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- EMDB-5158: Model of human low density lipoprotein and bound receptor based o... -

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Basic information

Entry
Database: EMDB / ID: EMD-5158
TitleModel of human low density lipoprotein and bound receptor based on CryoEM
Map dataLDLrLDL receptor
Sample
  • Sample: LDLrLDL receptor
  • Organelle or cellular component: LDLrLDL receptor
KeywordsLDL / Apolipoprotein B-100 / Cholesteryl ester / Electron CryoMicroscopy / LDL receptor
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 28.0 Å
AuthorsRen G / Rudenko G / Ludtke SJ / Deisenhofer J / Chiu W / Pownall HJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Model of human low-density lipoprotein and bound receptor based on cryoEM.
Authors: Gang Ren / Gabby Rudenko / Steven J Ludtke / Johann Deisenhofer / Wah Chiu / Henry J Pownall /
Abstract: Human plasma low-density lipoproteins (LDL), a risk factor for cardiovascular disease, transfer cholesterol from plasma to liver cells via the LDL receptor (LDLr). Here, we report the structures of ...Human plasma low-density lipoproteins (LDL), a risk factor for cardiovascular disease, transfer cholesterol from plasma to liver cells via the LDL receptor (LDLr). Here, we report the structures of LDL and its complex with the LDL receptor extracellular domain (LDL.LDLr) at extracellular pH determined by cryoEM. Difference imaging between LDL.LDLr and LDL localizes the site of LDLr bound to its ligand. The structural features revealed from the cryoEM map lead to a juxtaposed stacking model of cholesteryl esters (CEs). High density in the outer shell identifies protein-rich regions that can be accounted for by a single apolipoprotein (apo B-100, 500 kDa) leading to a model for the distribution of its alpha-helix and beta-sheet rich domains across the surface. The structural relationship between the apo B-100 and CEs appears to dictate the structural stability and function of normal LDL.
History
DepositionDec 17, 2009-
Header (metadata) releaseJan 22, 2010-
Map releaseJan 28, 2010-
UpdateNov 9, 2016-
Current statusNov 9, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5158.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLDLr
Voxel sizeX=Y=Z: 5.34375 Å
Density
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum0.0 - 2.09259105
Average (Standard dev.)0.04653585 (±0.22311571)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 513.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.343755.343755.34375
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z513.000513.000513.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
D min/max/mean-0.0002.0930.047

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Supplemental data

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Sample components

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Entire : LDLr

EntireName: LDLrLDL receptor
Components
  • Sample: LDLrLDL receptor
  • Organelle or cellular component: LDLrLDL receptor

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Supramolecule #1000: LDLr

SupramoleculeName: LDLr / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 2.6 MDa / Theoretical: 2.6 MDa

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Supramolecule #1: LDLr

SupramoleculeName: LDLr / type: organelle_or_cellular_component / ID: 1 / Name.synonym: LDL / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human / Organelle: plasma
Molecular weightExperimental: 2.6 MDa / Theoretical: 2.6 MDa

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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

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 50mM Tris-HCl buffer, 150 mM NaCl, pH 7.5
GridDetails: Cu 400 mesh holey
VitrificationCryogen name: HELIUM / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: Blot for 2 sec

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Electron microscopy

MicroscopeJEOL 3000SFF
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.4 mm
Sample stageSpecimen holder: JEOL / Specimen holder model: JEOL
TemperatureAverage: 4 K
Alignment procedureLegacy - Electron beam tilt params: 2
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 25 e/Å2
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: CTFIT
Final two d classificationNumber classes: 10
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 8500

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