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- EMDB-21045: Cryo-EM map of human symplekin CTD -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-21045
TitleCryo-EM map of human symplekin CTD
Map datahuman symplekin_CTD
Sample
  • Complex: The Symplekin C-terminal domain in histone cleavage complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsSun Y / Zhang Y / Walz T / Tong L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR35GM118093 United States
National Institutes of Health/National Institute of General Medical SciencesR01GM029832 United States
CitationJournal: Science / Year: 2020
Title: Structure of an active human histone pre-mRNA 3'-end processing machinery.
Authors: Yadong Sun / Yixiao Zhang / Wei Shen Aik / Xiao-Cui Yang / William F Marzluff / Thomas Walz / Zbigniew Dominski / Liang Tong /
Abstract: The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with ...The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with the canonical cleavage and polyadenylation machinery. We reconstituted an active human histone pre-mRNA processing machinery using 13 recombinant proteins and two RNAs and determined its structure by cryo-electron microscopy. The overall structure is highly asymmetrical and resembles an amphora with one long handle. We captured the pre-mRNA in the active site of the endonuclease, the 73-kilodalton subunit of the cleavage and polyadenylation specificity factor, poised for cleavage. The endonuclease and the entire cleavage module undergo extensive rearrangements for activation, triggered through the recognition of the duplex between the authentic pre-mRNA and U7 small nuclear RNA (snRNA). Our study also has notable implications for understanding canonical and snRNA 3'-end processing.
History
DepositionNov 28, 2019-
Header (metadata) releaseMar 4, 2020-
Map releaseMar 4, 2020-
UpdateMar 4, 2020-
Current statusMar 4, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0144
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0144
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21045.png

Downloads & links

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Map

FileDownload / File: emd_21045.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman symplekin_CTD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 334 pix.
= 357.38 Å		1.07 Å/pix.
x 334 pix.
= 357.38 Å		1.07 Å/pix.
x 334 pix.
= 357.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0144 / Movie #1: 0.0144
Minimum - Maximum-0.01852024 - 0.05167114
Average (Standard dev.)-0.00001601711 (±0.0014982913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 357.38 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z334334334
origin x/y/z0.0000.0000.000
length x/y/z357.380357.380357.380
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS334334334
D min/max/mean-0.0190.052-0.000

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Supplemental data

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Sample components

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Entire : The Symplekin C-terminal domain in histone cleavage complex

EntireName: The Symplekin C-terminal domain in histone cleavage complex
Components
  • Complex: The Symplekin C-terminal domain in histone cleavage complex

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Supramolecule #1: The Symplekin C-terminal domain in histone cleavage complex

SupramoleculeName: The Symplekin C-terminal domain in histone cleavage complex
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
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

Concentration0.3 mg/mL
BufferpH: 7.5 / Component - Concentration: 100.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 70.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 73.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.8 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
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

Image recording ID1
CTF correctionSoftware - Name: CTFFIND
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 19315
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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