[English] 日本語
Yorodumi
- EMDB-53919: Cryo-EM structure of a contractile injection system in Salmonella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53919
TitleCryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the baseplate portion in extended state.
Map dataC3 reconstruction.
Sample
  • Complex: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
    • Protein or peptide: Peptidoglycan-binding protein
    • Protein or peptide: Conserved hypothetical phage tail region protein
    • Protein or peptide: Baseplate protein J-like domain-containing protein
    • Protein or peptide: SalCis12
  • Protein or peptide: GPW/gp25 family protein
  • Protein or peptide: Phage tail sheath family protein
  • Protein or peptide: SalCis6
  • Protein or peptide: Type VI secretion system tip protein VgrG
  • Protein or peptide: SalCis10
Keywordscontractile injection system Salmonella / CONTRACTILE PROTEIN
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / PAAR motif / PAAR motif / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / LysM domain profile. / LysM domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Conserved hypothetical phage tail region protein / Uncharacterized conserved protein / Peptidoglycan-binding protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. salamae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsEjaz RN / Tillmann HP / Sofos NH / Siborova M / Taylor NMI
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Medical Sciences30342400-1201051001 Denmark
CitationJournal: Nat Commun / Year: 2026
Title: Structure of a contractile injection system in Salmonella enterica subsp. salamae.
Authors: Rooshanie N Ejaz / Kristin Funke / Claudia S Kielkopf / Freddie J O Martin / Marta Šiborová / Ivo A Hendriks / Nicholas H Sofos / Tillmann Pape / Eva M Steiner-Rebrova / Michael L Nielsen ...Authors: Rooshanie N Ejaz / Kristin Funke / Claudia S Kielkopf / Freddie J O Martin / Marta Šiborová / Ivo A Hendriks / Nicholas H Sofos / Tillmann Pape / Eva M Steiner-Rebrova / Michael L Nielsen / Marc Erhardt / Nicholas M I Taylor /
Abstract: Extracellular contractile injection systems (eCISs) are phage-derived nanomachines used by bacteria to deliver effectors into target cells. Well-studied examples include the Photorhabdus asymbiotica ...Extracellular contractile injection systems (eCISs) are phage-derived nanomachines used by bacteria to deliver effectors into target cells. Well-studied examples include the Photorhabdus asymbiotica virulence cassettes and the antifeeding prophage from Serratia entomophila, which have been engineered for heterologous cargo delivery. Recent genomic analyses identified eCIS gene clusters in the opportunistic human pathogen Salmonella enterica subspecies salamae, but their structure, function, and biotechnological potential remain unexplored. Here, we report a high-resolution cryo-electron microscopy structure of the S. enterica eCIS. Our atomic models reveal a distinctive sheath architecture, an expansive cage-like shell around a central spike, and an associated integral membrane protein. We identify a putative effector encoded within the operon exhibiting mild periplasmic toxicity and provide evidence that the S. enterica eCIS deviates from canonical eCISs by interacting with the inner membrane. Guided by these structural features, we uncover, to the best of our knowledge, a previously unannotated cluster of contractile injection systems (CISs). Together, our findings expand the known diversity of CISs' structures and functions, and lay the groundwork for engineering customisable protein delivery platforms.
History
DepositionMay 28, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53919.png

Downloads & links

-
Map

FileDownload / File: emd_53919.map.gz / Format: CCP4 / Size: 953.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC3 reconstruction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 630 pix.
= 456.75 Å		0.73 Å/pix.
x 630 pix.
= 456.75 Å		0.73 Å/pix.
x 630 pix.
= 456.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0678
Minimum - Maximum-0.43147695 - 0.6562294
Average (Standard dev.)0.0007682948 (±0.026841221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions630630630
Spacing630630630
CellA=B=C: 456.75 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_53919_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53919_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cryo-EM structure of a contractile injection system in Salmonella...

EntireName: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
Components
  • Complex: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
    • Protein or peptide: Peptidoglycan-binding protein
    • Protein or peptide: Conserved hypothetical phage tail region protein
    • Protein or peptide: Baseplate protein J-like domain-containing protein
    • Protein or peptide: SalCis12
  • Protein or peptide: GPW/gp25 family protein
  • Protein or peptide: Phage tail sheath family protein
  • Protein or peptide: SalCis6
  • Protein or peptide: Type VI secretion system tip protein VgrG
  • Protein or peptide: SalCis10

+
Supramolecule #1: Cryo-EM structure of a contractile injection system in Salmonella...

SupramoleculeName: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #9, #3
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)

+
Macromolecule #1: Peptidoglycan-binding protein

MacromoleculeName: Peptidoglycan-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 23.868895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKITIKSIT SKGTVAQTFS ATLNPNSIKH NFGISYTDKG PQQQGDISPT TVFKGYESEK LDFELLFDGT GVTGSTSTNT VQKQLATLK KVTYAYNGEQ HEPNPVVIAW GSSVNFQGRL TAISINYSLF DSSGNPLRAT VSLSFAKYLT QQEKSALKKQ S SPDLTHII ...String:
MEKITIKSIT SKGTVAQTFS ATLNPNSIKH NFGISYTDKG PQQQGDISPT TVFKGYESEK LDFELLFDGT GVTGSTSTNT VQKQLATLK KVTYAYNGEQ HEPNPVVIAW GSSVNFQGRL TAISINYSLF DSSGNPLRAT VSLSFAKYLT QQEKSALKKQ S SPDLTHII EFKAGDTLPM LCHKIYNDSS YYIDVARANN LVSARQITPG TKIYFPPLI

UniProtKB: Peptidoglycan-binding protein

+
Macromolecule #2: Conserved hypothetical phage tail region protein

MacromoleculeName: Conserved hypothetical phage tail region protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 17.506768 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVTAKGSGAA QGDGDWPLPA FYFSVSISGC ADDTAFQEVS GLEFQIETEE YREGGNNLVY HLPKTIKSSN LTLKRAVTDK ASRLLSWCL DILNDELSKP IQTKSVSINL LNEKGTTCKS WTASNAYPVK LKMAPFNSTQ NDIAIEEIEI CFHHLKRNL

UniProtKB: Conserved hypothetical phage tail region protein

+
Macromolecule #3: SalCis12

MacromoleculeName: SalCis12 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 93.034227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPAHSDWGVN STMSKTISKK DHNDNPNSFG HLYQLGLTYI QQLSGHLWTD YNTHDPGMTI LEQVCYALTD LIYRCEFEVT DYLSEPSGN IDYRAHGLAL AEDIIPSYPQ QPKEYEAWLL ARLPELDKVW LRNSENDSHL GIYTLNAQLN HFYALSQQRA V TGKHSVYT ...String:
MPAHSDWGVN STMSKTISKK DHNDNPNSFG HLYQLGLTYI QQLSGHLWTD YNTHDPGMTI LEQVCYALTD LIYRCEFEVT DYLSEPSGN IDYRAHGLAL AEDIIPSYPQ QPKEYEAWLL ARLPELDKVW LRNSENDSHL GIYTLNAQLN HFYALSQQRA V TGKHSVYT QQYAALHRIR HEYYRVRAVG EDLAAIELTG QHPLSLSAVI HISDDVADVT WLAACIYHRI HLWLESNQQN TP VNVIKES LLAEDGILQI DRLEFMQHSD NVSHDEQKAI DNIAPFSYLM LPEASAHSGI EIVQFQHPVN IDYADLAIQI EQI QYQQRN AQLKTPTPPA LPVGQYVDFT RYESIQTLFP RNYHLAPGTP IQYHAQQQAQ RHQLRSYLLL FDQLMANFCD DIAG LNALF SLSLTPEVTY HAHSLQDDEF YNIEKHYPRD ANAGLERLRA QLDNYPERKN RIFNYLLALY SERYPDWLHR QFNPY FSTQ TLEKEILKYK QAFILNIVTM TNGRGIGDNL LQPEHQGGYC QRLALLLGLF PSVDAAKGNV RTFARYSLNL VSDQDY FHS DTGRKALWLT TLEAQTSLQP IEENALTGYP KESDIHDTLL TAPLFREKIL PDALLQFGID NHRYRLLSRQ NHDVHQL FF HVDIDGHKRW FHIASHSDKQ ALILLCHQLQ RWLVQLNRDS EELYVVEPIL LRTEATSASL SDYANRVILV LPGYTARF S NLRFREQVEQ LIVENSPAHL LTQCLWLDFA MFNQFETLYT QWRQAKSNAL QHKERQPECD ATAQRLYLFL QRASIGADG VESQ

+
Macromolecule #4: GPW/gp25 family protein

MacromoleculeName: GPW/gp25 family protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 16.921131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MANDNTFLGT GWAFPPRFTG PNHQVVMSSD MQDIEQSLTL LLSTTPGERL MTPDFGCRIN QFVFEELTQT VLTQLSSEIR HAILFFESR IDVEDVHFLP EPLSGKLLIQ IDYSVITTNT RSNMVYPFYL NEGTLISPQL LPLANEWDIA

+
Macromolecule #5: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 57.35193 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGVMKTPGVY IVEQNAFPNS VVEVATAVPA FIGYTEKADN GGKSLSNKGW RITSMSEYRQ YFGGEPQHLF EISEISTTSN ANIREAFKQ SGKTYQITQS NTRHHLYYSM LFFFQNGGGP CYIVSVGNYS DDIDAAVLKG GILPLIKEAE PTMLLIPEAI Q LAEDDCIN ...String:
MGVMKTPGVY IVEQNAFPNS VVEVATAVPA FIGYTEKADN GGKSLSNKGW RITSMSEYRQ YFGGEPQHLF EISEISTTSN ANIREAFKQ SGKTYQITQS NTRHHLYYSM LFFFQNGGGP CYIVSVGNYS DDIDAAVLKG GILPLIKEAE PTMLLIPEAI Q LAEDDCIN VEQAMLGHCG GKMKNRVAIL DVWNGYKDRQ HPDGDCVESF RSKLGTHYLD YAAAYYPWLN TSIVQDSDVS FL NISNIDK LAELLSGEVA LMFSDLEGLS EEELSTGGNK LRATRKQAML DEIAKLSAEI SRPDAVLLHK ILSNMSPLYQ TIM ADIKFQ QNILPPSSAM AGIYTMVDNS RGVWKAPANV SVNAVVSPTV NISDDEQEDL NVTTQGKSIN AIRPFIGEGT LVWG ARTLD GNSVDWRYIN VRRTMIMLEE SIKLASKAYV FEPNVANTWV SMESMLSNFL YGIWKRGGLA GSTPGEAYNV SVGLG KTMT SNDILEGILR ITVLVAMVRP AEFIEITFQQ KMQES

+
Macromolecule #6: SalCis6

MacromoleculeName: SalCis6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 6.294013 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VPLEIKQLVI KSQTINDDNK SPSFGSDWPG IESEESVSAK VIPYPFMPSP DEVRER

+
Macromolecule #7: Type VI secretion system tip protein VgrG

MacromoleculeName: Type VI secretion system tip protein VgrG / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 63.170824 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAISPLSNNS TGVTTYTIKV GGKAIDSAIG VIAIHIHYQV NHIATAEITI SDGDMPTQRF DISDADTFKP GSTISISAGY ASDEQTIFD GIIISHGIEI AANNSSSLSV ICKDQAVAMT IAKHSQCFLG KSDSKIISTL LANYPNITAS VGRITDPHSE L VQFNSTDW ...String:
MAISPLSNNS TGVTTYTIKV GGKAIDSAIG VIAIHIHYQV NHIATAEITI SDGDMPTQRF DISDADTFKP GSTISISAGY ASDEQTIFD GIIISHGIEI AANNSSSLSV ICKDQAVAMT IAKHSQCFLG KSDSKIISTL LANYPNITAS VGRITDPHSE L VQFNSTDW DFILTRAEAN GFVVTNQSNK VTVDKPAISN AADLVVTYGT DLISFSAKVD ARNQLKSVTA TAWDPAKQSM VT GTGPAQS ISGQGNLTSS ELAKVLGISD YTLQTASTLS TDSLTRWADG QQVKAMLSKV RGSVTFQGNA SATINSLIEL AGV GERYNG SHYISGVHHS IEKGQWITTA ELGMSPMWSA DHRDIGAPPA SGYLPPVDGL QIGVVTKLDG DPESNYRIQI KIPT LNSEA NVIWARLASY YASSGFGNFF IPEVGDEVIV GCINQDPSNP IILGSLYSSK NKMPEEMTSD NYIKTLVTKS KMKII FDDE NSVMTLKTPN GNTVVISDKN KSITLADQNS NTICMDKNGI AITSSKDVMI SAKGGVNISS TRDTIVKATG DAKISG LNI SAQANTGLTL KGTATAELSC SGITTVKGAL VKIN

+
Macromolecule #8: SalCis10

MacromoleculeName: SalCis10 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 9.573319 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPFAARITDL QMCPMSTPGL PPIPHVGGPI IGPGVPTVLI GSLPAAVVGD SCVCVGPPST IVKGSATVLI GGKPAARMGD TTSHGGSIT IGCPTVIIGG

UniProtKB: Uncharacterized conserved protein

+
Macromolecule #9: Baseplate protein J-like domain-containing protein

MacromoleculeName: Baseplate protein J-like domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 150.611344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSRQQRQDE AINSSLFHPH ELSFEQLVGW AHQFAQQLPF RNLQDQADGH WGNLFQKSEI VVCAAISTSD TKHIQRQFKQ ALAHDENVT VEFLLILLKR LQAWYQHLPG APETAYQFKY YLLHEYQRHL SLPLSLVICR LPEQFRHSVQ ELDPLWNLDQ H TLDTASPV ...String:
MTSRQQRQDE AINSSLFHPH ELSFEQLVGW AHQFAQQLPF RNLQDQADGH WGNLFQKSEI VVCAAISTSD TKHIQRQFKQ ALAHDENVT VEFLLILLKR LQAWYQHLPG APETAYQFKY YLLHEYQRHL SLPLSLVICR LPEQFRHSVQ ELDPLWNLDQ H TLDTASPV LQHSSFTEQM RHCFAKIVFV IEQIKKQSQQ VLQAALMHQE NNPQQALYFA FLKLFERAQQ SLNQFTEKHL QF YYRQVLQ QEKQSARENA VYLKLSLNHP TSSSIQFEQG AKFSPGDDPD FKPIAYRSRY PIEVTDAEVS HVFNLTLQRD PLV SPEKES GLVCGVSGQR VQITAGATGD DFPKAQQFNI FNNKYKTEDS TQPMGLIISD PLFSMQQGKR VIEIIVHLKE VRSS IVAQE LLVVDDNNKT SAALTHIFAQ LLSLHVHLFE DWAARITASG LTKQISQEQL SQFRQLRPSQ RVWVAYKLFY LQTLQ YICS TPEKGMQYGL SKIDLLFRIV GQMVSRRCLY TSAWLTKTDI STALSGLKSI LVADPTAYTT IEELLSHSTT AAFYQI FQG GFDIEATTEN GWELIDNVEI YPCPPQECQI GFKVKCHIDT GFAPIIPRLA HLPHSASLKI TLKRQSNCFP YAIFRDF EL SKLAMSTQVC GVTQLQLFNP EGQVDSSQPF FLFGSQPYMD AYVVLANEEI ARKSISQLSL HLDWGNLPRG SDGFKQHY A EYHYPYTNAS FQMRAEVLNN GRWVEFGPTG FSLFTPASGA LRHDSHLHFL NMRNGYTPVT RPWPKTPYSN QSGLRNGLF KLLLTGPEPA FGHKDYAPLL SDTLTYNVTK KHKKTLPNQP YTPLVTHISI DYSAESTIDL LSVDRRSQSE IIHLYPFGEN IIYPPKQTS PVHRPRFFPN YKEDSHCFIG ITARELSGYL NIFFVFDGSA RLVMPYPSTS YRWYYLVDNE WQALNPHQII H DTTLNFLT TGIVTLDLPS EINTDHSVMP SGLFWLRVST NKGIDRYPDC LHVATHVVKV TGKGVPLADD GITPLSFSSW RS TPRKANL AAIAQLNAMI RIPDIESEQH FQMRVSENLR HKGKALTPWD YEHLILENFP EVGSVHCFPT RSYYSLNQEP GRV LIIVTP LNTDCDHSLC SPKQLDSSYL LAIRRFLLSV SRSHVQIEVR NPGYEKIQIR CKVTLKEGVS HGPALRRLEY AIKA QLCPW EADTLNTGPG FCLSLEKLSA FILKQKNVVK VSALSALKIS LDENTEYVLQ DSAATSQPIR AAYPWFLLIP EEHQY IQIS PDNLSHKPVT VGIGELVIGE QFIVSTSPTS PPKGAQNNG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 20065
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 20

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9rce:
Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the baseplate portion in extended state.

+
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