[English] 日本語
Yorodumi
- EMDB-71970: Cryo-EM structure of BAM from P. aeruginosa PAO1 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71970
TitleCryo-EM structure of BAM from P. aeruginosa PAO1 in complex with Pyocin L1
Map dataConsensus sharp map of BAM from P. aeruginosa with Pyocin L1
Sample
  • Complex: PAO1-BAM-PyocinL1
    • Complex: BamA
      • Protein or peptide: Outer membrane protein assembly factor BamA
    • Complex: BamB
      • Protein or peptide: Outer membrane protein assembly factor BamB
    • Complex: BamC
      • Protein or peptide: Outer membrane protein assembly factor BamC
    • Complex: BamD
      • Protein or peptide: Outer membrane protein assembly factor BamD
    • Complex: BamE
      • Protein or peptide: Outer membrane protein assembly factor BamE
    • Complex: Pyocin L1
      • Protein or peptide: Pyocin L1
Keywordsprotein complex / outer membrane / beta-barrel / protein folding / Gram-negative bacterial protein / L-type bacteriocin / pyocin / MEMBRANE PROTEIN
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity
Similarity search - Function
Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA ...Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamB / BamE-like / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamC / Bacteriocin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsMunder F / Venugopal H / Grinter R
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102150 Australia
CitationJournal: To Be Published
Title: A potent protein antibiotic kills Pseudomonas aeruginosa by inhibiting the BAM complex
Authors: Munder F / Johnson M / Samuels I / McCaughey L / Zdorevskyi O / Wang C / Kropp A / Price EP / Sarovich DS / Varshney S / Venugopal H / Sharma V / Doyle M / Short F / Ghosal D / Connolly J / Knott G / Grinter R
History
DepositionAug 5, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71970.png

Downloads & links

-
Map

FileDownload / File: emd_71970.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus sharp map of BAM from P. aeruginosa with Pyocin L1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 320 pix.
= 240. Å		0.75 Å/pix.
x 320 pix.
= 240. Å		0.75 Å/pix.
x 320 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.88768595 - 1.2469304
Average (Standard dev.)-0.000043613672 (±0.02850653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 240.0 Å
α=β=γ: 90.0 °

-
Supplemental data

+
Mask #1

Fileemd_71970_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Mask #2

Fileemd_71970_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Mask #3

Fileemd_71970_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Consensus map of BAM from P. aeruginosa with Pyocin L1

Fileemd_71970_additional_1.map
AnnotationConsensus map of BAM from P. aeruginosa with Pyocin L1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Local refined map of BamA from P. aeruginosa with Pyocin L1

Fileemd_71970_additional_2.map
AnnotationLocal refined map of BamA from P. aeruginosa with Pyocin L1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Local refined sharp map of BamA from P. aeruginosa with Pyocin L1

Fileemd_71970_additional_3.map
AnnotationLocal refined sharp map of BamA from P. aeruginosa with Pyocin L1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Local refined map of BamDE (BamC) from P. aeruginosa with Pyocin L1

Fileemd_71970_additional_4.map
AnnotationLocal refined map of BamDE (BamC) from P. aeruginosa with Pyocin L1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Local refined sharp map of BamDE (BamC) from...

Fileemd_71970_additional_5.map
AnnotationLocal refined sharp map of BamDE (BamC) from P. aeruginosa with Pyocin L1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Local refined map of BamB from P. aeruginosa with Pyocin L1

Fileemd_71970_additional_6.map
AnnotationLocal refined map of BamB from P. aeruginosa with Pyocin L1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Local refined sharp map of BamB from P. aeruginosa with Pyocin L1

Fileemd_71970_additional_7.map
AnnotationLocal refined sharp map of BamB from P. aeruginosa with Pyocin L1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: #2

Fileemd_71970_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: #1

Fileemd_71970_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : PAO1-BAM-PyocinL1

EntireName: PAO1-BAM-PyocinL1
Components
  • Complex: PAO1-BAM-PyocinL1
    • Complex: BamA
      • Protein or peptide: Outer membrane protein assembly factor BamA
    • Complex: BamB
      • Protein or peptide: Outer membrane protein assembly factor BamB
    • Complex: BamC
      • Protein or peptide: Outer membrane protein assembly factor BamC
    • Complex: BamD
      • Protein or peptide: Outer membrane protein assembly factor BamD
    • Complex: BamE
      • Protein or peptide: Outer membrane protein assembly factor BamE
    • Complex: Pyocin L1
      • Protein or peptide: Pyocin L1

+
Supramolecule #1: PAO1-BAM-PyocinL1

SupramoleculeName: PAO1-BAM-PyocinL1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: BAM from P. aeruginosa PAO1 in complex with Pyocin L1, Pre-inhibition complex
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 31 KDa

+
Supramolecule #2: BamA

SupramoleculeName: BamA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

+
Supramolecule #3: BamB

SupramoleculeName: BamB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

+
Supramolecule #4: BamC

SupramoleculeName: BamC / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

+
Supramolecule #5: BamD

SupramoleculeName: BamD / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

+
Supramolecule #6: BamE

SupramoleculeName: BamE / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

+
Supramolecule #7: Pyocin L1

SupramoleculeName: Pyocin L1 / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: C1433

+
Macromolecule #1: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 38.660914 KDa
SequenceString: MQVKHLLLIA ILALTAACSS NKETVDENLS ESQLYQQAQD DLNNKSYNSA VTKLKALESR YPFGRYAEQA QLELIYANYK NMEPEAARA AAERFIRLHP QHPNVDYAYY LKGLSSFDQD RGLLARFLPL DMTKRDPGAA RDSFNEFAQL TSRFPNSRYA P DAKARMVY ...String:
MQVKHLLLIA ILALTAACSS NKETVDENLS ESQLYQQAQD DLNNKSYNSA VTKLKALESR YPFGRYAEQA QLELIYANYK NMEPEAARA AAERFIRLHP QHPNVDYAYY LKGLSSFDQD RGLLARFLPL DMTKRDPGAA RDSFNEFAQL TSRFPNSRYA P DAKARMVY LRNLLAAYEV HVGHYYLKRQ AYVAAANRGR YVVENFQETP AVGDGLAIMV EAYRRLGLDD LASTSLETLK LN YPDNASL KDGEFVARES EADTRSWLAK ATLGLIEGGE PPPHMETQAA KDVIKQYEDA EREIPAELKP ENQDHSADDE KPE SDDDED SGRSWWSYMT FGLFD

UniProtKB: Outer membrane protein assembly factor BamD

+
Macromolecule #2: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 43.100664 KDa
SequenceString: MKRLAGLTAL ALVIGNTSGC GWLWGPEGYF RDRGDDYLGA RETPPMQLPE GVHSKPLDPL LPIPLNVATT HEKEGEYEVP RPQPLANAG DISDYSLQRS GDSRWVVAQR PPAEVWPVAR QFFEENGFRI ADERPQTGEF SSDWQSLSQL SAPLARRLSS R VSGVEPDG ...String:
MKRLAGLTAL ALVIGNTSGC GWLWGPEGYF RDRGDDYLGA RETPPMQLPE GVHSKPLDPL LPIPLNVATT HEKEGEYEVP RPQPLANAG DISDYSLQRS GDSRWVVAQR PPAEVWPVAR QFFEENGFRI ADERPQTGEF SSDWQSLSQL SAPLARRLSS R VSGVEPDG QARVRVRIEP GVQSNTSEVY VLSQTRAAGD TSSPSWPSKS VAPSLDAALL DEMVASMARS AEQGGSVSLL AA NSIYDTP GTFELSKDGS GNPVLTLQSD FDRSWVSVGR ALDNADIRVD DLNRSLGVYY VNIAEGAKKP DEDKPGFFSR LFG GGEKTK EEEDAKAQRY QVRLTTVSDA VQVTVDKDIN TSAPADVAQN VLEKLQESMR NAVRGSGQRK PGQFGLGEQF

UniProtKB: Outer membrane protein assembly factor BamC

+
Macromolecule #3: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 40.436656 KDa
SequenceString: MVQWKHAALL ALALAVVGCS SNSKKELPPA ELTDFKEEVV LSKQWSRSVG DGQGDLYNLL EPAVDGSTIY AASAEGRVMA IQRETGDVL WKKDLERPVS GGVGVGYGLV LVGTLRGDVI ALDEATGKKK WTKRVNSEVL SAPATNGDVV VVQTQDDKLI G LDAASGDQ ...String:
MVQWKHAALL ALALAVVGCS SNSKKELPPA ELTDFKEEVV LSKQWSRSVG DGQGDLYNLL EPAVDGSTIY AASAEGRVMA IQRETGDVL WKKDLERPVS GGVGVGYGLV LVGTLRGDVI ALDEATGKKK WTKRVNSEVL SAPATNGDVV VVQTQDDKLI G LDAASGDQ RWIYESTVPV LTLRGTGAPL IAGNMALAGL ASGKVVAVDV QRGLPIWEQR VAIPQGRSEL DRVVDIDGGL LL SGDTLYV VSYQGRAAAL DVNSGRLLWQ REASSYVGVA EGFGNIYVSQ ASGSVEGLDS RGASSLWNND ALARRQLSAP AVF SSNVVV GDLEGYVHLL SQVDGRFVGR ERVDSDGVRV RPLVVGSWMY VFGNGGKLVA YTIR

UniProtKB: Outer membrane protein assembly factor BamB

+
Macromolecule #4: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 92.258469 KDa
SequenceString: MKRFLLPALL SALMIAEVHA ESAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGSF TVSDIRVNGL QRVSAGSVFA ALPLNVGET IDDQALVQAT RSLFKTGFFQ DIQLGRDGNV LVVTVVERPS ISSIEIEGNK AISKEDLLKG LKQSGLAEGE I FQRATLEG ...String:
MKRFLLPALL SALMIAEVHA ESAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGSF TVSDIRVNGL QRVSAGSVFA ALPLNVGET IDDQALVQAT RSLFKTGFFQ DIQLGRDGNV LVVTVVERPS ISSIEIEGNK AISKEDLLKG LKQSGLAEGE I FQRATLEG VRNELQRQYV AQGRYSAEIN AEVIPQPRNR VALKININEG TVAAISHINV VGNTVFSEED LTDLFELKTT NW LSFFKND DKYAREKLSG DLERLRSYYL DRGYINMDIA STQVSITPDK KHVYITVNIN EGEKYTIRDV KLTGDLKVPE EEV KRLLLV QKGQVFSRKV MTTTSDLITR RLGNEGYTFA NVNGVPEAHD DDKTVSVTFV VDPGKRAYVN RINFRGNTKT EDEV LRREM RQMEGGWAST YLIDQSKARL ERLGYFKEVN VETPAVPGTD DQVDVNYSVE EQPSGSITAS VGFAQSAGLI LGGSI SQNN FLGTGNKVSI GLTRSEYQTR YNFGFVDPYW TVDGVSLGYN AFYRKTDYDE LDVDVASYSV NSLGAGMSIG YPISET SRL TYGLSVQRDQ IDTGRYTVDE IYDFLDKEGD NFTNFKASIG WSESTLNKGV LATRGHSQSL TLETTLPGSD LSFYKID YR GQVFAPLTDN YTMRFHTELG YGDGYGSTER LPFYENYYAG GFNSVRGFKD STLGPRSTPS VARNPDGTPM KNQGPDSK G RYTDPDQDPE AFGGNILITG GAELLFPLPF VKDQRQLRTV LFWDVGSTFD TDCPTKTTTN CDGIKTDNLA SSVGVGLTW ITALGPLSFS LATPIKKPDN AETQVFQFSL GQTF

UniProtKB: Outer membrane protein assembly factor BamA

+
Macromolecule #5: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 19.411865 KDa
SequenceString:
MQNAKLMLTC LAFAGLAALA GCSFPGVYKI DIQQGNVVTQ DMIDQLRPGM TRRQVRFIMG NPLIVDTFHA NRWDYLYSIQ PGGGRRQQE RVSLFFNDSD QLAGLNGDFM PGVSRDEAIL GKEGSTTVTQ PADQQKPEAQ KEEPPKPGST LEQLQREVDE A QPVPVPTP EPLDPSPQ

UniProtKB: Outer membrane protein assembly factor BamE

+
Macromolecule #6: Pyocin L1

MacromoleculeName: Pyocin L1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: C1433
Molecular weightTheoretical: 30.609574 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASSLAPRQV IRDGQFITSP NGKYKLVMQA DGNLVLYEDG TKPIWNTTPV GPGAKAVMEF NLNLYNKAG QVAWSSNVYT AYLFEEFKDE AYLNLQDDGD FGIFSDEAKW GSIVLSRPEV GVKNKIIPTG TVMVPGTEYI N GNYRLAFQ ...String:
MGSSHHHHHH SSGLVPRGSH MASSLAPRQV IRDGQFITSP NGKYKLVMQA DGNLVLYEDG TKPIWNTTPV GPGAKAVMEF NLNLYNKAG QVAWSSNVYT AYLFEEFKDE AYLNLQDDGD FGIFSDEAKW GSIVLSRPEV GVKNKIIPTG TVMVPGTEYI N GNYRLAFQ GDGNLVIYQI NPQVVIWATY TMGADRAVVQ EDGNFVIYKG TTALWHTHTA TGMPAYLKFT NTGKLFLSQP TL LWTLKRG SLSKPPKVIP GQHGPLDTTP IWSWPHDYP

UniProtKB: Bacteriocin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris-HCl
150.0 mMSodium chlorideNaCl

Details: LMNG detergent was removed by dilution in detergent-free buffer and concentration in 100kD cut-off concentrator
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 11513 / Average exposure time: 5.22 sec. / Average electron dose: 60.0 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: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3141875 / Details: Particles picked with TOPAZ trained picking model
CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 110600
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: AlphaFold, initial_model_type: in silico modelBamA-E
chain_id: F, source_name: PDB, initial_model_type: experimental model

4led

Output model

PDB-9pxi:
Cryo-EM structure of BAM from P. aeruginosa PAO1 in complex with Pyocin L1

+
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