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- EMDB-0598: Structure of a drug-like molecule stalled ribosome nascent chain ... -

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Basic information

Entry
Database: EMDB / Id: 598
TitleStructure of a drug-like molecule stalled ribosome nascent chain complex (PCSK9_RNC) in non-rotated state with PP tRNA
Map dataPF846 stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA. Map is sharpened.
SampleDrug-like molecule stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA:
nucleic-acidNucleic acid
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLi W / Cate JHD
CitationJournal: To be Published
Title: Structure of a drug-like molecule stalled PCSK9 ribosome nascent chain complex (PCSK9_RNC) in non-rotated state with PP tRNA
P-authors: Li W / Cate JHD
DateDeposition: Feb 21, 2019 / Header (metadata) release: Mar 20, 2019 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019

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Strvis

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

emd_0598.png

Downlink

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Map

Fileemd_0598.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.15 Å/pix.
= 460. Å		400 pix
1.15 Å/pix.
= 460. Å		400 pix
1.15 Å/pix.
= 460. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.022 (by author), 0.024 (movie #1):
Minimum - Maximum-0.057956874 - 0.10376459
Average (Standard dev.)0.000268779 (0.007156887)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 460.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z460.000460.000460.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0580.1040.000

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Supplemental data

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Sample components

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Entire Drug-like molecule stalled human ribosome nascent chain complex (...

EntireName: Drug-like molecule stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA
Number of components: 2

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Component #1: protein, Drug-like molecule stalled human ribosome nascent chain ...

ProteinName: Drug-like molecule stalled human ribosome nascent chain complex (PCSK9-RNC) in non-rotated state with PP tRNA
Recombinant expression: No
MassTheoretical: 4.3 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HeLa

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Component #2: nucleic-acid, human ribosome with nascent chain

Nucleic-acidName: human ribosome with nascent chain / Class: RNA
Details: Nascent chain sequence including CDH1 domain V and PCSK9 1-35
Structure: OTHER / Synthetic: No
Sequence:
SDVNDNAPIP EPRTIFFCER NPKPQVINII DADLPPNTSP FTAELTHGAS ANWTIQYNDP TQESIILKPK MALEVGDYKI NLKLMDNQNK DQVTTLEVSV CDCEGAAGVC RKAQPVEAGL QIPAILGILG MGTVSSRRSW WPLPLLLLLL LLLGPAGARA QEDED
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionPh: 7.8
Support filmunspecified
VitrificationCryogen name: ETHANE / Temperature: 4 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7214
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 80

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