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- PDB-9e9r: The Structure of ApoB100 from Human Low-Density Lipoprotein -

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Basic information

Entry
Database: PDB / ID: 9e9r
TitleThe Structure of ApoB100 from Human Low-Density Lipoprotein
ComponentsApolipoprotein B 100
KeywordsLIPID BINDING PROTEIN / apolipoprotein
Function / homology
Function and homology information


mature chylomicron / Scavenging by Class H Receptors / triglyceride mobilization / positive regulation of cholesterol storage / VLDL assembly / regulation of cholesterol biosynthetic process / lipase binding / LDL remodeling / Scavenging by Class B Receptors / VLDL clearance ...mature chylomicron / Scavenging by Class H Receptors / triglyceride mobilization / positive regulation of cholesterol storage / VLDL assembly / regulation of cholesterol biosynthetic process / lipase binding / LDL remodeling / Scavenging by Class B Receptors / VLDL clearance / triglyceride catabolic process / very-low-density lipoprotein particle assembly / low-density lipoprotein particle clearance / chylomicron remnant / intermediate-density lipoprotein particle / Chylomicron clearance / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / LDL clearance / Regulation of TLR by endogenous ligand / flagellated sperm motility / positive regulation of lipid storage / chylomicron / lipoprotein catabolic process / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / very-low-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / fertilization / cholesterol efflux / artery morphogenesis / lipoprotein transport / Scavenging by Class A Receptors / low-density lipoprotein particle receptor binding / Scavenging by Class F Receptors / Platelet sensitization by LDL / endoplasmic reticulum exit site / smooth endoplasmic reticulum / Retinoid metabolism and transport / lipid droplet / endocytic vesicle lumen / cholesterol metabolic process / lysosomal lumen / cholesterol homeostasis / post-embryonic development / endosome lumen / Cell surface interactions at the vascular wall / establishment of localization in cell / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / Heme signaling / response to virus / phospholipid binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / nervous system development / Cargo recognition for clathrin-mediated endocytosis / heparin binding / Clathrin-mediated endocytosis / spermatogenesis / in utero embryonic development / early endosome / endosome membrane / receptor ligand activity / endoplasmic reticulum lumen / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of gene expression / endoplasmic reticulum membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Lipid transport, open beta-sheet / Apolipoprotein B100 C-terminal / : / Domain of Unknown Function (DUF1081) / Apolipoprotein B100 C terminal / Vitellinogen, open beta-sheet, subdomain 1 / Vitellinogen, open beta-sheet / Vitellinogen, open beta-sheet / DUF1943 / Vitellogenin, N-terminal ...Lipid transport, open beta-sheet / Apolipoprotein B100 C-terminal / : / Domain of Unknown Function (DUF1081) / Apolipoprotein B100 C terminal / Vitellinogen, open beta-sheet, subdomain 1 / Vitellinogen, open beta-sheet / Vitellinogen, open beta-sheet / DUF1943 / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. / Lipoprotein N-terminal Domain / Armadillo-type fold
Similarity search - Domain/homology
Apolipoprotein B-100
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsBerndsen, Z.T. / Cassidy, C.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2025
Title: The structure of apolipoprotein B100 from human low-density lipoprotein.
Authors: Zachary T Berndsen / C Keith Cassidy /
Abstract: Low-density lipoprotein (LDL) has a central role in lipid and cholesterol metabolism and is a key agent in the development and progression of atherosclerosis, the leading cause of mortality worldwide. ...Low-density lipoprotein (LDL) has a central role in lipid and cholesterol metabolism and is a key agent in the development and progression of atherosclerosis, the leading cause of mortality worldwide. Apolipoprotein B100 (apoB100), one of the largest proteins in the genome, is the primary structural and functional component of LDL, yet its size and complex lipid associations have posed major challenges for structural studies. Here we present the structure of apoB100 resolved to subnanometre resolution in most regions using an integrative approach of cryo-electron microscopy, AlphaFold2 and molecular-dynamics-based refinement. The structure consists of a large globular N-terminal domain and an approximately 61-nm-long continuous amphipathic β-sheet that wraps around the LDL particle like a belt. Distributed quasi-symmetrically across the two sides of the β-belt are nine strategically located interstrand inserts that extend across the lipid surface to provide additional structural support through a network of long-range interactions. We further compare our structure to a comprehensive list of more than 200 intramolecular cross-links and find close agreement between the two. These results suggest a mechanism for how the various domains of apoB100 act in concert to maintain LDL shape and cohesion across a range of particle sizes. More generally, they advance our fundamental understanding of LDL synthesis, form and function, and will help to accelerate the design of potential therapeutics.
History
DepositionNov 8, 2024Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein B 100


Theoretical massNumber of molelcules
Total (without water)516,1671
Polymers516,1671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Apolipoprotein B 100 / Apo B-100


Mass: 516167.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOB / Production host: Homo sapiens (human) / References: UniProt: P04114
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: apolipoprotein B-100 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 550 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4particle selection
2SerialEMimage acquisition
4cryoSPARC4CTF correction
7NAMD3model fittingcascade MDFF protocol was used
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
11cryoSPARC4classification
12cryoSPARC43D reconstruction
13UCSF ChimeraX1.6.1model refinementISOLDE was used for manual refinement
14PHENIX1.2.0model refinementReal_space_refine used for refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 600000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52843 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Details: The Molecular Dynamics Flexible Fitting protocol was applied using NAMD 3.0
Atomic model buildingSource name: AlphaFold / Type: in silico model

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