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- EMDB-11017: CTC-primase, body 1 (contains primase, CIAO1, CIAO2B, MMS19 CTD) -

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Basic information

Entry
Database: EMDB / ID: EMD-11017
TitleCTC-primase, body 1 (contains primase, CIAO1, CIAO2B, MMS19 CTD)
Map data
Sample
  • Complex: MMS19-CIAO1-CIAO2B-primase complex
    • Complex: MMS19 CTD-CIAO1-CIAO2B CIA targeting complex
    • Complex: Primase
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsKassube SA / Thomae N
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 871-2014 Switzerland
European Research Council (ERC)666068 Switzerland
Swiss National Science FoundationCRSII3_160734 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structural insights into Fe-S protein biogenesis by the CIA targeting complex.
Authors: Susanne A Kassube / Nicolas H Thomä /
Abstract: The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. ...The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. The molecular mechanisms of client protein recognition and Fe-S cluster transfer remain unknown. Here, we report crystal structures of the CIA targeting complex (CTC), revealing that its CIAO2B subunit is centrally located and bridges CIAO1 and the client adaptor protein MMS19. Cryo-EM reconstructions of human CTC bound either to the DNA replication factor primase or to the DNA helicase DNA2, combined with biochemical, biophysical and yeast complementation assays, reveal an evolutionarily conserved, bipartite client recognition mode facilitated by CIAO1 and the structural flexibility of the MMS19 subunit. Unexpectedly, the primase Fe-S cluster is located ~70 Å away from the CTC reactive cysteine, implicating conformational dynamics of the CTC or additional maturation factors in the mechanism of Fe-S cluster transfer.
History
DepositionMay 9, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11017.png

Downloads & links

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Map

FileDownload / File: emd_11017.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.74 Å
Density
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.038803086 - 0.096690126
Average (Standard dev.)0.00042705203 (±0.0036799116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 306.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.741.741.74
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z306.240306.240306.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS176176176
D min/max/mean-0.0390.0970.000

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Supplemental data

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Sample components

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Entire : MMS19-CIAO1-CIAO2B-primase complex

EntireName: MMS19-CIAO1-CIAO2B-primase complex
Components
  • Complex: MMS19-CIAO1-CIAO2B-primase complex
    • Complex: MMS19 CTD-CIAO1-CIAO2B CIA targeting complex
    • Complex: Primase

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Supramolecule #1: MMS19-CIAO1-CIAO2B-primase complex

SupramoleculeName: MMS19-CIAO1-CIAO2B-primase complex / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 164.211 KDa

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Supramolecule #2: MMS19 CTD-CIAO1-CIAO2B CIA targeting complex

SupramoleculeName: MMS19 CTD-CIAO1-CIAO2B CIA targeting complex / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: Primase

SupramoleculeName: Primase / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration0.3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

11016

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42382
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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