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- EMDB-70561: Structure of the Bombyx mori bmCENP-HIKM-LN-T-OP complex without ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70561
TitleStructure of the Bombyx mori bmCENP-HIKM-LN-T-OP complex without the CS module
Map dataConsensus refinement of bmCENP-HIKM-LN-T-OP particles (lacking Centromeric Subunit Module), sharpened
Sample
  • Complex: Bombyx mori bmCENP-HIKM-LN-T-OP sub-complex
    • Protein or peptide: bmCENP-H
    • Protein or peptide: bmCENP-K
    • Protein or peptide: Centromere protein I
    • Protein or peptide: Centromere protein M
    • Protein or peptide: Centromere protein L
    • Protein or peptide: bmCENP-N
    • Protein or peptide: Centromere protein O
    • Protein or peptide: bmCENP-P
    • Protein or peptide: bmCENP-T
KeywordsCCAN / complex / segregation / DNA BINDING PROTEIN
Function / homology
Function and homology information


CENP-A containing chromatin assembly / inner kinetochore / mitotic sister chromatid segregation / chromosome, centromeric region / nucleus
Similarity search - Function
Centromere subunit L / Centromere protein L / Centromere protein Cenp-M / Centromere protein M (CENP-M) / Centromere protein I / Mis6 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Centromere protein O / Uncharacterized protein / Centromere protein M / Uncharacterized protein / Centromere protein I / Centromere protein L
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsYatskevich S / Ciferri C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2026
Title: Architecture and function of holocentric CENP-A-independent inner kinetochores.
Authors: Christine Yu / Sundar Ram Sankaranarayanan / Gaetan Cornilleau / Anna C Howes / Caleigh M Azumaya / Eric S Day / Inna Zilberleyb / Bobby Brillantes / Tommy K Cheung / Leonie Dec / Damarys ...Authors: Christine Yu / Sundar Ram Sankaranarayanan / Gaetan Cornilleau / Anna C Howes / Caleigh M Azumaya / Eric S Day / Inna Zilberleyb / Bobby Brillantes / Tommy K Cheung / Leonie Dec / Damarys Loew / Phong Tran / Christopher M Rose / Ines Anna Drinnenberg / Claudio Ciferri / Stanislau Yatskevich /
Abstract: Kinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of ...Kinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of kinetochores across diverse species remains poorly understood. We present the inner kinetochore constitutive centromere-associated network (CCAN) structure of the silkmoth , an insect that lacks the canonical centromere-specifying histone variant CENP-A and exhibits chromosome-wide centromeric activity (holocentric). The CCAN incorporates four previously uncharacterized centromeric subunit proteins that are structurally related to the Dam1/DASH complex but function in scaffolding the inner kinetochore rather than in microtubule binding. Similar to the yeast and human systems, the CCAN also entraps DNA within its central closed chamber. However, unlike these systems, the CCAN can also assemble in vitro into a self-contained head-to-head dimer via atypical histone-fold protein dimerization. On the basis of our findings, we propose that the holocentric organization may emerge from the modular arrangement of discrete kinetochore units.
History
DepositionMay 9, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70561.png

Downloads & links

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Map

FileReleased
AnnotationConsensus refinement of bmCENP-HIKM-LN-T-OP particles (lacking Centromeric Subunit Module), sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 335.2 Å		0.84 Å/pix.
x 400 pix.
= 335.2 Å		0.84 Å/pix.
x 400 pix.
= 335.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.838 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0526
Minimum - Maximum-0.43774506 - 0.67769736
Average (Standard dev.)-0.000060571994 (±0.009908337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus refinement of bmCENP-HIKM-LN-T-OP particles (lacking Centromeric Subunit...

Fileemd_70561_additional_1.map
AnnotationConsensus refinement of bmCENP-HIKM-LN-T-OP particles (lacking Centromeric Subunit Module), unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of bmCENP-HIKM-LN-T-OP particles

Fileemd_70561_half_map_1.map
AnnotationHalf-map A of bmCENP-HIKM-LN-T-OP particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of bmCENP-HIKM-LN-T-OP particles

Fileemd_70561_half_map_2.map
AnnotationHalf-map B of bmCENP-HIKM-LN-T-OP particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bombyx mori bmCENP-HIKM-LN-T-OP sub-complex

EntireName: Bombyx mori bmCENP-HIKM-LN-T-OP sub-complex
Components
  • Complex: Bombyx mori bmCENP-HIKM-LN-T-OP sub-complex
    • Protein or peptide: bmCENP-H
    • Protein or peptide: bmCENP-K
    • Protein or peptide: Centromere protein I
    • Protein or peptide: Centromere protein M
    • Protein or peptide: Centromere protein L
    • Protein or peptide: bmCENP-N
    • Protein or peptide: Centromere protein O
    • Protein or peptide: bmCENP-P
    • Protein or peptide: bmCENP-T

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Supramolecule #1: Bombyx mori bmCENP-HIKM-LN-T-OP sub-complex

SupramoleculeName: Bombyx mori bmCENP-HIKM-LN-T-OP sub-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bombyx mori (domestic silkworm)

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Macromolecule #1: bmCENP-H

MacromoleculeName: bmCENP-H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 27.71917 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAFKTLKEV SQNFEQELKQ LSNVLFSAKI GETFEDAVSK KLQELSLFSS KLKLLRAKPV SLTPQITEQV KTEEIIKEYG DVAAIKLLE KVTVKCVAQT HAVKKLITTP DRALDAEMLT RKQNIMEALT NYRDKETSLR HFEMILQEKQ YEHNLLRAEW D KSLGELRD ...String:
MSAFKTLKEV SQNFEQELKQ LSNVLFSAKI GETFEDAVSK KLQELSLFSS KLKLLRAKPV SLTPQITEQV KTEEIIKEYG DVAAIKLLE KVTVKCVAQT HAVKKLITTP DRALDAEMLT RKQNIMEALT NYRDKETSLR HFEMILQEKQ YEHNLLRAEW D KSLGELRD MKAAVSDDEE MDTNSAYYVR LRTLVSKMEM IRWLIGRLVV CRKESRNDPR RALQALKMAR QVLDVDTFMS D

UniProtKB: Uncharacterized protein

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Macromolecule #2: bmCENP-K

MacromoleculeName: bmCENP-K / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 24.760084 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTSKHNAETL DALKREIKTL QNNCLNVCNI IENAPPETPS ANQDEISDKC LSYIQALKTE IENPNTIITT DENLLTSQFL NEIKEKTGQ IEELTAFTKG SIRDVDEEIM RLKNQITIAQ EAMSKPIQKY GQVSSEHVKN AKEKFSQLKS ELHGLIYSMF P NTSALIIE ...String:
MTSKHNAETL DALKREIKTL QNNCLNVCNI IENAPPETPS ANQDEISDKC LSYIQALKTE IENPNTIITT DENLLTSQFL NEIKEKTGQ IEELTAFTKG SIRDVDEEIM RLKNQITIAQ EAMSKPIQKY GQVSSEHVKN AKEKFSQLKS ELHGLIYSMF P NTSALIIE FMGQLMAERL NPASSGYIQI TAENYQIAEL LKDTNIISTN PYNKMEVKLA Y

UniProtKB: Uncharacterized protein

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Macromolecule #3: Centromere protein I

MacromoleculeName: Centromere protein I / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 75.965023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MCDIGEIIDY IKSLKRGFDK DLFQSKIDEL GYIVDSVGLD YDDFHTLFKI WLNLSIPLTK WTSLGACLIP PDAVEEKTVD YAIQWILIN YGNQNSFTKT GFLLDWLTAA MECDCIDMKA LDFGYELFYS MMTYETLTPQ AVKLVYTLTK PSDVTRRRVI E ILDCAKKR ...String:
MCDIGEIIDY IKSLKRGFDK DLFQSKIDEL GYIVDSVGLD YDDFHTLFKI WLNLSIPLTK WTSLGACLIP PDAVEEKTVD YAIQWILIN YGNQNSFTKT GFLLDWLTAA MECDCIDMKA LDFGYELFYS MMTYETLTPQ AVKLVYTLTK PSDVTRRRVI E ILDCAKKR ESKKNLFRQL QILLGLFKSY KPECVPENVP AICVHTAFKK INKDLLGRFK RTQERRNRQS KEKQHLIWLN PI NMARGRN KKIVPLVPNM EFFNIGSKQY DQKEPQKNYL DFSDPASVVQ LAACGRAARP ARLRALLCGP ALLLAAAAAD QHA FLSHDL RHLLDNCFLD ISPYSYAEKQ DLLQRLALLQ STLLQGIPVI TRFLAQFLPL WNERDYFTEI LQLVEWVSVD SPDH LGYIV GPLIKIYHRA QPLEQCAILK SLTQMYINLV YASTRRRQFF MAIDTPKENY DVVLPRLAAE LGEMGEKALQ YNPDD MRVL FSNIWSVECR SRAHLLYNIG LGPIPGLLSL SLPLLGVSAA LIEKMAALLV IYKKIFTRLK STNAISATHT EQIQIL HRY SVDLSSLYTE ESLRGRGNGF VFDKLHPQLV SKLYHLIPEP DTKLSVRSHV AFAAYTYVAL GDVDERDADN KAWYRAF LE HEFSYLAKFF KKTVPELRM

UniProtKB: Centromere protein I

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Macromolecule #4: Centromere protein M

MacromoleculeName: Centromere protein M / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 20.135387 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSLLEEDAVI APWVGPMSAK NSLTAIVLSL NVEVIEKVSE ALSEVHKKSR FRWKLVVLRS FHLEEVVKQS DLTGRVAIDF VIIALDTSR LFCLEWAKKE LSQVHPDLRR RRVVLVNTSG LPVNAMAITA GELINFYTEN NVDLLTADIS NTENTTLLAQ K LLKYMEVS IGVRTGIPNI NV

UniProtKB: Centromere protein M

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Macromolecule #5: Centromere protein L

MacromoleculeName: Centromere protein L / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 34.22998 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSLRLDSCW EQEEDGNTSR HVTGDPIALI YNEGLWKINK VSPLYNLQYN GIKLKQYGSK ILQALVSSLQ MSNTAKYTVV LEELPLLKY SEEDSSGILI TVRSSQEDSN TKKVAYVAIL LSWGISISME NAIHLPYMLE RGEQRVGTVV KTILQTAFDC N IKQFSFTQ ...String:
MSSLRLDSCW EQEEDGNTSR HVTGDPIALI YNEGLWKINK VSPLYNLQYN GIKLKQYGSK ILQALVSSLQ MSNTAKYTVV LEELPLLKY SEEDSSGILI TVRSSQEDSN TKKVAYVAIL LSWGISISME NAIHLPYMLE RGEQRVGTVV KTILQTAFDC N IKQFSFTQ HQLLNFGFSF IDSDTSRSND QFTLVYRSPQ TEVKSKLSLS FDIGDVRLIW NGIKDETTKK ADLIILAYQI LQ NQIFSLG YLDVTVFDLS EINLTKAEIK CNGGVKMKTP EIVNCVFTVL NEICCDLWQD LNITE

UniProtKB: Centromere protein L

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Macromolecule #6: bmCENP-N

MacromoleculeName: bmCENP-N / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 36.882559 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKNSNKLKDL QMTIARMPLQ QCCVTVLPEF GVKWREVFRA VRLARLPMTA ASVARVLTRH IAKSLEAHEL NDILARLKLK LVASQNRMW HVVNMSEQHT AGPITELIET LPEVIENNLK KGKHRFTRPE VQTNLIGDLL YISVQLVSDT KEGSTLYVAT P PGESVALF ...String:
MKNSNKLKDL QMTIARMPLQ QCCVTVLPEF GVKWREVFRA VRLARLPMTA ASVARVLTRH IAKSLEAHEL NDILARLKLK LVASQNRMW HVVNMSEQHT AGPITELIET LPEVIENNLK KGKHRFTRPE VQTNLIGDLL YISVQLVSDT KEGSTLYVAT P PGESVALF STLSMSAQIK ACVDALGYRK YEDAKLHGKD IPSLLRINDR AWSGMAQNLA SVPDYAPKPI LTYNGINYTN RT YDAEYIE NILGPDPPLL TDLTIKTSKP FFDASMLSKN INMKITLKSE NVAETLKSWV VKGALAPTSE FFHIFHNIKS NNI SRNIDD TD

UniProtKB: Uncharacterized protein

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Macromolecule #7: Centromere protein O

MacromoleculeName: Centromere protein O / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 37.681129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKQTKITKLF QTKLVARRSS DDCDELQDEI EKLRENLKEK QNELFQLQRN SYKHKSSPVK KKSEQFVRPQ KIVLTNSIDS LKRNLELMS ILTGMEVQSY VVGEHCCVVY HMQHDSDNVV KHGLRIEMQA GANVVSKSSL PLGFNINAVM EEYDNIMMPE C LGAIRKAL ...String:
MKQTKITKLF QTKLVARRSS DDCDELQDEI EKLRENLKEK QNELFQLQRN SYKHKSSPVK KKSEQFVRPQ KIVLTNSIDS LKRNLELMS ILTGMEVQSY VVGEHCCVVY HMQHDSDNVV KHGLRIEMQA GANVVSKSSL PLGFNINAVM EEYDNIMMPE C LGAIRKAL VAYYDRLQQF EALKKMLNVE AQLFKLLDAS HIEISFSAQS AVEEDEHLNL VLVLDYRVYD IRPKQYSFKD LD IPAGAVA ALKEQCTVFK RKPLQRAFRD AFIDGVGPYQ MIHQIGFKPV ERKSHRRKRF KAHPYNHNND DTFRPEDCSD QSE EGPEP

UniProtKB: Centromere protein O

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Macromolecule #8: bmCENP-P

MacromoleculeName: bmCENP-P / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 71.10082 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPINKIHYDK KTLLLEKQSL LDNIVYCETR IAELLTKKCT NYIEDSDSSG SEDGFTLSID PGPTVSQLKL LQSSLQTCLQ ATQELTNLQ VLQSEVNVMV TEPELEGEPP VTESGAWREV TADCRIDLVP FSVQFYMHQP DRKFSAPSYR KLCVILVKAA H ETELAKSV ...String:
MPINKIHYDK KTLLLEKQSL LDNIVYCETR IAELLTKKCT NYIEDSDSSG SEDGFTLSID PGPTVSQLKL LQSSLQTCLQ ATQELTNLQ VLQSEVNVMV TEPELEGEPP VTESGAWREV TADCRIDLVP FSVQFYMHQP DRKFSAPSYR KLCVILVKAA H ETELAKSV LPHLTRPSDV VEVLKSYSVA YRSRRTSLAR LAEKYESSLY MEPAAEGGYL LRCANLLEVH WRLENKVSAV AP FYHRMKF DLEYMNESYV AKISEAHKQL SDPALSTDER TLLLSKIITV CLEVNGQETV EPSRLDTRQD ALDGDPAPNI MAP PKEIPR KLAKKPSKSL KRSQPDTANV SAKKGKSAPD DTTENQSDNI NIHNLVDNID SKKNNFEATT KNVVTSQSTN KDKS SGNTE LEKAQMIKKP IAENGGRGNK QSSNSEVNVK SVKSSAASKK IPTHKSRLAE KSSVASAEIK STSKNVAAIK SRTEK LNLN ENDKNVMNTN NKNNGNELIE KVTERNKHIT PNKRENVANI NVDNSRDKQK NDLQNKKIQK KILIKSHKNP SSKIKA GNN NVLSAGNTDA AKKSKIPQKV SSPVVDSIIK KNMLRISPRR LPANIKSSSE TSNKQRLIKT STSIPRLLKP TSKIK

UniProtKB: Uncharacterized protein

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Macromolecule #9: bmCENP-T

MacromoleculeName: bmCENP-T / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 116.758258 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPSSKIPSPA RSQGSLLTPR RHRTRSTRSV GSPARSNTPS RLTAIIMQNK EPSFVLSPLP TRRSVLNDDT EVEEPQRKSW WRKLDENSR DILEVLEGNK VGETYEAVEE ILNVEILSQE KKNYTSDLPD SSDSESINSI VMPQRKLFIQ KENVPKKKFG Q LIDNRESL ...String:
MPSSKIPSPA RSQGSLLTPR RHRTRSTRSV GSPARSNTPS RLTAIIMQNK EPSFVLSPLP TRRSVLNDDT EVEEPQRKSW WRKLDENSR DILEVLEGNK VGETYEAVEE ILNVEILSQE KKNYTSDLPD SSDSESINSI VMPQRKLFIQ KENVPKKKFG Q LIDNRESL ANVDKTTAHE KSVTVTTKSL FQNNKRKRVF PAAALNLSPN KTAVDKTKQC IVDPPQNQPR NIFGYRPAAK RK NMFAEFI VSESEDEISE IQPKVFEYQK QFEHRRSRAS NSRPIRETSP ASSITTDMEL DDWKYLPSST IVESHDQNLT ENH ANTIVL KEHDPKKQVS TQHAQQPNDE DHEMVCENNV DQKMFQDKET DNRQQGITPY NNDRGNNTSN KDQTQKEAVE VEHS HNEFQ ENQQNITNKQ KNAENISNVD NSGEQADIFT PQNEEIVEQE NENNDFRKPE NIGSQNNIDI EKHADNEKNN HVEEV DQNA ETEEKIHHSN NTDISSEQNA EVIASNEEEQ MNSHGNETGI EESDQNAESE ASCAEEEQEE TVNEECESEE NNSERA LED STVENNDETE IHERSGDQIR ESDEDLEIDE NMERSELGNE SNASNDDEHL YLSDDNDDEP ENSAGADINV NDNSPNT DN LDNNEITDRS ETVEKVNLPE AILHDKKNES DLFTMQGNNT DLRKTKSIML MSIRPSLLPP VESTSMTDGT RNSSAEGS G WDSHRTTRKT LRQTFGKDFT PRKSLRALVM EKSAKRQTAL VDAKEISKMP QANSTEIPEF NDDYHEAEES IEPTNHEIS KNTRQATLEI YLQKIKKSNM EKNMRIEQEV RNSLKAMKQC KQNVNIFKVP AKPLFARHST KPVQNKNKVR EMKSSMPLGD LPPELLEDM KYKPPKRYQP KNASWTTKRL YKYLEDKLEP KYDYKARVRA EKLVETIYHF TKEVKKHEVA PNDAVDVLKH E MARLDIVK THFDFYQFFH DFMPREIRVK VVPDIVNKIT IPRNGVFSEI LSGHAVHA

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 328750
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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