[English] 日本語
Yorodumi
- EMDB-72163: Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72163
TitleRad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP
Map dataconsensus
Sample
  • Complex: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
    • Protein or peptide: x 7 types
    • DNA: x 1 types
  • Ligand: x 4 types
KeywordsHomologous Recombination Complex / Rad51 Paralog Complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Shu complex / positive regulation of single-strand break repair via homologous recombination / Presynaptic phase of homologous DNA pairing and strand exchange / meiotic joint molecule formation / error-free postreplication DNA repair / heteroduplex formation / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / meiotic DNA recombinase assembly / methylated-DNA-[protein]-cysteine S-methyltransferase ...Shu complex / positive regulation of single-strand break repair via homologous recombination / Presynaptic phase of homologous DNA pairing and strand exchange / meiotic joint molecule formation / error-free postreplication DNA repair / heteroduplex formation / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / meiotic DNA recombinase assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / meiotic chromosome segregation / maintenance of rDNA / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / mitochondrial DNA repair / DNA recombinase assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / telomere maintenance via recombination / reciprocal meiotic recombination / recombinational repair / error-free translesion synthesis / ATP-dependent DNA damage sensor activity / nuclear chromosome / DNA replication origin binding / ATP-dependent activity, acting on DNA / replication fork / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / nucleotide-excision repair / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / methylation / DNA recombination / mitochondrial matrix / DNA repair / nucleolus / DNA binding / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Shu complex, component Psy3 / Chromosome segregation in meiosis protein 2 / Shu complex component Csm2, DNA-binding / Shu complex component Psy3, DNA-binding description / : / : / Methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC ...Shu complex, component Psy3 / Chromosome segregation in meiosis protein 2 / Shu complex component Csm2, DNA-binding / Shu complex component Psy3, DNA-binding description / : / : / Methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / : / SAM-like Helix-hairpin-helix tandem / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Suppressor of hydroxyurea sensitivity protein 2 / Methylated-DNA--protein-cysteine methyltransferase / DNA repair protein RAD57 / DNA repair protein RAD51 / Suppressor of HU sensitivity involved in recombination protein 1 / DNA repair protein RAD55 / Chromosome segregation in meiosis protein 2 / Platinum sensitivity protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsYatskevich S / Koo CW / Ciferri C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Rad51 Paralog Complex Dynamically Templates Rad51 Filament Nucleation
Authors: Yatskevich S / Koo CW / Ciferri C
History
DepositionAug 15, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72163.png

Downloads & links

-
Map

FileDownload / File: emd_72163.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 400 pix.
= 362.5 Å		0.91 Å/pix.
x 400 pix.
= 362.5 Å		0.91 Å/pix.
x 400 pix.
= 362.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.90625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.30927554 - 0.6950094
Average (Standard dev.)-0.00021159441 (±0.01654285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 362.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72163_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B

Fileemd_72163_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half A

Fileemd_72163_half_map_2.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA

EntireName: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
Components
  • Complex: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55
    • Protein or peptide: DNA repair protein RAD57
    • Protein or peptide: Chromosome segregation in meiosis protein 2
    • Protein or peptide: Platinum sensitivity protein 3
    • Protein or peptide: Suppressor of HU sensitivity involved in recombination protein 1
    • Protein or peptide: Suppressor of hydroxyurea sensitivity protein 2
    • Protein or peptide: DNA repair protein RAD51
    • DNA: ssDNA (9-mer)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: ZINC ION

+
Supramolecule #1: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA

SupramoleculeName: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 271.98 KDa

+
Macromolecule #1: Methylated-DNA--protein-cysteine methyltransferase,DNA repair pro...

MacromoleculeName: Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 70.243594 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSMDKDCEM KRTTLDSPLG KLELSGCEQG LHRIIFLGKG TSAADAVEVP APAAVLGGP EPLMQATAWL NAYFHQPEAI EEFPVPALHH PVFQQESFTR QVLWKLLKVV KFGEVISYSH LAALAGNPAA T AAVKTALS ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSMDKDCEM KRTTLDSPLG KLELSGCEQG LHRIIFLGKG TSAADAVEVP APAAVLGGP EPLMQATAWL NAYFHQPEAI EEFPVPALHH PVFQQESFTR QVLWKLLKVV KFGEVISYSH LAALAGNPAA T AAVKTALS GNPVPILIPC HRVVQGDLDV GGYEGGLAVK EWLLAHEGHR LGKPGLGGSE NLYFQGSMSL GIPLSQLIVE SP KPLSSGI TGLDEILNLG FQARSIYEIF GPPGIGKTNF GIQLVCNSLE GIQQSEINDD KILWIETFQE MPINILRERF QKF KIVEEN VKRVRITKFG QLLYFFQNLF KLSQSVRYKL VIIDGFSQLV CDHLCTLSKR GGGMIDKTIH ELKCRHLILI FTVM TKYTH STGSTIIVLN DCMNTAFQSN EFESLEEYYE ILDDGSNFFV NSNNERRKNN VHILKSALVA NIAMGSKDST WEVFL RDRI GLFRDWNEQV DETVFVKSKR VKASSSQSNE GCTTIKEMRI NKRNFENLRI AIVFNLHGED RKREGRNLKR SRSSDD RNY IVKFDFDKAT GQLRDIIDLK PDTANIASFP TLSTSSSSCS QVFNNIDSND NPLPNAEGKE EIIYDSEG

UniProtKB: Methylated-DNA--protein-cysteine methyltransferase, DNA repair protein RAD55

+
Macromolecule #2: DNA repair protein RAD57

MacromoleculeName: DNA repair protein RAD57 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 52.308301 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPRALSIKFD NTYMDLYDEL PESKLLYDEE FSYLLDAVRQ NGVCVVDFLT LTPKELARLI QRSINEVFRF QQLLVHEYNE KYLEICEKN SISPDNGPEC FTTADVAMDE LLGGGIFTHG ITEIFGESST GKSQLLMQLA LSVQLSEPAG GLGGKCVYIT T EGDLPTQR ...String:
MPRALSIKFD NTYMDLYDEL PESKLLYDEE FSYLLDAVRQ NGVCVVDFLT LTPKELARLI QRSINEVFRF QQLLVHEYNE KYLEICEKN SISPDNGPEC FTTADVAMDE LLGGGIFTHG ITEIFGESST GKSQLLMQLA LSVQLSEPAG GLGGKCVYIT T EGDLPTQR LESMLSSRPA YEKLGITQSN IFTVSCNDLI NQEHIINVQL PILLERSKGS IKLVIIDSIS HHLRVELQNK SF RESQENK NYLDRMAEKL QILAHDYSLS VVVANQVGDK PLANSPVAHR TYVTDYDYQL GWLVGWKNST ILYRQMNSLL GAS SNNDEI LSDDEDYMLI ERVMSTVNDR NYDFFSKKKP PIIENKTVER NSSSPISRQS KKRKFDYRVP NLGLTWSNHV STRI LLQKS FKASTIIQRG EAHLYKGGDS ASFWQVKRTM KVVYSTFAKP GQIAYQITKR GIETA

UniProtKB: DNA repair protein RAD57

+
Macromolecule #3: Chromosome segregation in meiosis protein 2

MacromoleculeName: Chromosome segregation in meiosis protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.98368 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEYEDLELIT IWPSPTKNKL CQFIKQNLSK EHVVTQLFFI DATSSFPLSQ FQKLVPPTLP ENVRIYENIR INTCLDLEEL SAITVKLLQ ILSMNKINAQ RGTEDAVTEP LKIILYINGL EVMFRNSQFK SSPQRSHELL RDTLLKLRVM GNDENENASI R TLLEFPKE ...String:
MEYEDLELIT IWPSPTKNKL CQFIKQNLSK EHVVTQLFFI DATSSFPLSQ FQKLVPPTLP ENVRIYENIR INTCLDLEEL SAITVKLLQ ILSMNKINAQ RGTEDAVTEP LKIILYINGL EVMFRNSQFK SSPQRSHELL RDTLLKLRVM GNDENENASI R TLLEFPKE QLLDYYLKKN NNTRTSSVRS KRRRIKNGDS LAEYIWKYYA DSLFE

UniProtKB: Chromosome segregation in meiosis protein 2

+
Macromolecule #4: Platinum sensitivity protein 3

MacromoleculeName: Platinum sensitivity protein 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 32.385123 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQM EVLKNIRIYP LSNFITSTKN YINLPNELRN LISEEQESKL GFLHIIESD FKPSVALQKL VNCTTGDEKI LIIDIVSIWS QQKQRQHGAI YMNSLSCINI TGLIVFLELL YDSPMDALRR C QVDNFNFQ ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQM EVLKNIRIYP LSNFITSTKN YINLPNELRN LISEEQESKL GFLHIIESD FKPSVALQKL VNCTTGDEKI LIIDIVSIWS QQKQRQHGAI YMNSLSCINI TGLIVFLELL YDSPMDALRR C QVDNFNFQ LRGIVIDNLS FLNFESDKNY DVINLSKFEK LFKILRKLRE FLGCWIITKS FPTDFYNGIE NTLVDKWSIK RK SGVTLYP TKLPDSYMKG MDLIIYREVV DGRPQYRRIA ALEE

UniProtKB: Platinum sensitivity protein 3

+
Macromolecule #5: Suppressor of HU sensitivity involved in recombination protein 1

MacromoleculeName: Suppressor of HU sensitivity involved in recombination protein 1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.138637 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MQFEERLQQL VESDWSLDQS SPNVLVIVLG DTARKYVELG GLKEHVTTNT VAGHVASRER VSVVFLGRVK YLYMYLTRMQ AQANGPQYS NVLVYGLWDL TATQDGPQQL RLLSLVLRQC LSLPSKVEFY PEPPSSSVPA RLLRFWDHII R

UniProtKB: Suppressor of HU sensitivity involved in recombination protein 1

+
Macromolecule #6: Suppressor of hydroxyurea sensitivity protein 2

MacromoleculeName: Suppressor of hydroxyurea sensitivity protein 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.179885 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQG SKDVIEYSKL FAKLVNTNDD TKLDDTIASF LYYMFPRELF IRAISLLES SDMFIYILDR VHNKEGNEHT SLIDVLVDEF YKGSSNSLLE YRLIVKDTND GAPPILVDIA HWFCSCEEFC K YFHEALEK ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQG SKDVIEYSKL FAKLVNTNDD TKLDDTIASF LYYMFPRELF IRAISLLES SDMFIYILDR VHNKEGNEHT SLIDVLVDEF YKGSSNSLLE YRLIVKDTND GAPPILVDIA HWFCSCEEFC K YFHEALEK TDEKEELHDV LINEVDDHLQ FSDDRFAQLD PHSLSKQWYF KFDKVCCSHL LAFSILLRSS INVLKFFTVN SN KVFVIAI DNIDEWLNLH INIVE

UniProtKB: Suppressor of hydroxyurea sensitivity protein 2

+
Macromolecule #7: DNA repair protein RAD51

MacromoleculeName: DNA repair protein RAD51 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.239727 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHG ENLYFQGSMS QVQEQHISES QLQYGNGSLM STVPADLSQS VVDGNGNGSS EDIEATNGSG DGGGLQEQAE AQGEMEDEA YDEAALGSFV PIEKLQVNGI TMADVKKLRE SGLHTAEAVA YAPRKDLLEI KGISEAKADK LLNEAARLVP M GFVTAADF ...String:
MHHHHHHHHG ENLYFQGSMS QVQEQHISES QLQYGNGSLM STVPADLSQS VVDGNGNGSS EDIEATNGSG DGGGLQEQAE AQGEMEDEA YDEAALGSFV PIEKLQVNGI TMADVKKLRE SGLHTAEAVA YAPRKDLLEI KGISEAKADK LLNEAARLVP M GFVTAADF HMRRSELICL TTGSKNLDTL LGGGVETGSI TELFGEFRTG KSQLCHTLAV TCQIPLDIGG GEGKCLYIDT EG TFRPVRL VSIAQRFGLD PDDALNNVAY ARAYNADHQL RLLDAAAQMM SESRFSLIVV DSVMALYRTD FSGRGELSAR QMH LAKFMR ALQRLADQFG VAVVVTNQVV AQVDGGMAFN PDPKKPIGGN IMAHSSTTRL GFKKGKGCQR LCKVVDSPCL PEAE CVFAI YEDGVGDPRE EDE

UniProtKB: DNA repair protein RAD51

+
Macromolecule #8: ssDNA (9-mer)

MacromoleculeName: ssDNA (9-mer) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.692778 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

+
Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #11: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 11 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

+
Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 56.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 11289
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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