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- EMDB-15090: Sodium pumping NADH-quinone oxidoreductase with substrate Q2 -

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Basic information

Entry
Database: EMDB / ID: EMD-15090
TitleSodium pumping NADH-quinone oxidoreductase with substrate Q2
Map dataNQR with substrate Q2
Sample
  • Complex: NQR complex with substrate Q2
    • Protein or peptide: x 6 types
  • Ligand: x 9 types
Keywordsquinone / MEMBRANE PROTEIN
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / Gram-negative-bacterium-type cell wall / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / respiratory electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / FMN binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) ...Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit D / NqrDE/RnfAE / Ion-translocating oxidoreductase NqrB/RnfD / Na(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Rnf-Nqr subunit, membrane protein / NQR2, RnfD, RnfE family / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) / NQRA C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit F / FMN-binding / FMN-binding domain / FMN_bind / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
Na(+)-translocating NADH-quinone reductase subunit E / Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NADH-quinone reductase subunit D / Na(+)-translocating NADH-quinone reductase subunit B / Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-translocating NADH-quinone reductase subunit A
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsHau J-L / Kaltwasser S / Vonck J / Fritz G / Steuber J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1488/8-2 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Conformational coupling of redox-driven Na-translocation in Vibrio cholerae NADH:quinone oxidoreductase.
Authors: Jann-Louis Hau / Susann Kaltwasser / Valentin Muras / Marco S Casutt / Georg Vohl / Björn Claußen / Wojtek Steffen / Alexander Leitner / Eckhard Bill / George E Cutsail / Serena DeBeer / ...Authors: Jann-Louis Hau / Susann Kaltwasser / Valentin Muras / Marco S Casutt / Georg Vohl / Björn Claußen / Wojtek Steffen / Alexander Leitner / Eckhard Bill / George E Cutsail / Serena DeBeer / Janet Vonck / Julia Steuber / Günter Fritz /
Abstract: In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH: ...In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na-NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na-NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na-NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na-NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na from a binding site localized in subunit NqrB.
History
DepositionJun 2, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15090.png

Downloads & links

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Map

FileDownload / File: emd_15090.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNQR with substrate Q2
Voxel sizeX=Y=Z: 0.9125 Å
Density
Contour LevelBy AUTHOR: 0.0133
Minimum - Maximum-0.025538774 - 0.05924016
Average (Standard dev.)0.0000891336 (±0.0022237466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 292.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15090_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15090_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15090_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NQR complex with substrate Q2

EntireName: NQR complex with substrate Q2
Components
  • Complex: NQR complex with substrate Q2
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit A
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit B
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit C
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit D
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit E
    • Protein or peptide: Na(+)-translocating NADH-quinone reductase subunit F
  • Ligand: RIBOFLAVIN
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: UBIQUINONE-2Coenzyme Q10
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: SODIUM IONSodium
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: water

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Supramolecule #1: NQR complex with substrate Q2

SupramoleculeName: NQR complex with substrate Q2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Na(+)-translocating NADH-quinone reductase subunit A

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit A / type: protein_or_peptide / ID: 1
Details: Subunit NqrA has at the N-terminus the residual residues Gly, Pro, His after cleavage of the N-terminal His-tag. These residues are listed with numbering 0 His, -1 Pro, -2 Gly.
Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 51.125391 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MGSSHHHHHH SSGLEVLFQG PHMITIKKGL DLPIAGTPSQ VISDGKAIKK VALLGEEYVG MRPTMHVRVG DEVKKAQILF EDKKNPGVK FTSPVSGKVV EINRGAKRVL QSVVIEVAGD DQVTFDKFEA NQLASLNRDA IKTQLVESGL WTAFRTRPFS K VPAIDSTS ...String:
MGSSHHHHHH SSGLEVLFQG PHMITIKKGL DLPIAGTPSQ VISDGKAIKK VALLGEEYVG MRPTMHVRVG DEVKKAQILF EDKKNPGVK FTSPVSGKVV EINRGAKRVL QSVVIEVAGD DQVTFDKFEA NQLASLNRDA IKTQLVESGL WTAFRTRPFS K VPAIDSTS EAIFVTAMDT NPLAAEPTVV INEQSEAFVA GLDVLSALTT GKVYVCKKGT SLPRSQQPNV EEHVFDGPHP AG LAGTHMH FLYPVSADHV AWSINYQDVI AVGQLFLTGE LYTQRVVSLA GPVVNKPRLV RTVMGASLEQ LVDSEIMPGE VRI ISGSVL SGTKATGPHA YLGRYHLQVS VLREGRDKEL FGWAMPGKNK FSVTRSFLGH LFKGQVYNMT TTTNGSDRSM VPIG NYEKV MPLDMEPTLL LRDLCAGDSD SAVRLGALEL DEEDLALCTF VCPGKYEYGQ LLRECLDKIE KEG

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit A

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Macromolecule #2: Na(+)-translocating NADH-quinone reductase subunit B

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 45.390883 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MGLKKFLEDI EHHFEPGGKH EKWFALYEAA ATLFYTPGLV TKRSSHVRDS VDLKRIMIMV WLAVFPAMFW GMYNAGGQAI AALNHLYSG DQLAAIVAGN WHYWLTEMLG GTMSSDAGWG SKMLLGATYF LPIYATVFIV GGFWEVLFCM VRKHEVNEGF F VTSILFAL ...String:
MGLKKFLEDI EHHFEPGGKH EKWFALYEAA ATLFYTPGLV TKRSSHVRDS VDLKRIMIMV WLAVFPAMFW GMYNAGGQAI AALNHLYSG DQLAAIVAGN WHYWLTEMLG GTMSSDAGWG SKMLLGATYF LPIYATVFIV GGFWEVLFCM VRKHEVNEGF F VTSILFAL IVPPTLPLWQ AALGITFGVV VAKEVFGGTG RNFLNPALAG RAFLFFAYPA QISGDLVWTA ADGYSGATAL SQ WAQGGAG ALINNATGQT ITWMDAFIGN IPGSIGEVST LALMIGAAFI VYMGIASWRI IGGVMIGMIL LSTLFNVIGS DTN AMFNMP WHWHLVLGGF AFGMFFMATD PVSASFTNSG KWAYGILIGV MCVLIRVVNP AYPEGMMLAI LFANLFAPLF DHVV VERNI KRRLARYGKQ

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit B

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Macromolecule #3: Na(+)-translocating NADH-quinone reductase subunit C

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 27.65227 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MASNNDSIKK TLFVVIALSL VCSIIVSAAA VGLRDKQKEN AALDKQSKIL QVAGIEAKGS KQIVELFNKS IEPRLVDFNT GDFVEGDAA NYDQRKAAKE ASESIKLTAE QDKAKIQRRA NVGVVYLVKD GDKTSKVILP VHGNGLWSMM YAFVAVETDG N TVSGLTYY ...String:
MASNNDSIKK TLFVVIALSL VCSIIVSAAA VGLRDKQKEN AALDKQSKIL QVAGIEAKGS KQIVELFNKS IEPRLVDFNT GDFVEGDAA NYDQRKAAKE ASESIKLTAE QDKAKIQRRA NVGVVYLVKD GDKTSKVILP VHGNGLWSMM YAFVAVETDG N TVSGLTYY EQGETPGLGG EVENPAWRAQ WVGKKLFDEN HKPAIKIVKG GAPQGSEHGV DGLSGATLTS NGVQNTFDFW LG DMGFGPF LTKVRDGGLN

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit C

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Macromolecule #4: Na(+)-translocating NADH-quinone reductase subunit D

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 22.853217 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MSSAKELKKS VLAPVLDNNP IALQVLGVCS ALAVTTKLET AFVMTLAVMF VTALSNFFVS LIRNHIPNSV RIIVQMAIIA SLVIVVDQI LKAYLYDISK QLSVFVGLII TNCIVMGRAE AFAMKSEPIP SFIDGIGNGL GYGFVLMTVG FFRELLGSGK L FGLEVLPL ...String:
MSSAKELKKS VLAPVLDNNP IALQVLGVCS ALAVTTKLET AFVMTLAVMF VTALSNFFVS LIRNHIPNSV RIIVQMAIIA SLVIVVDQI LKAYLYDISK QLSVFVGLII TNCIVMGRAE AFAMKSEPIP SFIDGIGNGL GYGFVLMTVG FFRELLGSGK L FGLEVLPL ISNGGWYQPN GLMLLAPSAF FLIGFMIWAI RTFKPEQVEA KE

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit D

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Macromolecule #5: Na(+)-translocating NADH-quinone reductase subunit E

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 21.481678 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MEHYISLLVK SIFIENMALS FFLGMCTFLA VSKKVKTSFG LGIAVIVVLT ISVPVNNLVY NLVLKPDALV EGVDLSFLNF ITFIGVIAA LVQILEMILD RFFPPLYNAL GIFLPLITVN CAIFGGVSFM VQRDYSFAES VVYGFGSGVG WMLAIVALAG I REKMKYSD ...String:
MEHYISLLVK SIFIENMALS FFLGMCTFLA VSKKVKTSFG LGIAVIVVLT ISVPVNNLVY NLVLKPDALV EGVDLSFLNF ITFIGVIAA LVQILEMILD RFFPPLYNAL GIFLPLITVN CAIFGGVSFM VQRDYSFAES VVYGFGSGVG WMLAIVALAG I REKMKYSD VPPGLRGLGI TFITAGLMAL GFMSFSGVQL

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit E

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Macromolecule #6: Na(+)-translocating NADH-quinone reductase subunit F

MacromoleculeName: Na(+)-translocating NADH-quinone reductase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (Na+-transporting)
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 45.113492 KDa
Recombinant expressionOrganism: Vibrio cholerae (bacteria)
SequenceString: MSTIIFGVVM FTLIILALVL VILFAKSKLV PTGDITISIN GDPEKAIVTQ PGGKLLTALA GAGVFVSSAC GGGGSCGQCR VKIKSGGGD ILPTELDHIS KGEAREGERL ACQVAVKADM DLELPEEIFG VKKWECTVIS NDNKATFIKE LKLAIPDGES V PFRAGGYI ...String:
MSTIIFGVVM FTLIILALVL VILFAKSKLV PTGDITISIN GDPEKAIVTQ PGGKLLTALA GAGVFVSSAC GGGGSCGQCR VKIKSGGGD ILPTELDHIS KGEAREGERL ACQVAVKADM DLELPEEIFG VKKWECTVIS NDNKATFIKE LKLAIPDGES V PFRAGGYI QIEAPAHHVK YADFDVPEKY RGDWDKFNLF RYESKVDEPI IRAYSMANYP EEFGIIMLNV RIATPPPNNP NV PPGQMSS YIWSLKAGDK CTISGPFGEF FAKDTDAEMV FIGGGAGMAP MRSHIFDQLK RLKSKRKMSY WYGARSKREM FYV EDFDGL AAENDNFVWH CALSDPQPED NWTGYTGFIH NVLYENYLKD HEAPEDCEYY MCGPPMMNAA VINMLKNLGV EEEN ILLDD FGG

UniProtKB: Na(+)-translocating NADH-quinone reductase subunit F

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Macromolecule #7: RIBOFLAVIN

MacromoleculeName: RIBOFLAVIN / type: ligand / ID: 7 / Number of copies: 1 / Formula: RBF
Molecular weightTheoretical: 376.364 Da
Chemical component information

ChemComp-RBF:
RIBOFLAVIN / Riboflavin

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Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 8 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #9: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 9 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #10: UBIQUINONE-2

MacromoleculeName: UBIQUINONE-2 / type: ligand / ID: 10 / Number of copies: 1 / Formula: UQ2
Molecular weightTheoretical: 318.407 Da
Chemical component information

ChemComp-UQ2:
UBIQUINONE-2

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Macromolecule #11: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 11 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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Macromolecule #12: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 12 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #13: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 13 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #14: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 14 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM / Flavin adenine dinucleotide

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Macromolecule #15: water

MacromoleculeName: water / type: ligand / ID: 15 / Number of copies: 386 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration4 mg/mL
BufferpH: 7.6
GridModel: C-flat-1.2/1.3 / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 276 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 191781 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 7 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 7647 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 496434
Startup modelType of model: OTHER / Details: ab initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 226672
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4p6v
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8a1v:
Sodium pumping NADH-quinone oxidoreductase with substrate Q2

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