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- EMDB-39780: Cryo-EM structure of the proximal rod-export apparatus of the pol... -

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Basic information

Entry
Database: EMDB / ID: EMD-39780
TitleCryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor
Map dataMain map
Sample
  • Complex: The polar flagellar motor-hook complex
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
KeywordsPolar flagellum / Polar flagellar motor / Proximal rod / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum assembly / protein secretion / bacterial-type flagellum-dependent cell motility / protein targeting ...bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum assembly / protein secretion / bacterial-type flagellum-dependent cell motility / protein targeting / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar basal-body rod FlgF / Flagellar biosynthetic protein FlhB / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Flagellar hook-basal body complex protein FliE / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar biosynthesis protein FliQ ...Flagellar basal-body rod FlgF / Flagellar biosynthetic protein FlhB / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Flagellar hook-basal body complex protein FliE / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Bacterial export protein family 3 / Bacterial export proteins, family 3 / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar basal body rod protein FlgB / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgF / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FlhB / Flagellar biosynthetic protein FliR / Flagellar biosynthetic protein FliP / Flagellar M-ring protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZhang L / Tan JX / Zhou Y / Zhu YQ
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)U23A20163 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: Protein Cell / Year: 2026
Title: Molecular basis of high-torque transmission of the Vibrio polar flagellar motor.
Authors: Ling Zhang / Jiaxing Tan / Xuemin Duan / Xiaofei Wang / Ting Wang / Keke Yuan / Michio Homma / Seiji Kojima / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission ...The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission of varying torques to flagellar filaments to grant bacteria diverse swimming capabilities. Compared to peritrichous flagellar motors, polar flagellar motors are faster machines that transmit higher torque to drive high-speed motility in liquids and empower swimming in viscous environments. However, structural basis of high-torque transmission of the polar flagellar motors is still unclear. Here we present a cryo-electron microscopy structure of the polar flagellar motor in complex with the hook from Vibrio alginolyticus, comprising 295 subunits from 18 proteins. Compared to the peritrichous flagellar rod, this structure reveals an increased number of inter-subunit interactions in the rod of the polar flagellar motor. Nine phospholipid molecules insert into the interface between the export apparatus and the proximal rod. The LP ring contains more electrostatic charges on the inner surface and has fewer physical contacts with the rod, while the HT ring tightly binds to the outer surface of the LP ring. FlrP, a protein of previously unknown function, is identified as a new component of the polar flagellar motor, and extensively participates in the interactions of 15 FliF peptides of the MS ring with the rod. In contrast to that in the peritrichous flagellum, the hook in the polar flagellum has two different conformational states, L- and R-types. These findings provide unprecedented insights into structural adaptations of the bacterial polar flagellar motors for high-torque transmission.
History
DepositionApr 18, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39780.png

Downloads & links

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Map

FileDownload / File: emd_39780.map.gz / Format: CCP4 / Size: 909.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 620 pix.
= 744. Å		1.2 Å/pix.
x 620 pix.
= 744. Å		1.2 Å/pix.
x 620 pix.
= 744. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.42
Minimum - Maximum-2.095469 - 2.8748376
Average (Standard dev.)-0.0010787722 (±0.10338749)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions620620620
Spacing620620620
CellA=B=C: 744.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_39780_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_39780_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The polar flagellar motor-hook complex

EntireName: The polar flagellar motor-hook complex
Components
  • Complex: The polar flagellar motor-hook complex
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar biosynthetic protein FlhB
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar basal-body rod protein FlgC
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate

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Supramolecule #1: The polar flagellar motor-hook complex

SupramoleculeName: The polar flagellar motor-hook complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148

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Macromolecule #1: Flagellar biosynthetic protein FliP

MacromoleculeName: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 31.314904 KDa
SequenceString: MTKGNPIRLL LSTLLLFVGV LFSSFSFAEA EESALPDNLA DGSSVTVQAM QSDTGASRAM SVSSGGGIPA FTMTTNPDGS EDYSVTLQI LALMTMLGFL PAMVILMTSF TRIVVVMSIL RQAMGLQQTP SNQVIIGIAL FLTFFVMSPV LNEINDKAVQ P YLNEQVTA ...String:
MTKGNPIRLL LSTLLLFVGV LFSSFSFAEA EESALPDNLA DGSSVTVQAM QSDTGASRAM SVSSGGGIPA FTMTTNPDGS EDYSVTLQI LALMTMLGFL PAMVILMTSF TRIVVVMSIL RQAMGLQQTP SNQVIIGIAL FLTFFVMSPV LNEINDKAVQ P YLNEQVTA REAFDAAQAP MKAFMLKQTR IKDLETFVTM SGEQVDNPED VSMAVLIPAF ITSELKTAFQ IGFMLFLPFL II DLVVASV LMAMGMMMLS PMIVSLPFKL MLFVLVDGWN LILSTLAGSF AL

UniProtKB: Flagellar biosynthetic protein FliP

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Macromolecule #2: Flagellar biosynthetic protein FliQ

MacromoleculeName: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 10.329615 KDa
SequenceString:
MTPEMFVELF REALWMVLIM VCAIIIPSLL IGLIVAIFQA ATSINEQTLS FLPRLIVTLL ALMLFGHWMT QMLMEYFYGL IERLPQVLY

UniProtKB: Flagellar biosynthetic protein FliQ

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Macromolecule #3: Flagellar basal-body rod protein FlgF

MacromoleculeName: Flagellar basal-body rod protein FlgF / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 26.987387 KDa
SequenceString: MDRALFLAMS GAKQNMQALQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG HPSRVFSMTE RPGHNFAQGS VITTGRDLDV TIEGSGWIS VLDHTGKEGL TRNGNLKVDQ NGMLTNASGH LVLGENDAPI TLPIPLSKIE IGRDGTISVL PQGAPAEEFQ A VDRIKLVK ...String:
MDRALFLAMS GAKQNMQALQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG HPSRVFSMTE RPGHNFAQGS VITTGRDLDV TIEGSGWIS VLDHTGKEGL TRNGNLKVDQ NGMLTNASGH LVLGENDAPI TLPIPLSKIE IGRDGTISVL PQGAPAEEFQ A VDRIKLVK PNDQSLFKDT NGLFRHKTPN QPYEADATVS LQTGAIEGSN VNAVGEMTAL IDLQRQFEMQ VKMMSTAEEM DK SSDSLLR MS

UniProtKB: Flagellar basal-body rod protein FlgF

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Macromolecule #4: Flagellar hook-basal body complex protein FliE

MacromoleculeName: Flagellar hook-basal body complex protein FliE / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Molecular weightTheoretical: 11.135679 KDa
SequenceString:
MKVDGIQAEM RAMMVEATNT APTASGAKVG ADFNDLLTKA INNVNTLQKA SGDLQTRFDR GDADVSLSDV MIARNKSSVA FDATVQIRN KLVEAYKDLM NMPV

UniProtKB: Flagellar hook-basal body complex protein FliE

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Macromolecule #5: Flagellar biosynthetic protein FlhB

MacromoleculeName: Flagellar biosynthetic protein FlhB / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 42.197297 KDa
SequenceString: MAESDGQERT EEATPRRLQQ AREKGQVARS KELASASVLI VGAISLMWFG EALARSLFSI MSRLFDLQRE EIFDTAKLFD IALGAMTDL LFPLFLVLAT LFTAAMIGAA GVGGISFSAQ AAMPKLSKMN PLSGLKRMVG MQSWVELIKS ILKVVLVTGV A IYLIQASQ ...String:
MAESDGQERT EEATPRRLQQ AREKGQVARS KELASASVLI VGAISLMWFG EALARSLFSI MSRLFDLQRE EIFDTAKLFD IALGAMTDL LFPLFLVLAT LFTAAMIGAA GVGGISFSAQ AAMPKLSKMN PLSGLKRMVG MQSWVELIKS ILKVVLVTGV A IYLIQASQ ADLIQLSMDV YPQNIFHALD ILLNFILLIS CSLLIVVAID IPFQIWQHAD QLKMTKQEVK DEYKETEGKP EV KGRIRML QREAAQRRMM ADVPQADVIV TNPEHFSVAL RYKQKTDRAP VVIAKGTDHM AMKIREVARE HDITIVPAPP LAR ALYHTT ELEQEIPDGL FTAVAQVLAF VFQLKQYRKR GGQRPKIQDY DLPIPPEHRH

UniProtKB: Flagellar biosynthetic protein FlhB

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Macromolecule #6: Flagellar biosynthetic protein FliR

MacromoleculeName: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 28.905535 KDa
SequenceString: MEYPTSVVLD WIANYFWPYV RISSMLMVMT VTGARFVSPR IRLYLGLAIT FAVMPAIPAV PQDIELLSFR GFMTIAEQMI IGIAMGMVT QFMIQTFVLL GQILGMQSSL GFASMVDPAN GQNTPLLGQL FMFLTTMFFL ATDGHLKMLQ LVVFSFKTLP I GSGSLNAV ...String:
MEYPTSVVLD WIANYFWPYV RISSMLMVMT VTGARFVSPR IRLYLGLAIT FAVMPAIPAV PQDIELLSFR GFMTIAEQMI IGIAMGMVT QFMIQTFVLL GQILGMQSSL GFASMVDPAN GQNTPLLGQL FMFLTTMFFL ATDGHLKMLQ LVVFSFKTLP I GSGSLNAV DFREMAGWLG IMFQTALSMS LSGIIALLTI NLSFGVMTRA APQLNIFSLG FAFALMVGLL LCWYILAGLY SH YEMFWTV GEAQICRLIR LEC

UniProtKB: Flagellar biosynthetic protein FliR

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Macromolecule #7: Flagellar M-ring protein

MacromoleculeName: Flagellar M-ring protein / type: protein_or_peptide / ID: 7 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 63.915605 KDa
SequenceString: MADKSTDLTV TEGGSDGALV ASSDVDVESQ NPDLEERSAS KFDMAVGDLD LLRQVVLVLS ISICVALIVM LFFWVKEPEM RPLGAYETE ELIPVLDYLD QQKINYKLDG NTISVESSEY NSIKLGMVRS GVNQATEAGD DILLQDMGFG VSQRLEQERL K LSRERQLA ...String:
MADKSTDLTV TEGGSDGALV ASSDVDVESQ NPDLEERSAS KFDMAVGDLD LLRQVVLVLS ISICVALIVM LFFWVKEPEM RPLGAYETE ELIPVLDYLD QQKINYKLDG NTISVESSEY NSIKLGMVRS GVNQATEAGD DILLQDMGFG VSQRLEQERL K LSRERQLA QAIEEMKQVR KARVLLALPK HSVFVRHNQE ASASVFLTLS TGTNLKQQEV DSIVDMVASA VPGMKTSRIT VT DQHGRLL SSGSQDPASA ARRKEQELER SQEQALREKI DSVLLPILGY GNYTAQVDIQ MDFSAVEQTR KRFDPNTPAT RSE YALEDY NNGNMVAGIP GALSNQPPAD ASIPQDVAQM KDGSVMGQGS VRKESTRNFE LDTTISHERK QTGTVARQTV SVAI KDRRQ VNPDTGEVTY TPMSESEINA IRQVLIGTVG FDQGRGDLLN VLSVKFAEPE AEQLEEPPIW EHPNFSDWVR WFASA LVII VVVLVLVRPA MKKLLNPTSD DEDEMYGPDG LPIGADGETS LIGSDIESSE LFEFGSSIDL PNLHKDEDVL KAVRAL VAN EPELAAQVVK NWMNDNG

UniProtKB: Flagellar M-ring protein

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Macromolecule #8: Flagellar basal body rod protein FlgB

MacromoleculeName: Flagellar basal body rod protein FlgB / type: protein_or_peptide / ID: 8 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 14.23995 KDa
SequenceString:
MAISFDNALG IHQHTVGVRE RNAEVISTNI AQANTPGYKA RGLDFAKELQ AATSGASIGL SRTDGRHIPA TTTLVGDKLY RLPTQPDTG DGNTVDLDLE RNLFMQNQIR HQASLDFLGS KFKNLTKAIK GE

UniProtKB: Flagellar basal body rod protein FlgB

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Macromolecule #9: Flagellar basal-body rod protein FlgC

MacromoleculeName: Flagellar basal-body rod protein FlgC / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 14.812569 KDa
SequenceString:
MSLFNVFNVT GSAMSAESVR LNTTSSNLAN ADSVSSSAKD TYKARHAVFG AELSNAMRGG DTVPVKVMGI VESDKPLSAE YNPDHPLAN EEGYIYKPNV NVMEEMANMI SASRAYQTNV QVADSSKQML LRTLQMGQ

UniProtKB: Flagellar basal-body rod protein FlgC

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Macromolecule #10: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 10 / Number of copies: 4 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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Macromolecule #11: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~...

MacromoleculeName: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate
type: ligand / ID: 11 / Number of copies: 5 / Formula: XKP
Molecular weightTheoretical: 495.587 Da
Chemical component information

ChemComp-XKP:
(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate

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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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 329955
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 58418
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8z5s:
Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor

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