[English] 日本語
Yorodumi
- EMDB-72963: Composite structure of the sheathed flagellar motor in Vibrio cho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72963
TitleComposite structure of the sheathed flagellar motor in Vibrio cholerae adopting a higher FOMC conformation
Map data
Sample
  • Cell: Vibrio cholerae DflhG
    • Protein or peptide: x 13 types
KeywordsMotor protein / Sheathed flagellar motor / Vibrio cholerae
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum stator complex / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum hook / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum ...bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum stator complex / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum hook / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity / plasma membrane / cytosol
Similarity search - Function
Flagellar protein FlgO / FlgO domain / FlgO protein / Flagellar basal-body rod FlgF / Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain ...Flagellar protein FlgO / FlgO domain / FlgO protein / Flagellar basal-body rod FlgF / Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / FlgT, N-terminal domain superfamily / MotY N-terminal domain / MotY N-terminal domain / Flagellar protein FlgP / Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Flagellar basal-body rod FlgG / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / Sel1 repeat / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Sel1-like repeat / Sel1-like repeats. / 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 / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Flagellar hook protein FlgE / Sodium-type flagellar protein MotX / Flagellar protein FlgT / FlgO domain-containing protein / Lipoprotein / Flagellar basal-body rod protein FlgF / Flagellar basal-body rod protein FlgG / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar M-ring protein ...Flagellar hook protein FlgE / Sodium-type flagellar protein MotX / Flagellar protein FlgT / FlgO domain-containing protein / Lipoprotein / Flagellar basal-body rod protein FlgF / Flagellar basal-body rod protein FlgG / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar M-ring protein / Sodium-type flagellar protein MotY / Chemotaxis protein PomB
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGuo WB / Yue J
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01AI189907 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI102584 United States
CitationJournal: To Be Published
Title: Composite structure of the sheathed flagellar motor in Vibrio cholerae adopting a higher FOMC conformation
Authors: Guo WB / Yue J
History
DepositionSep 30, 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

Downloads & links

-
Map

FileDownload / File: emd_72963.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 448 pix.
= 640.64 Å
1.43 Å/pix.
x 448 pix.
= 640.64 Å
1.43 Å/pix.
x 448 pix.
= 640.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.70033586 - 0.765521
Average (Standard dev.)0.0012537425 (±0.038007878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 640.63995 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72963_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: #1

Fileemd_72963_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: #2

Fileemd_72963_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: #3

Fileemd_72963_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: #4

Fileemd_72963_additional_4.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: #5

Fileemd_72963_additional_5.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_72963_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_72963_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : Vibrio cholerae DflhG

EntireName: Vibrio cholerae DflhG
Components
  • Cell: Vibrio cholerae DflhG
    • Protein or peptide: Flagellar basal-body rod protein FlgG
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar hook protein FlgE
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
    • Protein or peptide: Flagellar protein FlgT
    • Protein or peptide: Sodium-type flagellar protein MotY
    • Protein or peptide: Sodium-type flagellar protein MotX
    • Protein or peptide: FlgP
    • Protein or peptide: Chemotaxis protein PomB
    • Protein or peptide: FlgP
    • Protein or peptide: FlgO domain-containing protein
    • Protein or peptide: Flagellar M-ring protein

+
Supramolecule #1: Vibrio cholerae DflhG

SupramoleculeName: Vibrio cholerae DflhG / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

+
Macromolecule #1: Flagellar basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 1 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 28.11435 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: MQPALWVSKT GLDAQQTNIA TISNNLANAS TIGFKKGRAV FEDLFYQNIN QPGAQSSQNT RLPSGLMLGA GSKVVATQKV HTNGNVQTT SNSLDMMIEG DGFFQILMPD GNIAYSRNGQ FTLDDEGAIV TSGAGYRLQP EIIIPEDAIS ITIGNDGEVS V RVRGQQDN ...String:
MQPALWVSKT GLDAQQTNIA TISNNLANAS TIGFKKGRAV FEDLFYQNIN QPGAQSSQNT RLPSGLMLGA GSKVVATQKV HTNGNVQTT SNSLDMMIEG DGFFQILMPD GNIAYSRNGQ FTLDDEGAIV TSGAGYRLQP EIIIPEDAIS ITIGNDGEVS V RVRGQQDN QVLGQITTVD FINPGGLEPV GQNLYLPTGA SGEPQEGVPG LDGLGDIRQS MLETSNVNVT EELVNMIEAQ RV YEMNSKV ISAVDKMMSF VNQQL

UniProtKB: Flagellar basal-body rod protein FlgG

+
Macromolecule #2: Flagellar basal-body rod protein FlgF

MacromoleculeName: Flagellar basal-body rod protein FlgF / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 26.77827 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: MDRALFLAMS GAKQNMQAMQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG LPSRVFSMTE RPGHNFAQGS VITTGRDLDI TIQGDGWIS VLDKTGKEGL TRNGNLRIDE TGLLLNGNGH PVLGETGAPI TLPVPLNKVE IGGDGTISVR PQGAPADAME V VDRIKLVR ...String:
MDRALFLAMS GAKQNMQAMQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG LPSRVFSMTE RPGHNFAQGS VITTGRDLDI TIQGDGWIS VLDKTGKEGL TRNGNLRIDE TGLLLNGNGH PVLGETGAPI TLPVPLNKVE IGGDGTISVR PQGAPADAME V VDRIKLVR LNDQSLFKDV NGLFRATDPN TQFEADASVK ILTGALEGSN VNAIGEMTSL IDLQRQFEMQ VKMMSTAEEM DK ASDSLLR SS

UniProtKB: Flagellar basal-body rod protein FlgF

+
Macromolecule #3: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 3 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 46.880289 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: MSYVSLSGLS AAQMDLNTTS NNIANANTFG FKESRAEFGD VYSTSLFTNA KTTPGQGVQA AKVAQQFHEG SSIYTNNPLD LRIAGTGFF AVAKDRLVPQ QNELTRNGAF HLDKNSFMVT ANDEFLLGYE VNPDTGDVLS YEPKPINIPP QFGKPKQTAN I DLGANLPA ...String:
MSYVSLSGLS AAQMDLNTTS NNIANANTFG FKESRAEFGD VYSTSLFTNA KTTPGQGVQA AKVAQQFHEG SSIYTNNPLD LRIAGTGFF AVAKDRLVPQ QNELTRNGAF HLDKNSFMVT ANDEFLLGYE VNPDTGDVLS YEPKPINIPP QFGKPKQTAN I DLGANLPA NGDLKDPALF DITDPETYNR TTSSTIYDSM GQPYKLTTYY LKDMNQANTW QTYYTVTDKT GEKPINVVGG DA ASPTGHV GHTMRFNNDG TLSSLNNGQP IVTEPLGGGA NPVDLNGADV NQTLSFSLDS ATQFAAPFEL TKFDQDGATT GFL TKIDFD ENGSVLATYS NGINTTLGRV ALVRVANEQG LDKKGGTQWD ATQFSGAKIW GESNKGSFGS ISNGSLEQSN IDMT QELVD LISAQRNFQA NSRALEVHNG LQQNILQIR

UniProtKB: Flagellar hook protein FlgE

+
Macromolecule #4: Flagellar L-ring protein

MacromoleculeName: Flagellar L-ring protein / type: protein_or_peptide / ID: 4 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 24.25652 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: TTTVDAVEGD KSESNSGLTD ALRNRTDPVA GDPAWAPIHP KGKPEHYAAE TGSLFNLASS SSMYDDSKPR GVGDIITVTL NESTKAAKS ADADLNKKND ASMDPLAVGG KDLTIGDYNF SYALKNDNKF SGSAAANQSN SMSGSITVEV IEVLANGNLV I RGEKWLTL ...String:
TTTVDAVEGD KSESNSGLTD ALRNRTDPVA GDPAWAPIHP KGKPEHYAAE TGSLFNLASS SSMYDDSKPR GVGDIITVTL NESTKAAKS ADADLNKKND ASMDPLAVGG KDLTIGDYNF SYALKNDNKF SGSAAANQSN SMSGSITVEV IEVLANGNLV I RGEKWLTL NTGDEYIRLS GTIRPDDIDF DNTIASNRIS NARIQYSGTG TNQDMQEPGF LARFFNVSL

UniProtKB: Flagellar L-ring protein

+
Macromolecule #5: Flagellar P-ring protein

MacromoleculeName: Flagellar P-ring protein / type: protein_or_peptide / ID: 5 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 35.702562 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: ARIKDVAQVA GVRNNQLVGY GLVTGLPGTG ESTPFTDQSF NAMLQSFGIQ LPPGTKPKTK NVAAVIVTAD LPAFSKQGQT IDITVSSIG SAKSLRGGTL MQTFLKGLDG QVYAVAQGNL VVSGFSATGA DGSKIVGNNP TVGMISSGAI VEREVPNPFG R GDYITFNL ...String:
ARIKDVAQVA GVRNNQLVGY GLVTGLPGTG ESTPFTDQSF NAMLQSFGIQ LPPGTKPKTK NVAAVIVTAD LPAFSKQGQT IDITVSSIG SAKSLRGGTL MQTFLKGLDG QVYAVAQGNL VVSGFSATGA DGSKIVGNNP TVGMISSGAI VEREVPNPFG R GDYITFNL FESDFTTAQR LADAVNQFLG PQMASAVDAA SIKVRAPRDL SQRVAFLSAI ENLEFNPADS AAKIIVNSRT GT IVVGQNV RLKPAAVTHG GMTVAIKENL NVSQPNALGG GQTVVVPNTE IEVTEKQGKM FKLEPGVTLD DLVRAVNEVG AAP SDLMAI LQALKQAGAI EGQLIII

UniProtKB: Flagellar P-ring protein

+
Macromolecule #6: Flagellar protein FlgT

MacromoleculeName: Flagellar protein FlgT / type: protein_or_peptide / ID: 6 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 39.808223 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: YEVTGSAAIV SSEEVARLHA LEDALYKAVN FAGADIGSIS NLMPLLESDR REYLFANHEV RYILIEERKA INNVMYVRTR IDIYPSATA CHVEQYKKTM LIGNIDLASP QQAVMGQIYQ VGDDFAQVIN RRLEQESRSF VSVGTTQYDI DPKAPERIKM I AQDAGAQY ...String:
YEVTGSAAIV SSEEVARLHA LEDALYKAVN FAGADIGSIS NLMPLLESDR REYLFANHEV RYILIEERKA INNVMYVRTR IDIYPSATA CHVEQYKKTM LIGNIDLASP QQAVMGQIYQ VGDDFAQVIN RRLEQESRSF VSVGTTQYDI DPKAPERIKM I AQDAGAQY IMGGMITDLT ATIEQKTLQD DIINRQFAME ISVFDGKTGN EVMTRTYREV ARWPFPKTSQ IDTRSARFWA ST YGEMMLR VSRNIMLDLE SEISCKITLP QIVAKFGTTA TMDLGRIHGV KQGDKLSLWH TGAFIDQQGL PRNKVTQSEI TLT VSRVYE HEAELTVDQP ELAYSIQIGD VMHKQM

UniProtKB: Flagellar protein FlgT

+
Macromolecule #7: Sodium-type flagellar protein MotY

MacromoleculeName: Sodium-type flagellar protein MotY / type: protein_or_peptide / ID: 7 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 31.207955 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: LEVRYMATPQ QSTWQMATNT PLECRLVHPI PNYGDAEFSS RAGKKINLDF ELKMRRPMGD TRNVSLVSMP PVWRPGEGAD RITNLQFFK QFDGYIGGQT AWSLLSELEK GRYPTFSYQD WQSRDQRIEV ALSSVLFQQP YNEFSDCISK LLPYSFEDIS F TILHYDQG ...String:
LEVRYMATPQ QSTWQMATNT PLECRLVHPI PNYGDAEFSS RAGKKINLDF ELKMRRPMGD TRNVSLVSMP PVWRPGEGAD RITNLQFFK QFDGYIGGQT AWSLLSELEK GRYPTFSYQD WQSRDQRIEV ALSSVLFQQP YNEFSDCISK LLPYSFEDIS F TILHYDQG TSVELNKASQ KRLAQIAEYV RYNQDIDLVL VSTYTDSTDT NNNSQNLSEQ RAEVLREYFK SIGLPEDRIQ VQ GYGKRRP IADNASPIGK DKNRRVVISL GRTQ

UniProtKB: Sodium-type flagellar protein MotY

+
Macromolecule #8: Sodium-type flagellar protein MotX

MacromoleculeName: Sodium-type flagellar protein MotX / type: protein_or_peptide / ID: 8 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 21.244137 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString:
PVPIYSEAEL IKLIEENKHL ERVKADNCQI VEDIVARATR ISLPSYEFLY GDMLAWGVCV DQDVELGLYY MENAAHQGLP AALEQLGRY YSRGTLVQQD KERAIPYLRE AAAMGNLNAR IQLAELLLRD YGSPLDYEDA YRWLYNSVTA DQRTHNRIAL L RQGLERRM PENIIARAKR RETFW

UniProtKB: Sodium-type flagellar protein MotX

+
Macromolecule #9: FlgP

MacromoleculeName: FlgP / type: protein_or_peptide / ID: 9 / Number of copies: 52 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 1.506766 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString:
QQVPEKRQMT LF

UniProtKB: Lipoprotein

+
Macromolecule #10: Chemotaxis protein PomB

MacromoleculeName: Chemotaxis protein PomB / type: protein_or_peptide / ID: 10 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 17.542775 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString:
QQQAQAMSEQ METVAESIKK ALSREIEQGA IEVENLGQQI DIRIREKGAF PEGSAFLQPK FRPLVRQIAE LVKDIPGKVR VTGHTDNQK LDSELYRSNW DLSAQRAVSV AQEMEKVKDF DHLRLQVRGL ADTQPLGPND TEAQRATNRR VEISIL

UniProtKB: Chemotaxis protein PomB

+
Macromolecule #11: FlgP

MacromoleculeName: FlgP / type: protein_or_peptide / ID: 11 / Number of copies: 58 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 11.848299 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString:
PDDWLTAVGY ANISEQRGRD EAEKQVRAMR ASKIDAYREL AEQVYGMRIS GRAELQDQRL GTELTAGADG VIRGAEVVRS YKVGDSYVT ELRLDIRKMD KMRDY

UniProtKB: Lipoprotein

+
Macromolecule #12: FlgO domain-containing protein

MacromoleculeName: FlgO domain-containing protein / type: protein_or_peptide / ID: 12 / Number of copies: 58 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 21.395104 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString:
IYNGKEPYNG SQFMLMESPR HTLDFFVESM TEDLMLSNTS ITARTPIAVT SFVDLQNMDT TNWLGNSVSE GFIHQFQRRG FKVVDFKTT GSIQVTQQGD FAFSRDWKNL SSEQEVQYVL TGTMLRQEGG VIVNARVVGM HSRIVVATAQ GFLPADRIGR D LDTLNSIR TQDGVLIRSD PTITQPYTVI LR

UniProtKB: FlgO domain-containing protein

+
Macromolecule #13: Flagellar M-ring protein

MacromoleculeName: Flagellar M-ring protein / type: protein_or_peptide / ID: 13 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 21.495785 KDa
Recombinant expressionOrganism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
SequenceString: VSAARRKEQE LEKQQEEALR GKIDSVLIPI LGLGNYTAQV DIELDFSAVE QTRKVFDPNT PATRSEYTLE DYNNGNVVAG VPGALSNQP PADASIPQDV AQMKDGSVMG QGSVHKEATR NYELDTTISH ERKQSGVINR QTVAVAVKSR SSVNPDTGEV T YTPLSEAD ...String:
VSAARRKEQE LEKQQEEALR GKIDSVLIPI LGLGNYTAQV DIELDFSAVE QTRKVFDPNT PATRSEYTLE DYNNGNVVAG VPGALSNQP PADASIPQDV AQMKDGSVMG QGSVHKEATR NYELDTTISH ERKQSGVINR QTVAVAVKSR SSVNPDTGEV T YTPLSEAD LNSIRQVLIG TVGYSENRGD LLNVLSMPFA

UniProtKB: Flagellar M-ring protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C26 (26 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5068
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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