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- EMDB-12706: Murine CIII2 focus-refined from supercomplex CICIII2 -

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Basic information

Entry
Database: EMDB / ID: EMD-12706
TitleMurine CIII2 focus-refined from supercomplex CICIII2
Map datamurine CIII2 focus-refined from CICIII2
Sample
  • Complex: Murine complex CIII2 focus-refined from supercomplex CICIII2
    • Protein or peptide: x 11 types
  • Ligand: x 6 types
Keywordsmitochondria / respiratory chain / supercomplex / OXIDOREDUCTASE / complex III / complex IV / MEMBRANE PROTEIN
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / Respiratory electron transport / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex III ...Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / Respiratory electron transport / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex III / Mitochondrial protein degradation / : / : / response to alkaloid / quinol-cytochrome-c reductase / response to copper ion / ubiquinol-cytochrome-c reductase activity / response to glucagon / cellular respiration / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / electron transport coupled proton transport / response to hyperoxia / animal organ regeneration / response to cadmium ion / response to hormone / respiratory electron transport chain / hippocampus development / response to activity / mitochondrial membrane / metalloendopeptidase activity / response to toxic substance / 2 iron, 2 sulfur cluster binding / response to calcium ion / myelin sheath / response to ethanol / mitochondrial inner membrane / response to hypoxia / oxidoreductase activity / response to xenobiotic stimulus / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / 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 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 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 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsVercellino I / Sazanov LA
Funding support Austria, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission754411 Austria
CitationJournal: Nature / Year: 2021
Title: Structure and assembly of the mammalian mitochondrial supercomplex CIIICIV.
Authors: Irene Vercellino / Leonid A Sazanov /
Abstract: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is ...The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is debated. Supercomplexes CIIICIV (refs. ), CICIII (ref. ) and CICIIICIV (respirasome) exist in mammals, but in contrast to CICIII and the respirasome, to date the only known eukaryotic structures of CIIICIV come from Saccharomyces cerevisiae and plants, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIIICIV and its assembly intermediates, in different conformations. We describe the assembly of CIIICIV from the CIII precursor to the final CIIICIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. ) deep into CIII, while its C terminus is integrated into CIV. Our structures (which include CICIII and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIIICIV and has no role in the assembly of the respirasome. We show that CIII is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII, explaining the presence of one copy of CIV in CIIICIV in mammals. Finally, we show that CIII and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIIICIV in fine tuning the efficiency of electron transfer in the electron transport chain.
History
DepositionApr 1, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
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: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-7o3h
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12706.png

Downloads & links

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Map

FileDownload / File: emd_12706.map.gz / Format: CCP4 / Size: 77.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmurine CIII2 focus-refined from CICIII2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.5 Å/pix.
x 243 pix.
= 121.455 Å		0.5 Å/pix.
x 257 pix.
= 128.452 Å		0.5 Å/pix.
x 325 pix.
= 162.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.49981 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.08931874 - 0.3091969
Average (Standard dev.)0.014097222 (±0.028675193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions257325243
Spacing243257325
CellA: 121.4548 Å / B: 128.4522 Å / C: 162.43954 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.499814814814810.499813229571980.49981538461538
M x/y/z243257325
origin x/y/z0.0000.0000.000
length x/y/z121.455128.452162.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ243257325
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS325257243
D min/max/mean-0.0890.3090.014

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Supplemental data

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Sample components

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Entire : Murine complex CIII2 focus-refined from supercomplex CICIII2

EntireName: Murine complex CIII2 focus-refined from supercomplex CICIII2
Components
  • Complex: Murine complex CIII2 focus-refined from supercomplex CICIII2
    • 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: Cytochrome b-c1 complex subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
    • Protein or peptide: Cytochrome b-c1 complex subunit 9
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CARDIOLIPIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Murine complex CIII2 focus-refined from supercomplex CICIII2

SupramoleculeName: Murine complex CIII2 focus-refined from supercomplex CICIII2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 / Details: Dimer of Complex III
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD1 / Organ: heart / Tissue: cardiac muscle / Organelle: mitochondria / Location in cell: inner mitochondrial membrane
Molecular weightTheoretical: 500 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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 49.355301 KDa
SequenceString: TATFAQALQS VPETQVSILD NGLRVASEQS SHATCTVGVW IDAGSRYETE KNNGAGYFLE HLAFKGTKNR PGNALEKEVE SIGAHLNAY STREHTAYLI KALSKDLPKV VELLADIVQN SSLEDSQIEK ERDVILREMQ ENDASMQNVV FDYLHATAFQ G TPLAQAVE ...String:
TATFAQALQS VPETQVSILD NGLRVASEQS SHATCTVGVW IDAGSRYETE KNNGAGYFLE HLAFKGTKNR PGNALEKEVE SIGAHLNAY STREHTAYLI KALSKDLPKV VELLADIVQN SSLEDSQIEK ERDVILREMQ ENDASMQNVV FDYLHATAFQ G TPLAQAVE GPSENVRRLS RTDLTDYLNR HYKAPRMVLA AAGGVEHQQL LDLAQKHLSS VSRVYEEDAV PGLTPCRFTG SE IRHRDDA LPLAHVAIAV EGPGWANPDN VTLQVANAII GHYDCTYGGG VHLSSPLASV AVANKLCQSF QTFNISYSDT GLL GAHFVC DAMSIDDMVF FLQGQWMRLC TSATESEVTR GKNILRNALV SHLDGTTPVC EDIGRSLLTY GRRIPLAEWE SRIQ EVDAQ MLRDICSKYF YDQCPAVAGY GPIEQLPDYN RIRSGMFWLR F

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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 46.641773 KDa
SequenceString: SLKVAPKVKT SAAPGGVPLQ PQDLEFTKLP NGLVIASLEN YAPLSRIGLF VKAGSRYEDS NNLGTSHLLR LASSLTTKGA SSFKITRGI EAVGGKLSVT ATRENMAYTV EGIRSDIEIL MEFLLNVTTA PEFRRWEVAA LRSQLKIDKA VAFQNSQTRI I ENLHDVAY ...String:
SLKVAPKVKT SAAPGGVPLQ PQDLEFTKLP NGLVIASLEN YAPLSRIGLF VKAGSRYEDS NNLGTSHLLR LASSLTTKGA SSFKITRGI EAVGGKLSVT ATRENMAYTV EGIRSDIEIL MEFLLNVTTA PEFRRWEVAA LRSQLKIDKA VAFQNSQTRI I ENLHDVAY KNALANPLYC PDYRMGKITS EELHYFVQNH FTSARMALVG LGVSHSVLKQ VAEQFLNMRG GLGLAGAKAK YR GGEIREQ NGDNLVHAAI VAESAAIGNA EANAFSVLQH LLGAGPHIKR GNNTTSLLSQ SVAKGSHQPF DVSAFNASYS DSG LFGIYT ISQAAAAGEV INAAYNQVKA VAQGNLSSAD VQAAKNKLKA GYLMSVETSE GFLSEIGSQA LAAGSYMPPS TVLQ QIDSV ADADVVKAAK KFVSGKKSMA ASGNLGHTPF LDEL

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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 43.240305 KDa
SequenceString: MTNMRKTHPL FKIINHSFID LPAPSNISSW WNFGSLLGVC LMVQIITGLF LAMHYTSDTM TAFSSVTHIC RDVNYGWLIR YMHANGASM FFICLFLHVG RGLYYGSYTF METWNIGVLL LFAVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTT L VEWIWGGF ...String:
MTNMRKTHPL FKIINHSFID LPAPSNISSW WNFGSLLGVC LMVQIITGLF LAMHYTSDTM TAFSSVTHIC RDVNYGWLIR YMHANGASM FFICLFLHVG RGLYYGSYTF METWNIGVLL LFAVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTT L VEWIWGGF SVDKATLTRF FAFHFILPFI IAALAIVHLL FLHETGSNNP TGLNSDADKI PFHPYYTIKD ILGILIMFLI LM TLVLFFP DMLGDPDNYM PANPLNTPPH IKPEWYFLFA YAILRSIPNK LGGVLALILS ILILALMPFL HTSKQRSLMF RPI TQILYW ILVANLLILT WIGGQPVEHP FIIIGQLASI SYFSIILILM PISGIIEDKM LKLYP

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 / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 27.312188 KDa
SequenceString: SDLELHPPSY PWSHRGLLSS LDHTSIRRGF QVYKQVCSSC HSMDYVAYRH LVGVCYTEEE AKALAEEVEV QDGPNDDGEM FMRPGKLSD YFPKPYPNPE AARAANNGAL PPDLSYIVRA RHGGEDYVFS LLTGYCEPPT GVSLREGLYF NPYFPGQAIG M APPIYTEV ...String:
SDLELHPPSY PWSHRGLLSS LDHTSIRRGF QVYKQVCSSC HSMDYVAYRH LVGVCYTEEE AKALAEEVEV QDGPNDDGEM FMRPGKLSD YFPKPYPNPE AARAANNGAL PPDLSYIVRA RHGGEDYVFS LLTGYCEPPT GVSLREGLYF NPYFPGQAIG M APPIYTEV LEYDDGTPAT MSQVAKDVAT FLRWASEPEH DHRKRMGLKM LLMMGLLLPL TYAMKRHKWS VLKSRKLAYR PP K

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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 21.524398 KDa
SequenceString: SHTDVKVPDF SDYRRAEVLD STKSSKESSE ARKGFSYLVT ATTTVGVAYA AKNVVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLDRVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS ...String:
SHTDVKVPDF SDYRRAEVLD STKSSKESSE ARKGFSYLVT ATTTVGVAYA AKNVVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLDRVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS GRIRKGPAPL NLEVPAYEFT SDDVVVVG

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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 13.456336 KDa
SequenceString:
AGRSAVSASS KWLDGFRKWY YNAAGFNKLG LMRDDTLHET EDVKEAIRRL PEDLYNDRMF RIKRALDLTM RHQILPKDQW TKYEEDKFY LEPYLKEVIR ERKEREEWAK K

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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 9.652051 KDa
SequenceString:
GREFGNLARI RHVISYSLSP FEQRAFPSYF SKGIPNVLRR TRERILRVAP PFVVVYLIYT WGNQEFEQSK RKNPAMYEND K

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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 9.002015 KDa
SequenceString:
GDPKEEEEEE LVDPLTTVRE HCEQLEKCVK ARERLELCDN RVSSRSQTEE DCTEELFDFL HARDHCVAHK LFKNLK

UniProtKB: Cytochrome b-c1 complex subunit 6, mitochondrial

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Macromolecule #9: Cytochrome b-c1 complex subunit 9

MacromoleculeName: Cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 7.32633 KDa
SequenceString:
SSPTIPSRLY SLLFRRTSTF ALTIAVGALF FERAFDQGAD AIYEHINEGK LWKHIKHKYE NKE

UniProtKB: Cytochrome b-c1 complex subunit 9

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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: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 6.546627 KDa
SequenceString:
MLSRFLGPRY RELARNWIPT AGMWGTVGAV GLVWATDWRL ILDWVPYING KFKKDD

UniProtKB: Cytochrome b-c1 complex subunit 10

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Macromolecule #11: Cytochrome b-c1 complex subunit 9

MacromoleculeName: Cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Organ: heart
Molecular weightTheoretical: 7.900234 KDa
SequenceString:
MLSVAARSGP FAPVLSATSR GVAGALRPLL QGAVPAASEP PVLDVKRPFL CRESLSGQAA ARPLVATVGL NVPASVRF

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #12: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 12 / Number of copies: 8 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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Macromolecule #13: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 13 / Number of copies: 6 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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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: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 15 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 16 / 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 #17: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 17 / 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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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: 7.7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
2.0 mMC10H16N2O8EDTA
0.2 %C32H58N2O7SCHAPS

Details: CHAPS was added only upon freezing
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: 7245 / Average exposure time: 1.17 sec. / Average electron dose: 90.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 75000
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: 1500000
Details: multiple rounds of picking and classification performed, first with Relion LoG and then with Topaz, to extract the best particles from the non-pure starting material
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6qbx


Details: PDB 6qbx used for initial classification of CICIII2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: the final pool of particles was classified without alignment around the MPP cavity to separate the two orientations of Sub 9. the two classes were then refined, first globally and then ...Details: the final pool of particles was classified without alignment around the MPP cavity to separate the two orientations of Sub 9. the two classes were then refined, first globally and then focused on CIII, re-oriented along the C2 symmetry axis, to allow for subsequent 180 degrees flipping of one class and final re-pooled refinement with all particles having the same orientation of Sub 9
Number images used: 129
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 116400 / Software - Name: RELION (ver. 3.1)
Details: the particles were not evenly distributed in the classes. the good class contained 129k particles
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1ntz

source_name: PDB, initial_model_type: experimental model

3l75

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 65 / Target criteria: MAXIMAL LIKELIHOOD
Output model

PDB-7o3h:
Murine CIII2 focus-refined from supercomplex CICIII2

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

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