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- EMDB-4286: CryoEM structure of bovine cytochrome bc1 in complex with the ant... -

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Basic information

Entry
Database: EMDB / ID: EMD-4286
TitleCryoEM structure of bovine cytochrome bc1 in complex with the anti-malarial compound GSK932121
Map dataCryoEM map of bovine cytochrome bc1 in complex with antimalarial inhibitor GSK932121.
Sample
  • Complex: Cytochrome bc1 in complex with the antimalarial inhibitor GSK932121
    • Protein or peptide: x 10 types
  • Ligand: x 3 types
KeywordsCryo-EM / Inhibitor binding / Membrane protein / cytochrome bc1
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / hypothalamus development / midbrain development / ubiquinone binding / respiratory electron transport chain / hippocampus development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
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 / Cytochrome b-c1 complex subunit 9 / 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 family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJohnson RM / Amporndanai K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust109158/B/15/Z United Kingdom
CitationJournal: IUCrJ / Year: 2018
Title: X-ray and cryo-EM structures of inhibitor-bound cytochrome complexes for structure-based drug discovery.
Authors: Kangsa Amporndanai / Rachel M Johnson / Paul M O'Neill / Colin W G Fishwick / Alexander H Jamson / Shaun Rawson / Stephen P Muench / S Samar Hasnain / Svetlana V Antonyuk /
Abstract: Cytochrome , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. ...Cytochrome , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome that may be available from parasites, all efforts have been focused on homologous cytochrome complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.
History
DepositionFeb 5, 2018-
Header (metadata) releaseFeb 28, 2018-
Map releaseFeb 28, 2018-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.114
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.114
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fo0
  • Surface level: 0.114
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4286.png

Downloads & links

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Map

FileDownload / File: emd_4286.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of bovine cytochrome bc1 in complex with antimalarial inhibitor GSK932121.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 213. Å		1.07 Å/pix.
x 200 pix.
= 213. Å		1.07 Å/pix.
x 200 pix.
= 213. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114 / Movie #1: 0.114
Minimum - Maximum-0.279474 - 0.6473155
Average (Standard dev.)0.007950289 (±0.03478431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 213.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z213.000213.000213.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2790.6470.008

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Supplemental data

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Additional map: Unsharpened map of bc1 in complex with GSK932121

Fileemd_4286_additional.map
AnnotationUnsharpened map of bc1 in complex with GSK932121
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of bc1 in complex with GSK932121

Fileemd_4286_half_map_1.map
AnnotationHalf map of bc1 in complex with GSK932121
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map of bc1 in complex with GSK932121

Fileemd_4286_half_map_2.map
AnnotationSecond half map of bc1 in complex with GSK932121
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cytochrome bc1 in complex with the antimalarial inhibitor GSK932121

EntireName: Cytochrome bc1 in complex with the antimalarial inhibitor GSK932121
Components
  • Complex: Cytochrome bc1 in complex with the antimalarial inhibitor GSK932121
    • 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
    • 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 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Cytochrome b-c1 complex subunit 6, mitochondrial
    • Protein or peptide: Chain I/V
    • Protein or peptide: Cytochrome b-c1 complex subunit 9
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol
  • Ligand: HEME C

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Supramolecule #1: Cytochrome bc1 in complex with the antimalarial inhibitor GSK932121

SupramoleculeName: Cytochrome bc1 in complex with the antimalarial inhibitor GSK932121
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Heart / Location in cell: Mitochondria
Molecular weightTheoretical: 480 KDa

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

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 52.79641 KDa
SequenceString: MAASAVCRAA GAGTRVLLRT RRSPALLRSS DLRGTATYAQ ALQSVPETQV SQLDNGLRVA SEQSSQPTCT VGVWIDAGSR YESEKNNGA GYFVEHLAFK GTKNRPGNAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLAD IVQNCSLEDS Q IEKERDVI ...String:
MAASAVCRAA GAGTRVLLRT RRSPALLRSS DLRGTATYAQ ALQSVPETQV SQLDNGLRVA SEQSSQPTCT VGVWIDAGSR YESEKNNGA GYFVEHLAFK GTKNRPGNAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLAD IVQNCSLEDS Q IEKERDVI LQELQENDTS MRDVVFNYLH ATAFQGTPLA QSVEGPSENV RKLSRADLTE YLSRHYKAPR MVLAAAGGLE HR QLLDLAQ KHFSGLSGTY DEDAVPTLSP CRFTGSQICH REDGLPLAHV AIAVEGPGWA HPDNVALQVA NAIIGHYDCT YGG GAHLSS PLASIAATNK LCQSFQTFNI CYADTGLLGA HFVCDHMSID DMMFVLQGQW MRLCTSATES EVLRGKNLLR NALV SHLDG TTPVCEDIGR SLLTYGRRIP LAEWESRIAE VDARVVREVC SKYFYDQCPA VAGFGPIEQL PDYNRIRSGM FWLRF

UniProtKB: Cytochrome b-c1 complex subunit 1, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 48.204418 KDa
SequenceString: MKLLTRAGSL SRFYSLKVAP KVKATEAPAG VPPHPQDLEF TRLPNGLVIA SLENYAPASR IGLFIKAGSR YENSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTSTRENM AYTVECLRDD VDILMEFLLN VTTAPEFRRW EVAALQPQLR I DKAVALQN ...String:
MKLLTRAGSL SRFYSLKVAP KVKATEAPAG VPPHPQDLEF TRLPNGLVIA SLENYAPASR IGLFIKAGSR YENSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTSTRENM AYTVECLRDD VDILMEFLLN VTTAPEFRRW EVAALQPQLR I DKAVALQN PQAHVIENLH AAAYRNALAN SLYCPDYRIG KVTPVELHDY VQNHFTSARM ALIGLGVSHP VLKQVAEQFL NI RGGLGLS GAKAKYHGGE IREQNGDSLV HAALVAESAA IGSAEANAFS VLQHVLGAGP HVKRGSNATS SLYQAVAKGV HEP FDVSAF NASYSDSGLF GFYTISQAAS AGDVIKAAYN QVKTIAQGNL SNPDVQAAKN KLKAGYLMSV ESSEGFLDEV GSQA LAAGS YTPPSTVLQQ IDAVADADVI NAAKKFVSGR KSMAASGNLG HTPFIDEL

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

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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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 42.62034 KDa
SequenceString: MTNIRKSHPL MKIVNNAFID LPAPSNISSW WNFGSLLGIC LILQILTGLF LAMHYTSDTT TAFSSVTHIC RDVNYGWIIR YMHANGASM FFICLYMHVG RGLYYGSYTF LETWNIGVIL LLTVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTN L VEWIWGGF ...String:
MTNIRKSHPL MKIVNNAFID LPAPSNISSW WNFGSLLGIC LILQILTGLF LAMHYTSDTT TAFSSVTHIC RDVNYGWIIR YMHANGASM FFICLYMHVG RGLYYGSYTF LETWNIGVIL LLTVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTN L VEWIWGGF SVDKATLTRF FAFHFILPFI IMAIAMVHLL FLHETGSNNP TGISSDVDKI PFHPYYTIKD ILGALLLILA LM LLVLFAP DLLGDPDNYT PANPLNTPPH IKPEWYFLFA YAILRSIPNK LGGVLALAFS ILILALIPLL HTSKQRSMMF RPL SQCLFW ALVADLLTLT WIGGQPVEHP YITIGQLASV LYFLLILVLM PTAGTIENKL LKW

UniProtKB: Cytochrome b

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Macromolecule #4: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 35.34377 KDa
SequenceString: MAAAAATLRG AMVGPRGAGL PGARARGLLC GARPGQLPLR TPQAVSLSSK SGLSRGRKVI LSALGMLAAG GAGLAVALHS AVSASDLEL HPPSYPWSHR GLLSSLDHTS IRRGFQVYKQ VCSSCHSMDY VAYRHLVGVC YTEDEAKALA EEVEVQDGPN E DGEMFMRP ...String:
MAAAAATLRG AMVGPRGAGL PGARARGLLC GARPGQLPLR TPQAVSLSSK SGLSRGRKVI LSALGMLAAG GAGLAVALHS AVSASDLEL HPPSYPWSHR GLLSSLDHTS IRRGFQVYKQ VCSSCHSMDY VAYRHLVGVC YTEDEAKALA EEVEVQDGPN E DGEMFMRP GKLSDYFPKP YPNPEAARAA NNGALPPDLS YIVRARHGGE DYVFSLLTGY CEPPTGVSLR EGLYFNPYFP GQ AIGMAPP IYNEVLEFDD GTPATMSQVA KDVCTFLRWA AEPEHDHRKR MGLKMLLMMG LLLPLVYAMK RHKWSVLKSR KLA YRPPK

UniProtKB: Cytochrome c1, heme protein, mitochondrial

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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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 29.586842 KDa
SequenceString: MLSVAARSGP FAPVLSATSR GVAGALRPLV QAAVPATSES PVLDLKRSVL CRESLRGQAA GRPLVASVSL NVPASVRYSH TDIKVPDFS DYRRPEVLDS TKSSKESSEA RKGFSYLVTA TTTVGVAYAA KNVVSQFVSS MSASADVLAM SKIEIKLSDI P EGKNMAFK ...String:
MLSVAARSGP FAPVLSATSR GVAGALRPLV QAAVPATSES PVLDLKRSVL CRESLRGQAA GRPLVASVSL NVPASVRYSH TDIKVPDFS DYRRPEVLDS TKSSKESSEA RKGFSYLVTA TTTVGVAYAA KNVVSQFVSS MSASADVLAM SKIEIKLSDI P EGKNMAFK WRGKPLFVRH RTKKEIDQEA AVEVSQLRDP QHDLERVKKP EWVILIGVCT HLGCVPIANA GDFGGYYCPC HG SHYDASG RIRKGPAPLN LEVPSYEFTS DDMVIVG

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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 13.502387 KDa
SequenceString:
MAGRPAVSAS SRWLEGIRKW YYNAAGFNKL GLMRDDTIHE NDDVKEAIRR LPENLYDDRV FRIKRALDLS MRQQILPKEQ WTKYEEDKS YLEPYLKEVI RERKEREEWA KK

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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 9.737223 KDa
SequenceString:
MGRQFGHLTR VRHVITYSLS PFEQRAFPHY FSKGIPNVLR RTRACILRVA PPFVAFYLVY TWGTQEFEKS KRKNPAAYEN DR

UniProtKB: Cytochrome b-c1 complex subunit 8

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Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 10.638744 KDa
SequenceString:
MGLEDEQRML TGSGDPKEEE EEEEELVDPL TTVREQCEQL EKCVKARERL ELCDERVSSR SQTEEDCTEE LLDFLHARDH CVAHKLFNS LK

UniProtKB: Cytochrome b-c1 complex subunit 6, mitochondrial

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Macromolecule #9: Chain I/V

MacromoleculeName: Chain I/V / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 1.81611 KDa
SequenceString:
RPVVASVSLN VPASVRY

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Macromolecule #10: Cytochrome b-c1 complex subunit 9

MacromoleculeName: Cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.469621 KDa
SequenceString:
MVAPTLTARL YSLLFRRTST FALTIVVGAL FFERAFDQGA DAIYEHINEG KLWKHIKHKY ENKE

UniProtKB: Cytochrome b-c1 complex subunit 9

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Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 11 / 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 #12: 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phe...

MacromoleculeName: 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol
type: ligand / ID: 12 / Number of copies: 2 / Formula: G8U
Molecular weightTheoretical: 425.786 Da
Chemical component information

ChemComp-G8U:
3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol

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Macromolecule #13: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 13 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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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

Concentration5.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMTris-HCl
100.0 mMSodium chlorideNaCl
0.5 mMEDTA
0.015 %DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blot for 6 seconds with a blot force of 6 before plunge-freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 8840 / Average exposure time: 1.5 sec. / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 79000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 466865
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5d6u


Details: The pdb file of an existing crystal structure was back-filtered to 60 A.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 232910
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6fo0:
CryoEM structure of bovine cytochrome bc1 in complex with the anti-malarial compound GSK932121

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