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- EMDB-5295: 3D reconstruction of negatively stained PCSK9 in complex with a Fab -

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Basic information

Entry
Database: EMDB / ID: 5295
Title3D reconstruction of negatively stained PCSK9 in complex with a Fab
KeywordsPCSK9-Fab complex
Samplehuman PCSK9 in complex with a Fab
SourceHomo sapiens / human
Map data3D reconstruction of negatively stained PCSK9-Fab complex
Methodsingle particle reconstruction, at 25 A resolution
AuthorsWu S / Avila-Sakar A / Kim J / Booth DS / Greenberg CH / Rossi A / Liao M / Alian A / Griner SL / Juge N / Mergel CM / Chaparro-Riggers J / Strop P / Tampe R / Edwards RH / Stroud RM / Craik CS / Cheng Y
CitationStructure, 2012, 20, 582-592

Structure, 2012, 20, 582-592 StrPapers
Fabs enable single particle cryoEM studies of small proteins.
Shenping Wu / Agustin Avila-Sakar / JungMin Kim / David S Booth / Charles H Greenberg / Andrea Rossi / Maofu Liao / Xueming Li / Akram Alian / Sarah L Griner / Narinobu Juge / Yadong Yu / Claudia M Mergel / Javier Chaparro-Riggers / Pavel Strop / Robert Tampé / Robert H Edwards / Robert M Stroud / Charles S Craik / Yifan Cheng

DateDeposition: May 23, 2011 / Header (metadata) release: Oct 26, 2011 / Map release: May 29, 2012 / Last update: May 23, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
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Slabnear <=> far

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Orientation
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Supplemental images

Downloads & links

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Map

Fileemd_5295.map.gz (map file in CCP4 format, 845 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
4.26 A/pix
= 255.6 A
60 pix
4.26 A/pix
= 255.6 A
60 pix
4.26 A/pix
= 255.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.26 A
Density
Contour Level:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum-0.82391357 - 3.13429093
Average (Standard dev.)0.00072357 (0.1562008)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin000
Limit595959
Spacing606060
CellA=B=C: 255.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.264.264.26
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z255.600255.600255.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-0.8243.1340.001

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Supplemental data

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Sample components

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Entire human PCSK9 in complex with a Fab

EntireName: human PCSK9 in complex with a Fab / Number of components: 2 / Oligomeric State: monomer
MassTheoretical: 120 kDa / Experimental: 120 kDa

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Component #1: protein, PCSK9

ProteinName: PCSK9 / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 2
MassTheoretical: 120 kDa / Experimental: 120 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Support film200 mesh copper grid
Staininguranyl formate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 30 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: each particle / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.5 nm
Specimen HolderHolder: single tilt / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 60 deg.
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3876 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Fourier space / Software: Frealign / CTF correction: each particle / Resolution: 25 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 2PMW

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