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- EMDB-51939: Cryo-EM structure of the atovaquone-inhibited Complex III from th... -

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Basic information

Entry
Database: EMDB / ID: EMD-51939
TitleCryo-EM structure of the atovaquone-inhibited Complex III from the Chlorocebus sabaeus respirasome
Map data
Sample
  • Complex: mitochondrial respirasome from Chlorocebus sabaeus Vero cells inhibited by atovaquone
    • Protein or peptide: x 10 types
  • Ligand: x 10 types
Keywordscomplex III / respirasome / mitochondria / green african monkey / atovaquone / ELECTRON TRANSPORT
Function / homology
Function and homology information


subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / mitochondrial respiratory chain complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c ...subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / mitochondrial respiratory chain complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / hippocampus development / respiratory electron transport chain / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / proteolysis / nucleoplasm / metal ion binding
Similarity search - Function
Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / 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 ...Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / 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. / 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-like domain superfamily
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Complex III subunit 9 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 6 / Cytochrome b
Similarity search - Component
Biological speciesChlorocebus sabaeus (green monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsMaclean A / Muhleip A
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex.
Authors: Andrew E MacLean / Shikha Shikha / Mariana Ferreira Silva / Max J Gramelspacher / Aaron Nilsen / Katherine M Liebman / Sovitj Pou / Rolf W Winter / Amit Meir / Michael K Riscoe / J Stone ...Authors: Andrew E MacLean / Shikha Shikha / Mariana Ferreira Silva / Max J Gramelspacher / Aaron Nilsen / Katherine M Liebman / Sovitj Pou / Rolf W Winter / Amit Meir / Michael K Riscoe / J Stone Doggett / Lilach Sheiner / Alexander Mühleip /
Abstract: The apicomplexan mitochondrial electron transport chain is essential for parasite survival and displays a divergent subunit composition. Here we report cryo-electron microscopy structures of an ...The apicomplexan mitochondrial electron transport chain is essential for parasite survival and displays a divergent subunit composition. Here we report cryo-electron microscopy structures of an apicomplexan III-IV supercomplex and of the drug target complex III. The supercomplex structure reveals how clade-specific subunits form an apicomplexan-conserved III-IV interface with a unique, kinked architecture, suggesting that supercomplexes evolved independently in different eukaryotic lineages. A knockout resulting in supercomplex disassembly challenges the proposed role of III-IV in electron transfer efficiency as suggested for mammals. Nevertheless, knockout analysis indicates that III-IV is critical for parasite fitness. The complexes from the model parasite Toxoplasma gondii were inhibited with the antimalarial atovaquone, revealing interactions underpinning species specificity. They were also inhibited with endochin-like quinolone (ELQ)-300, an inhibitor in late-stage preclinical development. Notably, in the apicomplexan binding site, ELQ-300 is flipped compared with related compounds in the mammalian enzyme. On the basis of the binding modes and parasite-specific interactions discovered, we designed more potent ELQs with subnanomolar activity against T. gondii. Our findings reveal critical evolutionary differences in the role of supercomplexes in mitochondrial biology and provide insight into cytochrome b inhibition, informing future drug discovery.
History
DepositionOct 29, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51939.png

Downloads & links

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Map

FileDownload / File: emd_51939.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 600 pix.
= 592.482 Å		0.99 Å/pix.
x 600 pix.
= 592.482 Å		0.99 Å/pix.
x 600 pix.
= 592.482 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98747 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.276048 - 8.553283
Average (Standard dev.)0.0012486359 (±0.15456647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 592.482 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51939_msk_1.map
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Half map: #2

Fileemd_51939_half_map_1.map
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Half map: #1

Fileemd_51939_half_map_2.map
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Sample components

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Entire : mitochondrial respirasome from Chlorocebus sabaeus Vero cells inh...

EntireName: mitochondrial respirasome from Chlorocebus sabaeus Vero cells inhibited by atovaquone
Components
  • Complex: mitochondrial respirasome from Chlorocebus sabaeus Vero cells inhibited by atovaquone
    • Protein or peptide: Cytochrome c1
    • 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: Complex III subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 6
    • Protein or peptide: Ubiquinol-cytochrome c reductase core protein 2
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Ubiquinol-cytochrome c reductase core protein 1
    • Protein or peptide: UQCRB
  • Ligand: HEME C
  • Ligand: ZINC ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: CARDIOLIPIN
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

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Supramolecule #1: mitochondrial respirasome from Chlorocebus sabaeus Vero cells inh...

SupramoleculeName: mitochondrial respirasome from Chlorocebus sabaeus Vero cells inhibited by atovaquone
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Chlorocebus sabaeus (green monkey) / Strain: Vero cell line

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Macromolecule #1: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 35.268703 KDa
SequenceString: MAAAAASLRG VVLGPRGAGL PGARARGLLC SARPGQLPLR TPQAVALSSK SGLSRGRKVV LSALGMLAAG GAGLAVALHS AVSASDVAL HPPSYPWSHS GFLSSLDHTS IRRGFQVYKQ VCSSCHSMNF VAYRHLVGVC YTEDEAKALA AEVEVQDGPN E NGEMFMRP ...String:
MAAAAASLRG VVLGPRGAGL PGARARGLLC SARPGQLPLR TPQAVALSSK SGLSRGRKVV LSALGMLAAG GAGLAVALHS AVSASDVAL HPPSYPWSHS GFLSSLDHTS IRRGFQVYKQ VCSSCHSMNF VAYRHLVGVC YTEDEAKALA AEVEVQDGPN E NGEMFMRP GKLFDYFPKP YPNSEAARAA NNGALPPDLS YIARARHGGE DYIFSLLTGY CEPPTGVSLR EGLYFNPYFP GQ AIAMAPP IYTDVLEFDD GTPATMSQIA KDVCTFLRWA SEPEHDHRKR MALKMLTMMA LLIPLTYIMK RHKWSVLKSR KLA YRPPK

UniProtKB: Cytochrome c1, heme protein, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 29.817166 KDa
SequenceString: MLSVAARSGP FAPVLSATSR GVAGALRPLV QATVPATPEP PVLDLKRPFL SRESLSGQAV RRPLVASVGL NVPASVCYSH TDVKVPDFY DYRRLEVLDS TKSSRESSEA RKGFSYLVTA VTTVGVAYAA KNVVTQFISS MSASADVLAM AKIEINLSDI P EGKNMAFK ...String:
MLSVAARSGP FAPVLSATSR GVAGALRPLV QATVPATPEP PVLDLKRPFL SRESLSGQAV RRPLVASVGL NVPASVCYSH TDVKVPDFY DYRRLEVLDS TKSSRESSEA RKGFSYLVTA VTTVGVAYAA KNVVTQFISS MSASADVLAM AKIEINLSDI P EGKNMAFK WRGKPLFVRH RTQKEIEQEA AVELSQLRDP QHDLDRVKKP EWVILIGVCT HLGCVPIANA GDFGGYYCPC HG SHYDASG RIRLGPAPLN LEVPPYEFTR DDMVVVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #3: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 13.54045 KDa
SequenceString:
MAGKQAVSAS GKWLDGIRKW YYNAAGFNKL GLLRDDTMYE DEDVKEAIRR LPDNLYNDRM FRIKRALDLN LKHQILPKEQ WTKYEEENF YLEPYLKEVI RERKEREEWA KK

UniProtKB: Cytochrome b-c1 complex subunit 7

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Macromolecule #4: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 9.748262 KDa
SequenceString:
MGREFGNLTR IRHVISYSLS PLEQRALPHV LSKGVPNMLR RVRESFFRVV PQFVVFYLLY TWGTEEFEKS KRKNPAAYEN DK

UniProtKB: Cytochrome b-c1 complex subunit 8

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Macromolecule #5: Complex III subunit 9

MacromoleculeName: Complex III subunit 9 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 7.320473 KDa
SequenceString:
MAAVAFTSKL YSLLFRRTST FALTIVVGVL FFERAFDQGA DAIYDHINEG KLWKHIKHKY ENK

UniProtKB: Complex III subunit 9

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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: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 10.803954 KDa
SequenceString:
MGLEDERKML TESGDPEEEE EEEEELVDPL TTVREQCEQL EKCVKARERL ELCDERVSSR SHTEEDCMEE LLDFLYARDH CVAHKLFNN LK

UniProtKB: Cytochrome b-c1 complex subunit 6

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Macromolecule #7: Ubiquinol-cytochrome c reductase core protein 2

MacromoleculeName: Ubiquinol-cytochrome c reductase core protein 2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 48.592984 KDa
SequenceString: MKLLTRAGSF SRFYSLKVAP KVKATAAPAG APPQPQDLEF TKLPNGLVIA SLENYAPLSR IGLFIKAGSR YEDSNNLGTT HLLRLASSL TTKGASSFKI TRGIEAVGSK LSVTATRETM AYTVECLRGD VDILMEFLLN VTTAPEFRRW EVADLQPQLK I DKAVAFQN ...String:
MKLLTRAGSF SRFYSLKVAP KVKATAAPAG APPQPQDLEF TKLPNGLVIA SLENYAPLSR IGLFIKAGSR YEDSNNLGTT HLLRLASSL TTKGASSFKI TRGIEAVGSK LSVTATRETM AYTVECLRGD VDILMEFLLN VTTAPEFRRW EVADLQPQLK I DKAVAFQN PQTHVIENLH AAAYRNALAN PLYCPDYRIG KVTSEELHYF VQNHFTSARM ALIGLGVSHP VLKQVAEQFL NM RGGFGLS GVKAKYRGGE IREQNGDSLV HAALVAESAV AGSAEANAFS VLQHVLGAGP HIKRGSNTTS HLYQAVAKAT QQP FDVSAF NANYSDSGLF GIYTISQATA AGDVIKAAYN QVKTIAQGNL SNTDVQAAKN KLKAGYLMSV ESSERFLEEV GSQA LVAGS YVPPSTVLQQ IDSVANADVI NAAKKFVSGQ KSMVASGNLG HTPFVDEL

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

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Macromolecule #8: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 43.07077 KDa
SequenceString: MTPMRKSNPI MKMINHSLID LPTPSNISMW WNFGSLLAFC LILQIITGLF LAMHYSPDTS SAFSSIAHIT RDVNHGWIIR YLHANGASM FFICLFLHVG RGLYYGSFLL LKTWNTGIML LFLTMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VQWIWGGY ...String:
MTPMRKSNPI MKMINHSLID LPTPSNISMW WNFGSLLAFC LILQIITGLF LAMHYSPDTS SAFSSIAHIT RDVNHGWIIR YLHANGASM FFICLFLHVG RGLYYGSFLL LKTWNTGIML LFLTMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VQWIWGGY SIGNPTLSRF FTLHFILPFI ITALTMVHLL FLHETGSNNP CGISSDSDKI PFHPYYTIKD ILGLVLLLFI LT TLTLLSP NLLNDPDNYI PADPLNTPPH IKPEWYFLFA YAILRSVPNK LGGVLALFLS ILILSIIPTL HNSKQQSMMF RPL SQFLFW FLITTLLTLT WIGSQPVSQP FIFIGQLAST MYFTTVLILM PLTSLIENNL LKWT

UniProtKB: Cytochrome b

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Macromolecule #9: Ubiquinol-cytochrome c reductase core protein 1

MacromoleculeName: Ubiquinol-cytochrome c reductase core protein 1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 52.885816 KDa
SequenceString: MAASVVCRAA TSGAQVLLRA RRSPTLLRTP ALRSTATFAQ ALQFVPETQV SLLDNGLRVA SEQSSQPTCT VGVWIDVGSR FETEKNNGA GYFLEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKVVELLGD IVQNCSLEDS Q IEKERDVI ...String:
MAASVVCRAA TSGAQVLLRA RRSPTLLRTP ALRSTATFAQ ALQFVPETQV SLLDNGLRVA SEQSSQPTCT VGVWIDVGSR FETEKNNGA GYFLEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKVVELLGD IVQNCSLEDS Q IEKERDVI LREMQENDAS MRDVVFDYLH ATAFQGTPLA QTVEGPSENV RKLSRADLTE YLSTHYKAPR MVLAAAGGVE HQ QLLDLAQ KHLGDIPWTY AEDTMPALTP CRFTGSEIRH RDDALPFAHV AIAVEGPGWA SPDNVALQVA NAIIGHYDCT YGG GVHLSS PLASGAVANK LCQSFQTFSI CYADTGLLGA HFVCDRMKID DMMFVLQGQW MRLCTSATES EVARGKNILR NALV SHLDG TTPVCEDIGR SLLTYGRRIP LAEWESRIAE VDASVVREIC SKYIYDQCPA VAGYGPIEQL PDYNRIRSGM FWLRF

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Macromolecule #10: UQCRB

MacromoleculeName: UQCRB / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus sabaeus (green monkey)
Molecular weightTheoretical: 6.62371 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString:
MMTRFLGPRY RQLVKNWIPT AYTWGAVGTL GLAWAADWRL ILDWVPYVNG RFKKDD

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Macromolecule #11: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 11 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

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Macromolecule #14: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 14 / Number of copies: 4 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #15: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 15 / Number of copies: 2 / 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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Macromolecule #16: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione

MacromoleculeName: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione
type: ligand / ID: 16 / Number of copies: 2 / Formula: AOQ
Molecular weightTheoretical: 366.837 Da
Chemical component information

ChemComp-AOQ:
2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione / medication, Antimicrobial*YM

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Macromolecule #17: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 17 / Number of copies: 6 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

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

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Macromolecule #18: 2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHA...

MacromoleculeName: 2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE
type: ligand / ID: 18 / Number of copies: 2 / Formula: AFI
Molecular weightTheoretical: 366.837 Da
Chemical component information

ChemComp-AFI:
2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE

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Macromolecule #19: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 19 / 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 #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 14 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 301 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 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: INSILICO MODEL / In silico model: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 637526
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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

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