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- PDB-9bde: Middle Region of Apolipoprotein B 100 bound to Low Density Lipopr... -

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Basic information

Entry
Database: PDB / ID: 9bde
TitleMiddle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor
Components
  • (Legobody 8D3 Fab ...) x 2
  • ApoB100 nanobody 4
  • Apolipoprotein B 100
  • Low-density lipoprotein receptor
  • Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
KeywordsLIPID TRANSPORT / Apolipoprotein B 100 / ApoB100 / LDLreceptor
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 / receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / lipase binding / plasma lipoprotein particle clearance ...mature chylomicron / Scavenging by Class H Receptors / triglyceride mobilization / positive regulation of cholesterol storage / VLDL assembly / regulation of cholesterol biosynthetic process / receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / lipase binding / plasma lipoprotein particle clearance / LDL remodeling / Scavenging by Class B Receptors / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / VLDL clearance / triglyceride catabolic process / negative regulation of microglial cell activation / very-low-density lipoprotein particle assembly / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / clathrin heavy chain binding / negative regulation of receptor recycling / positive regulation of triglyceride biosynthetic process / intestinal cholesterol absorption / negative regulation of low-density lipoprotein particle clearance / chylomicron remnant / intermediate-density lipoprotein particle / low-density lipoprotein particle receptor activity / response to caloric restriction / Chylomicron clearance / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / 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 / high-density lipoprotein particle clearance / chylomicron / regulation of protein metabolic process / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / very-low-density lipoprotein particle / low-density lipoprotein particle remodeling / endolysosome membrane / positive regulation of macrophage derived foam cell differentiation / negative regulation of amyloid fibril formation / fertilization / IgG binding / cholesterol efflux / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / lipoprotein transport / Scavenging by Class A Receptors / cellular response to fatty acid / low-density lipoprotein particle receptor binding / Scavenging by Class F Receptors / Platelet sensitization by LDL / detection of maltose stimulus / sorting endosome / maltose transport complex / amyloid-beta clearance / lipoprotein particle binding / endoplasmic reticulum exit site / carbohydrate transport / cellular response to low-density lipoprotein particle stimulus / carbohydrate transmembrane transporter activity / maltose binding / long-term memory / maltose transport / maltodextrin transmembrane transport / phagocytosis / smooth endoplasmic reticulum / retinoid metabolic process / Retinoid metabolism and transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / clathrin-coated pit / somatodendritic compartment / lipid droplet / endocytic vesicle lumen / receptor-mediated endocytosis / cholesterol metabolic process / ATP-binding cassette (ABC) transporter complex / lysosomal lumen / cholesterol homeostasis / post-embryonic development / endosome lumen / cell chemotaxis / Cell surface interactions at the vascular wall / establishment of localization in cell / Post-translational protein phosphorylation
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 / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / : / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / Lysin motif / LysM domain superfamily / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / Low-density lipoprotein receptor domain class A / YSIRK type signal peptide / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / YSIRK Gram-positive signal peptide / Six-bladed beta-propeller, TolB-like / LPXTG cell wall anchor motif / Coagulation Factor Xa inhibitory site / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / EGF-type aspartate/asparagine hydroxylation site / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Armadillo-type fold
Similarity search - Domain/homology
Low-density lipoprotein receptor / Immunoglobulin G-binding protein A / Apolipoprotein B-100 / Maltose/maltodextrin-binding periplasmic protein / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
Staphylococcus aureus (bacteria)
Streptococcus sp. 'group G' (bacteria)
Camelus bactrianus (Bactrian camel)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 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 11, 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
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Revision 1.1Mar 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Legobody 8D3 Fab Heavy Chain
A: Apolipoprotein B 100
L: Legobody 8D3 Fab light chain
B: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
N: ApoB100 nanobody 4
R: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)735,93518
Polymers734,5496
Non-polymers1,38712
Water00
1


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

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Components

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Protein , 2 types, 2 molecules AR

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


Mass: 516167.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04114
#6: Protein Low-density lipoprotein receptor / LDL receptor


Mass: 95477.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Cell line (production host): HEK 293T GnTI- / Production host: Homo sapiens (human) / References: UniProt: P01130

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Antibody , 4 types, 4 molecules HLBN

#1: Antibody Legobody 8D3 Fab Heavy Chain


Mass: 25252.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody Legobody 8D3 Fab light chain


Mass: 24095.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Antibody Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / Staphylococcal protein A / SpA / IgG-binding protein G


Mass: 59233.246 Da / Num. of mol.: 1
Fragment: residues 27-384 (Uniprot numbering),residues 278-327 (Uniprot numbering),103-151 (Uniprot numbering),residues 440-497 (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Streptococcus sp. 'group G' (bacteria)
Gene: malE, b4034, JW3994, spa, SAOUHSC_00069, spg / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: P02976, UniProt: P19909
#5: Antibody ApoB100 nanobody 4


Mass: 14322.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)

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Sugars / Non-polymers , 2 types, 12 molecules

#7: 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.: 5
Source method: isolated from a genetically manipulated 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
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca

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Details

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

ComponentName: Middle of ApoB100 bound to LDL receptor and Legobody / Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
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
VitrificationCryogen name: ETHANE

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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
Particle selectionNum. of particles selected: 3689076 / Details: Picked with Topaz
3D reconstructionResolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 527598 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 165.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002217537
ELECTRON MICROSCOPYf_angle_d0.578823896
ELECTRON MICROSCOPYf_chiral_restr0.04232792
ELECTRON MICROSCOPYf_plane_restr0.00383118
ELECTRON MICROSCOPYf_dihedral_angle_d5.12872519

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