[English] 日本語
Yorodumi
- EMDB-60320: Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60320
TitleCryo-EM structure of Metyltetraprole-bound porcine bc1 complex
Map data
Sample
  • Complex: Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex
    • Protein or peptide: x 11 types
  • Ligand: x 6 types
KeywordsMetyltetraprole / Inhibitor / Complex / PROTEIN BINDING
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex III / quinol-cytochrome-c reductase ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / hippocampus development / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 / Cytochrome b-c1 complex subunit 10 / Cytochrome b
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsWang YX / Sun JY / Cui GR / Yang GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Am Chem Soc / Year: 2024
Title: Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome Complex Enabling Rational Design of Inhibitors.
Authors: Yu-Xia Wang / Ying Ye / Zhi-Wen Li / Guang-Rui Cui / Xing-Xing Shi / Ying Dong / Jia-Jia Jiang / Jia-Yue Sun / Ze-Wei Guan / Nan Zhang / Qiong-You Wu / Fan Wang / Xiao-Lei Zhu / Guang-Fu Yang /
Abstract: Cytochrome (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QI) that combats ...Cytochrome (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QI) that combats the G143A mutated isolate, which confers high resistance to strobilurin fungicides such as pyraclostrobin (PYR). The binding mode and antiresistance mechanism of MET remain unclear. Here, we determined the high-resolution structures of inhibitor-bound complex III (MET, 2.52 Å; PYR, 2.42 Å) and inhibitor-bound porcine complex III (MET, 2.53 Å; PYR, 2,37 Å) by cryo-electron microscopy. The distinct binding modes of MET and PYR were observed for the first time. Notably, the MET exhibited different binding modes in the two species. In , the binding site of MET was the same as PYR, serving as a -type inhibitor of the Q site. However, in porcine, MET acted as a dual-target inhibitor of both Q and Q. Based on the structural insights, a novel inhibitor (YF23694) was discovered and demonstrated excellent fungicidal activity against downy mildew and powdery mildew fungi. This work provides a new starting point for the design of the next generation of inhibitors to overcome the resistance.
History
DepositionMay 29, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_60320.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 300 pix.
= 288. Å
0.96 Å/pix.
x 300 pix.
= 288. Å
0.96 Å/pix.
x 300 pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density
Contour LevelBy AUTHOR: 0.798
Minimum - Maximum-5.3669434 - 8.863431
Average (Standard dev.)-0.0002567069 (±0.22286887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60320_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_60320_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex

EntireName: Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex
Components
  • Complex: Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1, heme protein, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 1, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 6
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Complex III subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
  • Ligand: 1-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]-3-methyl-phenyl]-4-methyl-1,2,3,4-tetrazol-5-one
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: CARDIOLIPIN
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

+
Supramolecule #1: Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex

SupramoleculeName: Cryo-EM structure of Metyltetraprole-bound porcine bc1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Sus scrofa (pig)

+
Macromolecule #1: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 42.70952 KDa
SequenceString: TNIRKSHPLM KIINNAFIDL PAPSNISSWW NFGSLLGICL ILQILTGLFL AMHYTSDTTT AFSSVTHICR DVNYGWVIRY LHANGASMF FICLFIHVGR GLYYGSYMFL ETWNIGVVLL FTVMATAFMG YVLPWGQMSF WGATVITNLL SAIPYIGTDL V EWIWGGFS ...String:
TNIRKSHPLM KIINNAFIDL PAPSNISSWW NFGSLLGICL ILQILTGLFL AMHYTSDTTT AFSSVTHICR DVNYGWVIRY LHANGASMF FICLFIHVGR GLYYGSYMFL ETWNIGVVLL FTVMATAFMG YVLPWGQMSF WGATVITNLL SAIPYIGTDL V EWIWGGFS VDKATLTRFF AFHFILPFII TALAAVHLLF LHETGSNNPT GISSDMDKIP FHPYYTIKDI LGALFMMLIL LI LVLFSPD LLGDPDNYTP ANPLNTPPHI KPEWYFLFAY AILRSIPNKL GGVLALVASI LILILMPMLH TSKQRSMMFR PLS QCLFWM LVADLITLTW IGGQPVEHPF IIIGQLASIL YFLIILVLMP ITSIIENNLL KW

UniProtKB: Cytochrome b

+
Macromolecule #2: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 27.373357 KDa
SequenceString: TDLELHAPSY PWSHRGLLSS LDHTSIRRGF QVYKQVCSSC HSMDYVAYRH LVGVCYTEEE AKALAEEVEV QDGPNEDGEM FMRPGKLSD YFPKPYPNPE AARAANNGAL PPDLSYIVRA RHGGEDYVFS LLTGYCEPPT GVSLREGLYF NPYFPGQAIA M APPIYNEV ...String:
TDLELHAPSY PWSHRGLLSS LDHTSIRRGF QVYKQVCSSC HSMDYVAYRH LVGVCYTEEE AKALAEEVEV QDGPNEDGEM FMRPGKLSD YFPKPYPNPE AARAANNGAL PPDLSYIVRA RHGGEDYVFS LLTGYCEPPT GVSLREGLYF NPYFPGQAIA M APPIYNEV LEFDDGTPAT MSQVAKDVCT FLRWASEPEH DHRKRMGLKM LMMMGLLLPL VYAMKRHKWS VLKSRKLAYR PP K

UniProtKB: Cytochrome c1, heme protein, mitochondrial

+
Macromolecule #3: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.610492 KDa
SequenceString: SHTDIRVPDF SDYRRAEVLD STKSSKESSD ARKGFSYLIT ATTTVGVAYA AKNAVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLERVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS ...String:
SHTDIRVPDF SDYRRAEVLD STKSSKESSD ARKGFSYLIT ATTTVGVAYA AKNAVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLERVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS GRIRKGPAPL NLEVPTYEFT SDDLVIVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

+
Macromolecule #4: Cytochrome b-c1 complex subunit 1, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.270133 KDa
SequenceString: TATYAQALQS VPETQVSQLD NGLRVASEQS SQPTCTVGVW IDAGSRYENE KNNGAGYFVE HLAFKGTKNR PGSALEKEVE SMGAHLNAY STREHTAYYI KALSKDLPKA VELLADIVQN CSLEDSQIEK ERDVILQELQ ENDSSMRDVV FDYLHATAFQ G TPLAQSVE ...String:
TATYAQALQS VPETQVSQLD NGLRVASEQS SQPTCTVGVW IDAGSRYENE KNNGAGYFVE HLAFKGTKNR PGSALEKEVE SMGAHLNAY STREHTAYYI KALSKDLPKA VELLADIVQN CSLEDSQIEK ERDVILQELQ ENDSSMRDVV FDYLHATAFQ G TPLAQSVE GPSENVRKLS RADLTEYVSQ HYKAPRMVLA AAGGVEHRQL LDLAQKHFSS LSGTYVEDAV PAFTPCRFTG SE IRHRDDA LPLAHVAIAV EGPGWANPDN VPLQVANAII GHYDSTYGGG THMSSTLASV AATRKLCQSF QTFNICYAET GLL GAHFVC DNMSIDDMMF FLQGQWMRLC TSATESEVVR GKNILRNALV SHLDGTTPVC EDIGRSLLTY GRRIPLAEWE SRIA EVDAS VVREVCSKYF YDQCPAVAGL GPIEQLPDYN RIRSGMFWLR F

UniProtKB: Cytochrome b-c1 complex subunit 1, mitochondrial

+
Macromolecule #5: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 44.616098 KDa
SequenceString: PQDLEFTRLP NGLVIASLEN YAPASRIGLF IKAGSRYEDS NNLGTSHLLR LASSLTTKGA SSFKITRGIE AVGGKLSVTS TRESMAYTV ECLRDDIEIL MEFLLNVTAA PEFRRWEVAA LQSQLRIDKA VAFQNPQAQV LENLHAAAYR NALANSLYCP D YRIGKVTP ...String:
PQDLEFTRLP NGLVIASLEN YAPASRIGLF IKAGSRYEDS NNLGTSHLLR LASSLTTKGA SSFKITRGIE AVGGKLSVTS TRESMAYTV ECLRDDIEIL MEFLLNVTAA PEFRRWEVAA LQSQLRIDKA VAFQNPQAQV LENLHAAAYR NALANSLYCP D YRIGKVTP DQLHYYVQNH FTSARMALIG LGVSHPVLKQ VAERFLNMRG GLGLSGAKAK YRGGEIRDQN GDSLVHAALV AE SAATGSA EANAFSVLQH VLGAGPHVKR GSNATSSLYQ AVAKGVHQPF DVSAFNASYS DSGLFGIYTI SQAASAGDVI KSA YDQVKA IAQGNLSNTD VQAAKNKLKA GYLMSVESSE GFLDEVGSQA LVAGSYMQPS TVLQQIDSVA DADVINAAKK FVSG RKSMA ASGNLGHTPF VDE

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

+
Macromolecule #6: Cytochrome b-c1 complex subunit 6

MacromoleculeName: Cytochrome b-c1 complex subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.592541 KDa
SequenceString:
DPLTTVREQC EQIEKCIKAR ERLELCDQRV SSRSQTEEDC TEELFDFLHA RDHCVAHKLF NSLK

UniProtKB: Cytochrome b-c1 complex subunit 6

+
Macromolecule #7: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.043888 KDa
SequenceString:
AVAASSKWLE GIRKWYYNAA GFNKLGLMRD DTIYEDDDVK EAIRRLPENL YNDRVFRIKR ALDLTMRQQI LPKEQWTKYE EDKFYLEPY LKEVIRERKE REEWAKK

UniProtKB: Cytochrome b-c1 complex subunit 7

+
Macromolecule #8: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 9.408876 KDa
SequenceString:
GREFGHLTRM RHVITYSLSP FEQRAFPHYF TKGIPNVLRR TRACILRVAP PFVVFYLVYT WGTQEFEKSK RKNPAAYEN

UniProtKB: Cytochrome b-c1 complex subunit 8

+
Macromolecule #9: Complex III subunit 9

MacromoleculeName: Complex III subunit 9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.15222 KDa
SequenceString:
AAPTLTARLY SLLFRRTSTF ALTIAVGALF FERAFDQGAD AIYEHINQGK LWKHIKHKYE NK

UniProtKB: Complex III subunit 9

+
Macromolecule #10: Cytochrome b-c1 complex subunit 10

MacromoleculeName: Cytochrome b-c1 complex subunit 10 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 6.058093 KDa
SequenceString:
MLSRFLGPRY RELARNWIPT ASMWGAVGAV GLVWATDWRL ILDWVPYING KF

UniProtKB: Cytochrome b-c1 complex subunit 10

+
Macromolecule #11: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.790676 KDa
SequenceString:
MLSVASRSGP FAPVLSATSR GVAGALRPLV QAALPATSES PVLDAKRSFL CRESLSG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

+
Macromolecule #12: 1-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]-3-methyl-phenyl]...

MacromoleculeName: 1-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]-3-methyl-phenyl]-4-methyl-1,2,3,4-tetrazol-5-one
type: ligand / ID: 12 / Number of copies: 4 / Formula: A1D6P
Molecular weightTheoretical: 396.83 Da

+
Macromolecule #13: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 13 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #14: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 14 / Number of copies: 2 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

+
Macromolecule #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

+
Macromolecule #16: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 16 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #17: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 17 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.72 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: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 411418
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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