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- EMDB-11020: CTC-DNA2, body 1 (contains DNA2, CIAO1, CIAO2B, and the CTD of MMS19) -

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Basic information

Entry
Database: EMDB / ID: EMD-11020
TitleCTC-DNA2, body 1 (contains DNA2, CIAO1, CIAO2B, and the CTD of MMS19)
Map data
Sample
  • Complex: MMS19(CTD)-CIAO1-CIAO2B-DNA2 complex
    • Complex: MMS19-CIAO1-CIAO2B CIA targeting complex
    • Complex: DNA2
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.2 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 10, 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: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11020.png

Downloads & links

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Map

FileDownload / File: emd_11020.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.01597349 - 0.036642097
Average (Standard dev.)0.0000872201 (±0.0011015588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0160.0370.000

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Supplemental data

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Sample components

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Entire : MMS19(CTD)-CIAO1-CIAO2B-DNA2 complex

EntireName: MMS19(CTD)-CIAO1-CIAO2B-DNA2 complex
Components
  • Complex: MMS19(CTD)-CIAO1-CIAO2B-DNA2 complex
    • Complex: MMS19-CIAO1-CIAO2B CIA targeting complex
    • Complex: DNA2

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Supramolecule #1: MMS19(CTD)-CIAO1-CIAO2B-DNA2 complex

SupramoleculeName: MMS19(CTD)-CIAO1-CIAO2B-DNA2 complex / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 119.447 KDa

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

SupramoleculeName: MMS19-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: DNA2

SupramoleculeName: DNA2 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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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

Concentration0.4 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.9 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69894
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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