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- EMDB-48370: RECQL5 and RNA polymerase II map U -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48370
TitleRECQL5 and RNA polymerase II map U
Map dataRECQL5 and RNA polymerase II map U
Sample
  • Complex: RECQL5-RNA polymerase II complex
    • Complex: RNA polymerase II
    • Complex: RECQL5
KeywordsHelicase / transcription / polymerase
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSyau D / Steinruecke F / Farnung L
Funding support United States, 4 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research Foundation United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)DP2-ES036404 United States
Richard and Susan Smith Family Foundation United States
National Science Foundation (NSF, United States)DGE 2140743 United States
CitationJournal: To Be Published
Title: Structure and function of IWS1 in transcription elongation
Authors: Syau D / Steinruecke F / Farnung L
History
DepositionDec 19, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48370.png

Downloads & links

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Map

FileDownload / File: emd_48370.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRECQL5 and RNA polymerase II map U
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 350 pix.
= 385. Å		1.1 Å/pix.
x 350 pix.
= 385. Å		1.1 Å/pix.
x 350 pix.
= 385. 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: 0.16
Minimum - Maximum-0.22163509 - 0.5821998
Average (Standard dev.)0.0005422579 (±0.020991696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 385.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: RECQL5-Pol II Half map QA

Fileemd_48370_half_map_1.map
AnnotationRECQL5-Pol II Half map QA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RECQL5-Pol II half map QB

Fileemd_48370_half_map_2.map
AnnotationRECQL5-Pol II half map QB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RECQL5-RNA polymerase II complex

EntireName: RECQL5-RNA polymerase II complex
Components
  • Complex: RECQL5-RNA polymerase II complex
    • Complex: RNA polymerase II
    • Complex: RECQL5

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Supramolecule #1: RECQL5-RNA polymerase II complex

SupramoleculeName: RECQL5-RNA polymerase II complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: RECQL5

SupramoleculeName: RECQL5 / type: complex / ID: 3 / Parent: 1
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
Component:
ConcentrationFormulaName
20.0 mMHEPES(2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid)
150.0 mMNaClsodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
3.0 mMMgCl2magnesium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.038 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 227 / Average exposure time: 3.99 sec. / Average electron dose: 13.045 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 52539
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15305
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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