[English] 日本語
Yorodumi
- EMDB-50416: Structure of human APC3loop 375-381 bound to the NCP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50416
TitleStructure of human APC3loop 375-381 bound to the NCP
Map data
Sample
  • Complex: APC3 motif bound to the NCP acidic patch
    • Protein or peptide: Cell division cycle protein 27 homolog
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • DNA: DNA (132-MER)
    • DNA: DNA (131-MER)
  • Protein or peptide: Histone H2A type 2-A
  • Protein or peptide: Histone H2B type 1-B
  • Ligand: water
KeywordsArginine anchor / NCP / APC3 / Complex / CELL CYCLE
Function / homology
Function and homology information


Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination ...Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / regulation of mitotic cell cycle / Inhibition of DNA recombination at telomere / APC/C:Cdc20 mediated degradation of Cyclin B / Meiotic synapsis / APC-Cdc20 mediated degradation of Nek2A / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Defective pyroptosis / Assembly of the pre-replicative complex / HDACs deacetylate histones / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / nucleosome / nucleosome assembly / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / protein ubiquitination / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / cell division / centrosome / protein-containing complex / DNA binding
Similarity search - Function
Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histone H2B signature. / Histone H2B ...Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Cell division cycle protein 27 homolog / Histone H2B type 1-B / Histone H4 / Histone H3.1 / Histone H2A type 2-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsYoung RVC / Muhammad R / Alfieri C
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
The Institute of Cancer Research (ICR) United Kingdom
CitationJournal: To be published
Title: Spatial control of the APC/C ensures the rapid degradation of Cyclin B1
Authors: Cirillo L / Young RVC / Veerapathiran S / Roberti A / Martin M / Abubacar A / Perosa C / Coates C / Muhammad R / Roumeliotis TI / Choudhary JS / Alfieri C / Pines J
History
DepositionMay 24, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50416.png

Downloads & links

-
Map

FileDownload / File: emd_50416.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 216 pix.
= 224.64 Å		1.04 Å/pix.
x 216 pix.
= 224.64 Å		1.04 Å/pix.
x 216 pix.
= 224.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.049518753 - 0.11865268
Average (Standard dev.)0.0002654244 (±0.003245794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 224.63998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_50416_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_50416_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : APC3 motif bound to the NCP acidic patch

EntireName: APC3 motif bound to the NCP acidic patch
Components
  • Complex: APC3 motif bound to the NCP acidic patch
    • Protein or peptide: Cell division cycle protein 27 homolog
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • DNA: DNA (132-MER)
    • DNA: DNA (131-MER)
  • Protein or peptide: Histone H2A type 2-A
  • Protein or peptide: Histone H2B type 1-B
  • Ligand: water

-
Supramolecule #1: APC3 motif bound to the NCP acidic patch

SupramoleculeName: APC3 motif bound to the NCP acidic patch / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #6-#7
Details: Recombinant protein sample of residues 375-381 of APC3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cell division cycle protein 27 homolog

MacromoleculeName: Cell division cycle protein 27 homolog / type: protein_or_peptide / ID: 1
Details: This is a disorder loop of human APC3 residues 177-446 fused to a SpyTag via a 27 residue GSA linker.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.788488 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGSASNCLPN SCTTQVPNHS LSHRQPETVL TETPQDTIEL NRLNLESSNS KYSLNTDSSV SYIDSAVISP DTVPLGTGTS ILSKQVQNK PKTGRSLLGG PAALSPLTPS FGILPLETPS PGDGSYLQNY TNTPPVIDVP STGAPSKKSV ARIGQTGTKS V FSQSGNSR ...String:
GGSASNCLPN SCTTQVPNHS LSHRQPETVL TETPQDTIEL NRLNLESSNS KYSLNTDSSV SYIDSAVISP DTVPLGTGTS ILSKQVQNK PKTGRSLLGG PAALSPLTPS FGILPLETPS PGDGSYLQNY TNTPPVIDVP STGAPSKKSV ARIGQTGTKS V FSQSGNSR EVTPILAQTQ SSGPQTSTTP QVLSPTITSP PNALPRRSSR LFTSDSSTTK ENSKKLKMKF PPKIPNRKTK SK TNKGGIT QPNINDSLEI TKLDSSIISE GKISTITGSA GSAGSAGSAG SAGSAGSAGS AGSARGVPHI VMVDAYKRYK

UniProtKB: Cell division cycle protein 27 homolog

-
Macromolecule #2: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 2 / Details: Human histone H3.1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

-
Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Details: Human histone H4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

-
Macromolecule #4: Histone H2A type 2-A

MacromoleculeName: Histone H2A type 2-A / type: protein_or_peptide / ID: 4
Details: This is a H2A/H2B fusion protein with a SpyCatcher tag attached
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.125549 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 2-A

-
Macromolecule #5: Histone H2B type 1-B

MacromoleculeName: Histone H2B type 1-B / type: protein_or_peptide / ID: 5
Details: This is a H2A/H2B fusion protein with a SpyCatcher tag attached,This is a H2A/H2B fusion protein with a SpyCatcher tag attached
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.445771 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VTTLSGLSGE QGPSGDMTTE EDSATHIKFS KRDEDGRELA GATMELRDSS GKTISTWISD GHVKDFYLYP GKYTFVETAA PDGYEVATP IEFTVNEDGQ VTVDGEATEG DAHTGSAWSH PQFEKGSAGS AAGSGAGWSH PQFEKGSAMP EPSKSAPAPK K GSKKAITK ...String:
VTTLSGLSGE QGPSGDMTTE EDSATHIKFS KRDEDGRELA GATMELRDSS GKTISTWISD GHVKDFYLYP GKYTFVETAA PDGYEVATP IEFTVNEDGQ VTVDGEATEG DAHTGSAWSH PQFEKGSAGS AAGSGAGWSH PQFEKGSAMP EPSKSAPAPK K GSKKAITK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SR EIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-B

-
Macromolecule #6: DNA (132-MER)

MacromoleculeName: DNA (132-MER) / type: dna / ID: 6
Details: The Widom 147 bp sequence with 32 nucleotides of DNA on either side
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.911336 KDa
SequenceString: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DA)(DG)(DA) (DA) (DT)(DC)(DC)(DC)(DG)(DG) ...String:
(DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(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)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT)(DT) (DT) (DG)(DC)(DC)(DG)(DG)(DG)(DT)(DA)(DT)(DT) (DT)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC) (DC)(DG)(DC)(DG)(DC)(DT)(DA)(DA)(DG)(DA) (DT)

-
Macromolecule #7: DNA (131-MER)

MacromoleculeName: DNA (131-MER) / type: dna / ID: 7
Details: Widom 147 DNA sequence flanked with 32 nucleotides on either side
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.382633 KDa
SequenceString: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT) (DG) (DT)(DA)(DT)(DA)(DT)(DA) ...String:
(DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT) (DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (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)(DG)(DA)(DT)(DT) (DT) (DG)(DC)(DC)(DG)(DG)(DG)(DT)(DA)(DT)(DT) (DT)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC) (DC)(DG)(DC)(DG)(DC)(DT)(DA)(DA)(DG)(DA) (DT)

-
Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 75 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPEs
50.0 mMNaClSodium chloride
0.5 mMC9H15O6PTCEP

Details: 20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2698450
Details: Template base particel picking and Topaz trained particle picking
Startup modelType of model: OTHER / Details: A previous map generated by the lab
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta-latest) / Number images used: 414277
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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://pdbjlvh1.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