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- EMDB-39339: Cryo-EM structure of the human DSS1-INTAC-PEC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39339
TitleCryo-EM structure of the human DSS1-INTAC-PEC complex
Map datalocal resolution filtered map using Relion
Sample
  • Complex: DSS1-INTAC-PEC
KeywordsDSS1 / Integrator / INTAC / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsZheng H / Xu Y / Cheng J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Stabilization of Integrator/INTAC by the small but versatile DSS1 protein.
Authors: Xu C / Zhou Q / Zheng H / Song A / Zhao W / Xiong Y / Huang Z / Xu Y / Cheng J / Chen FX
History
DepositionMar 1, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39339.png

Downloads & links

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Map

FileDownload / File: emd_39339.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered map using Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 420 pix.
= 442.68 Å		1.05 Å/pix.
x 420 pix.
= 442.68 Å		1.05 Å/pix.
x 420 pix.
= 442.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.05341603 - 0.14230254
Average (Standard dev.)0.0008607928 (±0.005888014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 442.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: multibody refined map focusing on PEC module filtered by deepEMhancer

Fileemd_39339_additional_1.map
Annotationmultibody refined map focusing on PEC module filtered by deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: multibody refined map focusing on INTAC phosphatase module...

Fileemd_39339_additional_2.map
Annotationmultibody refined map focusing on INTAC phosphatase module filtered by deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: multibody refined map focusing on INTAC endonuclease module...

Fileemd_39339_additional_3.map
Annotationmultibody refined map focusing on INTAC endonuclease module filtered by deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: this is a composite map derived from multibody refinement

Fileemd_39339_additional_4.map
Annotationthis is a composite map derived from multibody refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: multibody refined map focusing on INTAC core module...

Fileemd_39339_additional_5.map
Annotationmultibody refined map focusing on INTAC core module filtered by deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: consensus map without post process

Fileemd_39339_additional_6.map
Annotationconsensus map without post process
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39339_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39339_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DSS1-INTAC-PEC

EntireName: DSS1-INTAC-PEC
Components
  • Complex: DSS1-INTAC-PEC

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Supramolecule #1: DSS1-INTAC-PEC

SupramoleculeName: DSS1-INTAC-PEC / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 843523
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ycx

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 26822
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
Final angle assignmentType: OTHER / Software - Name: RELION / Details: relion
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ycx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model


PDB Unreleased entry

PDB-9vd9:
Cryo-EM structure of the human DSS1-INTAC-PEC complex

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