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- EMDB-60307: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60307
TitleCryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
Map data
Sample
  • Complex: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
    • Protein or peptide: x 10 types
  • Ligand: x 8 types
KeywordsPlant complex / mitochondria / pyraclostrobin / PLANT PROTEIN
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion ...respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Probable transposase, Ptta/En/Spm, plant / Plant transposase (Ptta/En/Spm family) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / 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 ...Probable transposase, Ptta/En/Spm, plant / Plant transposase (Ptta/En/Spm family) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / 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 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / 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
Ubiquinol-cytochrome c reductase complex 6.7 kDa protein / Cytochrome b-c1 complex subunit 6 / Cytochrome c domain-containing protein / Mitochondrial-processing peptidase subunit beta / Complex III subunit 9 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Mitochondrial-processing peptidase subunit alpha / Cytochrome b-c1 complex subunit 8 / Cytochrome b
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsCui GR / Wang YX / Yang GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
Authors: Cui GR / Wang YX / Yang GF
History
DepositionMay 28, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60307.png

Downloads & links

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Map

FileDownload / File: emd_60307.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.586
Minimum - Maximum-4.3288383 - 8.780233000000001
Average (Standard dev.)-0.00020173885 (±0.22985697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 307.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60307_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_60307_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 : Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex

EntireName: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
Components
  • Complex: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
    • Protein or peptide: Mitochondrial-processing peptidase subunit alpha
    • Protein or peptide: Mitochondrial-processing peptidase subunit beta
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c domain-containing protein
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Cytochrome b-c1 complex subunit 6
    • Protein or peptide: Complex III subunit 9
    • Protein or peptide: Ubiquinol-cytochrome c reductase complex 6.7 kDa protein
  • Ligand: ZINC ION
  • Ligand: CARDIOLIPIN
  • Ligand: methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-~{N}-methoxy-carbamate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex

SupramoleculeName: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 500 kDa/nm

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Macromolecule #1: Mitochondrial-processing peptidase subunit alpha

MacromoleculeName: Mitochondrial-processing peptidase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 49.77932 KDa
SequenceString: APPLDFPLPG VTLPSPLPDH VAPGKTIVTT LPNGIKLASE TSAGPAASIG LYVDCGSIYE TPLTFGATHL LERMAFKSTR NRTHFRVVR EVEAIGGNVQ ASASREQMGY TFDALKTHVP EMVELLVDCV RNPVFLDWEV NEQLLKVKAE VGEASKNPQD L LLEAIHSA ...String:
APPLDFPLPG VTLPSPLPDH VAPGKTIVTT LPNGIKLASE TSAGPAASIG LYVDCGSIYE TPLTFGATHL LERMAFKSTR NRTHFRVVR EVEAIGGNVQ ASASREQMGY TFDALKTHVP EMVELLVDCV RNPVFLDWEV NEQLLKVKAE VGEASKNPQD L LLEAIHSA GYSGALANPL LASESALNGL NGSILEEFVA ENYTAPRIVL AASGVEHEEL LSIAEPLLSD LPNVPRPEEP KS VYTGGDY RCHTESGHIL NGQRTHFALA FELPGGWHKL KDAMVLTVLQ MLLGGGGSFS AGGPGKGMYS RLYLRVLNEY PQF HSISAF NNIYNNTGIF GIQVTTGSDF VSKAIDITVN ELLAVATSGQ VDQVQLDRAK QATKSAILMN LESRMVVSED IGRQ VLTYG ERKPVEDFLK AVDEVTLKDI ASISQKLISS PLTMASYGDV IYVPNYESVS SKFRS

UniProtKB: Mitochondrial-processing peptidase subunit alpha

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Macromolecule #2: Mitochondrial-processing peptidase subunit beta

MacromoleculeName: Mitochondrial-processing peptidase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 54.822918 KDa
SequenceString: SPPPPNAMVY DRLAEAVKAK LRQLENPDPR FLKYGSPRPT LTDHTRILAA PETRVTTLPN GLRVATESSL AARTATVGVW IDAGSRFET EESNGTAHFL EHMIFKGTEK RNARELEEEI ENMGGHLNAY TSREQTTYYA KVADKDVPKA LDILADILQN S RFDENRIS ...String:
SPPPPNAMVY DRLAEAVKAK LRQLENPDPR FLKYGSPRPT LTDHTRILAA PETRVTTLPN GLRVATESSL AARTATVGVW IDAGSRFET EESNGTAHFL EHMIFKGTEK RNARELEEEI ENMGGHLNAY TSREQTTYYA KVADKDVPKA LDILADILQN S RFDENRIS RERDVILREM EEVEGQTEEV IFDHLHATAF QYTPLGRTIL GPAQNIKTIT KDHLQNYIQT HYTAPRMVIA AS GAVKHED IVEQVKKLFT KLSTDPTTAS QLVAKEPAIF TGSEVRMLDD EIPLAQFAVA FEGASWKDPD SIALMVMQAM LGS WNKTAG GGKHMGSELA QRVGINEVAE SMMAFNTNYK DTGLFGVYAV AKPDCLDDLS YAIMYETTKL AYRVSDDDVT RARN QLKSS LLLYIDGTSP VAEDIGRQLL TYGRRIPFAE LFARIDAVDA STIKRVANRF IYDKDIAIAA MGPIQRLPDY NWFRR RTYW NRY

UniProtKB: Mitochondrial-processing peptidase subunit beta

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Macromolecule #3: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 43.36052 KDa
SequenceString: MRNQRFSLLK QPISSTLNQH LIDYPTPSNL SYWWGFGSLA GICLVIQIVT GVFLAMHYTP HVDLAFNSVE HVMRDVEGGW LLRYMHANG ASMFLIVVHL HIFRGLYHAS YSSPREFVRC LGVVIFLLMI VTAFTGYVPP WGQMSFWGAT VITSLASAIP V VGDTIVTW ...String:
MRNQRFSLLK QPISSTLNQH LIDYPTPSNL SYWWGFGSLA GICLVIQIVT GVFLAMHYTP HVDLAFNSVE HVMRDVEGGW LLRYMHANG ASMFLIVVHL HIFRGLYHAS YSSPREFVRC LGVVIFLLMI VTAFTGYVPP WGQMSFWGAT VITSLASAIP V VGDTIVTW LWGGFSVDNA TLNRFFSLHH LLPFILVGAS LLHLAALHQY GSNNPLGVHS EMDQISFYPY FYVKDLVGWV AF AIFFSIW IFYAPNVLGH PDNYIPANPM PTPPHIVPEW YFLPIHAILR SIPDKSGGVA AIAPVFICLL ALPFFKSMYV RSS SFRPIH QGIFWLLLAD RLLLGWIGCQ PVEAPFVTIG QIPPLVFFLF FAITPIPGRV GRGIPNSYTD

UniProtKB: Cytochrome b

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Macromolecule #4: Cytochrome c domain-containing protein

MacromoleculeName: Cytochrome c domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 26.894418 KDa
SequenceString: EAEHGLACPS YPWPHQGILS SYDHASIRRG HQVYTQVCAS CHSMSLISYR DLVGVAYTEE EVKAMAAEIE VVDGPNDEGE MFTRPGKLS DRFPQPYANE AAARFANGGA YPPDLSLITK APHNGQNYVF ALLTGYRDPP AGVSIREGLH YNPYFPGGAI A MPKMLNDG ...String:
EAEHGLACPS YPWPHQGILS SYDHASIRRG HQVYTQVCAS CHSMSLISYR DLVGVAYTEE EVKAMAAEIE VVDGPNDEGE MFTRPGKLS DRFPQPYANE AAARFANGGA YPPDLSLITK APHNGQNYVF ALLTGYRDPP AGVSIREGLH YNPYFPGGAI A MPKMLNDG AVEYEDGTPA TESQMGKDVV SFLSWAAEPE MEERKLMGFK WIFVLTLALL QAGYYRRLRW SVLKSRKLVL DV VN

UniProtKB: Cytochrome c domain-containing protein

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

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 21.779992 KDa
SequenceString: EIPATVAAVK NPSSKIVYDE HNHERYPPGD PSKRAFAYFV LTGGRFVYAS LVRLLILKFV LSMSASKDVL ALASLEVDLS SIEPGTTVT VKWRGKPVFI RRRTEDDIKL ANSVDVGSLR DPQQDAERVK NPEWLIVIGV CTHLGCIPLP NAGDFGGWFC P CHGSHYDI ...String:
EIPATVAAVK NPSSKIVYDE HNHERYPPGD PSKRAFAYFV LTGGRFVYAS LVRLLILKFV LSMSASKDVL ALASLEVDLS SIEPGTTVT VKWRGKPVFI RRRTEDDIKL ANSVDVGSLR DPQQDAERVK NPEWLIVIGV CTHLGCIPLP NAGDFGGWFC P CHGSHYDI SGRIRKGPAP YNLEVPTYTF LEENKLLI

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #6: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 14.022236 KDa
SequenceString:
QSFIDPKKNW FAAQHMKAIS KRLRRFGLRY DDLYDPYYDL DVKEALNRLP KEVVDARHQR LKRAMDLSMK HEYLPEDLQA MQTPFRGYL QEMLALVKRE KAERESLGGL PLYQRTIP

UniProtKB: Cytochrome b-c1 complex subunit 7

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Macromolecule #7: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 8.102475 KDa
SequenceString:
KGFVPMKAVT YGLSPFQQKI MPGLWKDLPT KIHHKVSENW ISATLLLGPL VGVYSYVQNY QEKEKLSHRY

UniProtKB: Cytochrome b-c1 complex subunit 8

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Macromolecule #8: Cytochrome b-c1 complex subunit 6

MacromoleculeName: Cytochrome b-c1 complex subunit 6 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 7.448683 KDa
SequenceString:
PVDQKKYLEE SCKPKCVKAL LEYQACVKRI QGDETGNKHC TGQYFDYWSC IDKCVAQKLF SKLK

UniProtKB: Cytochrome b-c1 complex subunit 6

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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: Arachis hypogaea (peanut)
Molecular weightTheoretical: 6.86785 KDa
SequenceString:
GGIFEALYKV LMRRNSVYVT FVIAGAFVGE RAVDYGVHKL WEHNNVGKRY EDISVLGQRQ

UniProtKB: Complex III subunit 9

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Macromolecule #10: Ubiquinol-cytochrome c reductase complex 6.7 kDa protein

MacromoleculeName: Ubiquinol-cytochrome c reductase complex 6.7 kDa protein
type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arachis hypogaea (peanut)
Molecular weightTheoretical: 3.073544 KDa
SequenceString:
IQPTDVKAAA MWGVAAATGG LYLIQPWGW

UniProtKB: Ubiquinol-cytochrome c reductase complex 6.7 kDa protein

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 12 / Number of copies: 6 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #13: methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]...

MacromoleculeName: methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-~{N}-methoxy-carbamate
type: ligand / ID: 13 / Number of copies: 2 / Formula: A1D6K
Molecular weightTheoretical: 387.817 Da

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Macromolecule #14: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 14 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #15: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 15 / Number of copies: 12 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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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

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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

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Macromolecule #18: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 18 / Number of copies: 1 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 49.48 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95092
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8zom:
Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex

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