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- EMDB-54924: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-54924
TitleChromosomal Passenger Complex in complex with H3T3ph Nucleosome
Map data
Sample
  • Complex: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome
    • Protein or peptide: Borealin
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: Baculoviral IAP repeat-containing protein 5
    • Protein or peptide: Inner centromere protein
KeywordsNucleosome-binding DNA-binding Stabilising Nucleosome Acidic-patch interaction / CELL CYCLE
Function / homology
Function and homology information


central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis ...central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / interphase microtubule organizing center / lateral element / chromosome passenger complex / protein-containing complex localization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cobalt ion binding / mitotic metaphase chromosome alignment / nuclear chromosome / mitotic spindle assembly checkpoint signaling / spindle midzone / pericentric heterochromatin / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / mitotic cytokinesis / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / chromosome, centromeric region / cysteine-type endopeptidase inhibitor activity / mitotic spindle assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / chromosome organization / protein localization to CENP-A containing chromatin / intercellular bridge / Replacement of protamines by nucleosomes in the male pronucleus / cytoplasmic microtubule / CENP-A containing nucleosome / Packaging Of Telomere Ends / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / centriole / EML4 and NUDC in mitotic spindle formation / tubulin binding / Inhibition of DNA recombination at telomere / positive regulation of mitotic cell cycle / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Resolution of Sister Chromatid Cohesion / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / molecular function activator activity / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / mitotic spindle organization / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / spindle microtubule / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / chromosome segregation / HDACs deacetylate histones / lipopolysaccharide binding / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / sensory perception of sound / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / kinetochore / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / small GTPase binding / Pre-NOTCH Transcription and Translation / G2/M transition of mitotic cell cycle / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / Separation of Sister Chromatids / UCH proteinases / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin
Similarity search - Function
Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / : ...Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / : / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5 / Histone H2B type 1-J / Histone H2A type 1 / Histone H4 / Histone H3.2 / Borealin / Inner centromere protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsGireesh A / Abad MA / Sotelo-Parrilla P / Jeyaprakash AA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: CPC mediated centromeric chromatin protection is essential for error-free chromosome segregation
Authors: Gireesh A / Abad MA / Parrilla PS / Jeyaprakash AA
History
DepositionAug 28, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54924.png

Downloads & links

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Map

FileDownload / File: emd_54924.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 279.168 Å		0.73 Å/pix.
x 384 pix.
= 279.168 Å		0.73 Å/pix.
x 384 pix.
= 279.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.061
Minimum - Maximum-0.32538873 - 0.9028934
Average (Standard dev.)-0.0004064405 (±0.028908184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 279.168 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_54924_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54924_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54924_half_map_2.map
Projections & Slices
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Sample components

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Entire : Chromosomal Passenger Complex in complex with H3T3ph Nucleosome

EntireName: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome
Components
  • Complex: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome
    • Protein or peptide: Borealin
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: Baculoviral IAP repeat-containing protein 5
    • Protein or peptide: Inner centromere protein

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Supramolecule #1: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome

SupramoleculeName: Chromosomal Passenger Complex in complex with H3T3ph Nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: Cryo-EM Structure of CPC in complex with H3T3ph Nucleosome
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 341 KDa

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Macromolecule #1: Borealin

MacromoleculeName: Borealin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.376041 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAPRKGSSRV AKTNSLRRRK LASFLKDFDR EVEIRIKQIE SDRQNLLKEV DNLYNIEILR LPKALREMNW LDYFALGGNK QALEEAATA DLDITEINKL TAEAIQTPLK SAKTRKVIQV DEMIVEEEEE EENERKNLQT ARVKRCPPSK KRTQSIQGKG K GKRSSRAN ...String:
MAPRKGSSRV AKTNSLRRRK LASFLKDFDR EVEIRIKQIE SDRQNLLKEV DNLYNIEILR LPKALREMNW LDYFALGGNK QALEEAATA DLDITEINKL TAEAIQTPLK SAKTRKVIQV DEMIVEEEEE EENERKNLQT ARVKRCPPSK KRTQSIQGKG K GKRSSRAN TVTPAVGRLE VSMVKPTPGL TPRFDSRVFK TPGLRTPAAG ERIYNISGNG SPLADSKEIF LTVPVGGGES LR LLASDLQ RHSIAQLDPE ALGNIKKLSN RLAQICSSIR THK

UniProtKB: Borealin

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Macromolecule #2: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.990342 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1

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Macromolecule #5: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.804045 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #8: Baculoviral IAP repeat-containing protein 5

MacromoleculeName: Baculoviral IAP repeat-containing protein 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.414736 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MGAPTLPPAW QPFLKDHRIS TFKNWPFLEG CACTPERMAE AGFIHCPTEN EPDLAQCFFC FKELEGWEPD DDPIEEHKKH SSGCAFLSV KKQFEELTLG EFLKLDRERA KNKIAKETNN KKKEFEETAK KVRRAIEQLA AMD

UniProtKB: Baculoviral IAP repeat-containing protein 5

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Macromolecule #9: Inner centromere protein

MacromoleculeName: Inner centromere protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.620344 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGTTAPGPIH LLELCDQKLM EFLCNMDNKD LVWLEEIQEE AERMFTREFS KEPELMPKTP SQKNRRKKRR ISYVQDENRD PIRRRLSRR KSRSSQLSSR RLRSKDSVEK LATVVGENGS VLRRVTRAAA AAAAATMALA APSSPTPESP TMLTKKPEDN H TQCQLVPV ...String:
MGTTAPGPIH LLELCDQKLM EFLCNMDNKD LVWLEEIQEE AERMFTREFS KEPELMPKTP SQKNRRKKRR ISYVQDENRD PIRRRLSRR KSRSSQLSSR RLRSKDSVEK LATVVGENGS VLRRVTRAAA AAAAATMALA APSSPTPESP TMLTKKPEDN H TQCQLVPV VEIGISERQN AEQHVTQLMS TEPLPRTLSP TPASATAPTS QGIPTSDEES TPKKSKARIL ESITVSSLMA TP QDPKGQG VGTGRSASKL RIAQVSPGPR DSPAFPDSPW RERVLAPILP DNFSTPTGSR TDSQSVRHSP IAPSSPSPQV LAQ KYSLVA KQESVVRRAS RRLAKKTAEE PAASGRIICH SYLERLLNVE VPQKVGSEQK EPPEEAEPVA AAEPEVPENN GNNS WPHND TEIANSTPNP KPAASSPETP SAGQQEAKTD QADGPREPPQ SARRKRSYKQ AVSELDEEQH LEDEELQPPR SKTPS SPCP ASKVVRPLRT FLHTVQRNQM LMTPTSAPRS VMKSFIKRNT PLRMDPKCSF VEKERQRLEN LRRKEEAEQL RRQKVE EDK RRRLEEVKLK REERLRKVLQ ARERVEQMKE EKKKQIEQKF AQIDEKTEKA KEERLAEEKA KKKAAAKKME EVEARRK QE EEARRLRWLQ QEEEERRHQE LLQKKKEEEQ ERLRKAAEAK RLAEQREQER REQERREQER REQERREQER REQERQLA E QERRREQERL QAERELQERE KALRLQKEQL QRELEEKKKK EEQQRLAERQ LQEEQEKKAK EAAGASKALN VTVDVQSPA CTSYQMTPQG HRAPPKINPD NYGMDLNSDD STDDEAHPRK PIPTWARGTP LSQAIIHQYY HPPNLLELFG TILPLDLEDI FKKSKPRYH KRTSSAVWNS PPLQGARVPS SLAYSLKKH

UniProtKB: Inner centromere protein

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.64407 KDa
SequenceString: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(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)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG)

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Macromolecule #7: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.105727 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (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) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (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)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DC)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)

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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

Concentration.115 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 75653
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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