[English] 日本語
Yorodumi
- EMDB-70560: Structure of the monomeric Bombyx mori CCAN bound to linear DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70560
TitleStructure of the monomeric Bombyx mori CCAN bound to linear DNA
Map dataComposite map of monomeric Bombyx mori CCAN bound to DNA, unsharpened
Sample
  • Complex: Bombyx mori CCAN monomer bound to DNA
    • Protein or peptide: x 13 types
    • DNA: x 2 types
KeywordsCCAN / complex / protein-DNA / segregation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / Uncharacterized protein / Centromere protein I / Centromere protein L
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsYatskevich S / Ciferri C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Architecture and Function of Holocentric CENP-A-Independent Inner Kinetochores
Authors: Yatskevich S / Ciferri C
History
DepositionMay 9, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70560.png

Downloads & links

-
Map

FileDownload / File: emd_70560.map.gz / Format: CCP4 / Size: 296.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of monomeric Bombyx mori CCAN bound to DNA, unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 427 pix.
= 309.575 Å		0.73 Å/pix.
x 427 pix.
= 309.575 Å		0.73 Å/pix.
x 426 pix.
= 308.85 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0332
Minimum - Maximum-0.12773517 - 0.5107111
Average (Standard dev.)0.0011505454 (±0.008696665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-4-2-4
Dimensions427426427
Spacing426427427
CellA: 308.85 Å / B: 309.575 Å / C: 309.575 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Consensus refinement of monomeric Bombyx mori CCAN bound...

Fileemd_70560_additional_1.map
AnnotationConsensus refinement of monomeric Bombyx mori CCAN bound to DNA, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local refinement of monomeric Bombyx mori CCAN bound...

Fileemd_70560_additional_2.map
AnnotationLocal refinement of monomeric Bombyx mori CCAN bound to DNA, focusing on bmCENP-HIK-T head group, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Composite map of monomeric Bombyx mori CCAN bound to DNA, sharpened

Fileemd_70560_additional_3.map
AnnotationComposite map of monomeric Bombyx mori CCAN bound to DNA, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Consensus bmCCAN reconstruction half-map A

Fileemd_70560_half_map_1.map
AnnotationConsensus bmCCAN reconstruction half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Consensus bmCCAN reconstruction half-map B

Fileemd_70560_half_map_2.map
AnnotationConsensus bmCCAN reconstruction half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Bombyx mori CCAN monomer bound to DNA

EntireName: Bombyx mori CCAN monomer bound to DNA
Components
  • Complex: Bombyx mori CCAN monomer bound to DNA
    • 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
    • Protein or peptide: CS-1
    • Protein or peptide: DASH complex subunit DAD4
    • Protein or peptide: CS-4
    • Protein or peptide: CS-2
    • DNA: DNA (36-MER)
    • DNA: DNA (36-MER)

+
Supramolecule #1: Bombyx mori CCAN monomer bound to DNA

SupramoleculeName: Bombyx mori CCAN monomer bound to DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bombyx mori (domestic silkworm)

+
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: Trichoplusia ni (cabbage looper)
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

+
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: Trichoplusia ni (cabbage looper)
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

+
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: Trichoplusia ni (cabbage looper)
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

+
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: Trichoplusia ni (cabbage looper)
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

+
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: Trichoplusia ni (cabbage looper)
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

+
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: 36.883547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 LTYNGIDYTN RT YDAEYIE NILGPDPPLL TDLTIKTSKP FFDASMLSKN INMKITLKSE NVAETLKSWV VKGALAPTSE FFHIFHNIKS NNI SRNIDD TD

UniProtKB: Uncharacterized protein

+
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: Trichoplusia ni (cabbage looper)
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

+
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: Trichoplusia ni (cabbage looper)
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

+
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: Trichoplusia ni (cabbage looper)
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

+
Macromolecule #10: CS-1

MacromoleculeName: CS-1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 10.754051 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAQLQQLQQD LQNELITTNQ LLHLIGNELQ QIICLTSSGG EIEKNIKKNA SLMSILANLQ HIDIENIPLV TRNQVTSNQN TEELNLQRN VLDETD

+
Macromolecule #11: DASH complex subunit DAD4

MacromoleculeName: DASH complex subunit DAD4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 8.577579 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSNNSETSLS QRDKAAELPM ELESIRALNA CLQAYLEHIR NVKRNLLAMN DNYRDLEDVN RQWQEVVEFR RE

UniProtKB: Uncharacterized protein

+
Macromolecule #12: CS-4

MacromoleculeName: CS-4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 9.175406 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MNSTVSDDLT RENSASEISK CISRLSANNR NLSLLHKELL EINLSVKAYV QESKKRLQGL RLDLAHEARS SHQVVELLTE K

+
Macromolecule #13: CS-2

MacromoleculeName: CS-2 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 9.122198 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MTSVAPSDSE SNVSGFVRYS DKSFKHLYTS VLEKLELINQ DILQIENNLK NLIQHAGPLE SQLSAVLHSL PKPNTNTAME TE

+
Macromolecule #14: DNA (36-MER)

MacromoleculeName: DNA (36-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.095101 KDa
SequenceString:
(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG)(DA)(DC)(DA)(DG)(DC)(DT)

+
Macromolecule #15: DNA (36-MER)

MacromoleculeName: DNA (36-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.064092 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 241975
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9okd:
Structure of the monomeric Bombyx mori CCAN bound to linear DNA

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more