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- PDB-9bd1: beta/alpha1 region of ApoB 100 -

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Basic information

Entry
Database: PDB / ID: 9bd1
Titlebeta/alpha1 region of ApoB 100
ComponentsApolipoprotein B-100
KeywordsLIPID TRANSPORT / Apolipoprotien B 100 / alpha/beta 1 region / LDL
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: 5.4 Å
AuthorsDearborn, A.D. / Reimund, M. / Graziano, G. / Lei, H. / Kumar, A. / Neufeld, E.B. / Remaley, A.T. / Marcotrigiano, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2025
Title: Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor.
Authors: Mart Reimund / Altaira D Dearborn / Giorgio Graziano / Haotian Lei / Anthony M Ciancone / Ashish Kumar / Ronald Holewinski / Edward B Neufeld / Francis J O'Reilly / Alan T Remaley / Joseph Marcotrigiano /
Abstract: Apolipoprotein B100 (apoB100) is a structural component of low-density lipoprotein (LDL) and a ligand for the LDL receptor (LDLR). Mutations in apoB100 or in LDLR cause familial ...Apolipoprotein B100 (apoB100) is a structural component of low-density lipoprotein (LDL) and a ligand for the LDL receptor (LDLR). Mutations in apoB100 or in LDLR cause familial hypercholesterolaemia, an autosomal dominant disease that is characterized by a marked increase in LDL cholesterol (LDL-C) and a higher risk of cardiovascular disease. The structure of apoB100 on LDL and its interaction with LDLR are poorly understood. Here we present the cryo-electron microscopy structures of apoB100 on LDL bound to the LDLR and a nanobody complex, which can form a C-symmetric, higher-order complex. Using local refinement, we determined high-resolution structures of the interfaces between apoB100 and LDLR. One binding interface is formed between several small-ligand-binding modules of LDLR and a series of basic patches that are scattered along a β-belt formed by apoB100, encircling LDL. The other binding interface is formed between the β-propeller domain of LDLR and the N-terminal domain of apoB100. Our results reveal how both interfaces are involved in LDL dimer formation, and how LDLR cycles between LDL- and self-bound conformations. In addition, known mutations in either apoB100 or LDLR, associated with high levels of LDL-C, are located at the LDL-LDLR interface.
History
DepositionApr 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein B-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,3892
Polymers516,1671
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Apolipoprotein B-100 / Apo B-48


Mass: 516167.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04114
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1Apolipoprotein B 100 on LDL with LDL receptor and LegobodyCOMPLEX#10MULTIPLE SOURCES
2Low Density Lipoprotein ApoB 100COMPLEX#11NATURAL
3LDL receptorCOMPLEX1RECOMBINANT
4Legobody FabCOMPLEX1RECOMBINANT
5Legobody MBP/IgG-binding protein A/IgG-binding protein G FusionCOMPLEX1RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Mus musculus (house mouse)10090
55Escherichia coli (E. coli)562
65Staphylococcus aureus (bacteria)1280
75Streptococcus sp. group G (bacteria)1320
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Homo sapiens (human)9606
24Homo sapiens (human)9606
35Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 51.38 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 287079 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 284.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00296988
ELECTRON MICROSCOPYf_angle_d0.58789552
ELECTRON MICROSCOPYf_chiral_restr0.04411173
ELECTRON MICROSCOPYf_plane_restr0.00431239
ELECTRON MICROSCOPYf_dihedral_angle_d4.9254988

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