O
Centromere protein O in PDB entry 7r5v, assembly 1, front view.
Centromere protein O in PDB entry 7r5v, assembly 1, side view.
Centromere protein O in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9BU64  
130020406080100120140160180200220240260280300
 
100200300MEQANPLRPDGESKGGVLAHLERLETQVSRSRKQSEELQSVQAQEGALGTKIHKLRRLRDELRAVVRHRRASVKACIANVEPNQTVEINEQEALEEKLENVKAILQAYHFTGLSGKLTSRGVCVCISTAFEGNLLDSYFVDLVIQKPLRIHHHSVPVFIPLEEIAAKYLQTNIQHFLFSLCEYLNAYSGRKYQADRLQSDFAALLTGPLQRNPLCNLLSFTYKLDPGGQSFPFCARLLYKDLTATLPTDVTVTCQGVEVLSTSWEEQRASHETLFCTKPLHQVFASFTRKGEKLDMSLVS
UniProt
Q9BU64
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
Molecule details ›

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Centromere protein P
Chain: P
Length: 288 amino acids
Theoretical weight: 33.21 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6IPU0 (Residues: 1-288; Coverage: 100%)
Gene name: CENPP
Pfam: CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P
InterPro: Centromere protein P
Centromere protein P in PDB entry 7r5v, assembly 1, front view.
Centromere protein P in PDB entry 7r5v, assembly 1, side view.
Centromere protein P in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q6IPU0  
128820406080100120140160180200220240260280
 
100200MDAELAEVRALQAEIAALRRACEDPPAPWEEKSRVQKSFQAIHQFNLEGWKSSKDLKNQLGHLESELSFLSTLTGINIRNHSKQTEDLTSTEMTEKSIRKVLQRHRLSGNCHMVTFQLEFQILEIQNKERLSSAVTDLNIIMEPTECSELSEFVSRAEERKDLFMFFRSLHFFVEWFEYRKRTFKHLKEKYPDAVYLSEGPSSCSMGIRSASRPGFELVIVWRIQIDEDGKVFPKLDLLTKVPQRALELDKNRAIETAPLSFRTLVGLLGIEAALESLIKSLCAEENN
UniProt
Q6IPU0
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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Centromere protein Q
Chain: Q
Length: 268 amino acids
Theoretical weight: 30.65 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7L2Z9 (Residues: 1-268; Coverage: 100%)
Gene names: C6orf139, CENPQ
Pfam: CENP-Q, a CENPA-CAD centromere complex subunit
InterPro: Centromere protein Q
Centromere protein Q in PDB entry 7r5v, assembly 1, front view.
Centromere protein Q in PDB entry 7r5v, assembly 1, side view.
Centromere protein Q in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q7L2Z9  
126820406080100120140160180200220240260
 
100200MSGKANASKKNAQQLKRNPKRKKDNEEVVLSENKVRNTVKKNKNHLKDLSSEGQTKHTNLKHGKTAASKRKTWQPLSKSTRDHLQTMMESVIMTILSNSIKEKEEIQYHLNFLKKRLLQQCETLKVPPKKMEDLTNVSSLLNMERARDKANEEGLALLQEEIDKMVETTELMTGNIQSLKNKIQILASEVEEEEERVKQMHQINSSGVLSLPELSQKTLKAPTLQKEILALIPNQNALLKDLDILHNSSQMKSMSTFIEEAYKKLDAS
UniProt
Q7L2Z9
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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Centromere protein U
Chain: U
Length: 418 amino acids
Theoretical weight: 47.61 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q71F23 (Residues: 1-418; Coverage: 100%)
Gene names: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1
Pfam: CENP-A nucleosome associated complex (NAC) subunit
InterPro: Centromere protein U
Centromere protein U in PDB entry 7r5v, assembly 1, front view.
Centromere protein U in PDB entry 7r5v, assembly 1, side view.
Centromere protein U in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q71F23  
141850100150200250300350400
 
100200300400MAPRGRRRPRPHRSEGARRSKNTLERTHSMKDKAGQKCKPIDVFDFPDNSDVSSIGRLGENEKDEETYETFDPPLHSTAIYADEEEFSKHCGLSLSSTPPGKEAKRSSDTSGNEASEIESVKISAKKPGRKLRPISDDSESIEESDTRRKVKSAEKISTQRHEVIRTTASSELSEKPAESVTSKKTGPLSAQPSVEKENLAIESQSKTQKKGKISHDKRKKSRSKAIGSDTSDIVHIWCPEGMKTSDIKELNIVLPEFEKTHLEHQQRIESKVCKAAIATFYVNVKEQFIKMLKESQMLTNLKRKNAKMISDIEKKRQRMIEVQDELLRLEPQLKQLQTKYDELKERKSSLRNAAYFLSNLKQLYQDYSDVQAQEPNVKETYDSSSLPALLFKARTLLGAESHLRNINHQLEKLLDQG
UniProt
Q71F23
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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Centromere protein R
Chain: R
Length: 177 amino acids
Theoretical weight: 20.23 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13352 (Residues: 1-177; Coverage: 100%)
Gene names: CENPR, ITGB3BP, NRIF3
Pfam: Kinetochore component, CENP-R
InterPro: Centromere protein R
Centromere protein R in PDB entry 7r5v, assembly 1, front view.
Centromere protein R in PDB entry 7r5v, assembly 1, side view.
Centromere protein R in PDB entry 7r5v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q13352  
117720406080100120140160
 
50100150MPVKRSLKLDGLLEENSFDPSKITRKKSVITYSPTTGTCQMSLFASPTSSEEQKHRNGLSNEKRKKLNHPSLTESKESTTKDNDEFMMLLSKVEKLSEEIMEIMQNLSSIQALEGSRELENLIGISCASHFLKREMQKTKELMTKVNKQKLFEKSTGLPHKASRHLDSYEFLKAILN
UniProt
Q13352
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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DNA chain J
Name: DNA (171-MER)
Representative chains: J
Length: 171 nucleotides
Theoretical weight: 52.8 KDa
DNA (171-MER) in PDB entry 7r5v, assembly 1, front view.
DNA (171-MER) in PDB entry 7r5v, assembly 1, side view.
DNA (171-MER) in PDB entry 7r5v, assembly 1, top view.
117120406080100120140160
 
50100150
Chains
Chain C (auth J)
Interaction interfaces
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DNA chain i
Name: DNA (171-MER)
Representative chains: i
Length: 171 nucleotides
Theoretical weight: 52.71 KDa
DNA (171-MER) in PDB entry 7r5v, assembly 1, front view.
DNA (171-MER) in PDB entry 7r5v, assembly 1, side view.
DNA (171-MER) in PDB entry 7r5v, assembly 1, top view.
117120406080100120140160
 
50100150
Chains
Chain L (auth i)
Interaction interfaces
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