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- PDB-9bdt: Apolipoprotein B 100 bound to LDL receptor and legobody -

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Basic information

Entry
Database: PDB / ID: 9bdt
TitleApolipoprotein B 100 bound to LDL receptor and legobody
Components
  • (Legobody 8D3 Fab ...) x 2
  • ApoB100 nanobody 4
  • Apolipoprotein B-100
  • Low-density lipoprotein receptor
  • Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
KeywordsLIPID TRANSPORT / LDL / ApoB100 / LDL receptor
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 / regulation of protein metabolic process / Chylomicron assembly / LDL clearance / flagellated sperm motility / Regulation of TLR by endogenous ligand / positive regulation of lipid storage / high-density lipoprotein particle clearance / chylomicron / 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 / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / endoplasmic reticulum exit site / cellular response to low-density lipoprotein particle stimulus / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / long-term memory / maltodextrin transmembrane transport / smooth endoplasmic reticulum / phagocytosis / 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 / 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 / lipid metabolic process / positive regulation of inflammatory response
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 / Lysin motif / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LysM domain superfamily / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / LysM domain profile. / LysM domain / 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
Maltodextrin-binding protein / Low-density lipoprotein receptor / Apolipoprotein B-100 / Immunoglobulin G-binding protein G / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
Staphylococcus aureus (bacteria)
Homo sapiens (human)
Camelus bactrianus (Bactrian camel)
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 12, 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein B-100
H: Legobody 8D3 Fab Heavy Chain
L: Legobody 8D3 Fab Light Chain
B: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
I: Low-density lipoprotein receptor
N: ApoB100 nanobody 4
R: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)831,61619
Polymers830,0267
Non-polymers1,59012
Water00
1


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

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Components

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Protein , 2 types, 3 molecules AIR

#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
#5: Protein Low-density lipoprotein receptor / LDL receptor


Mass: 95477.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: Homo sapiens (human) / References: UniProt: P01130

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Antibody , 4 types, 4 molecules HLBN

#2: 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): Expi293T / Production host: Mus musculus (house mouse)
#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): Expi293T / Production host: Homo sapiens (human)
#4: Antibody Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G / IgG-binding protein A / Staphylococcal protein A / SpA / IgG-binding protein G


Mass: 59233.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Staphylococcus aureus (bacteria)
Gene: malE, malE_1, A9X72_23600, ACN81_05700, ACU57_23670, AM464_13530, B6R31_000964, BANRA_05111, BCB93_001091, BF481_003801, BG944_002391, BGM66_004246, BJI68_06200, BJJ90_24825, BK292_00970, BTB68_ ...Gene: malE, malE_1, A9X72_23600, ACN81_05700, ACU57_23670, AM464_13530, B6R31_000964, BANRA_05111, BCB93_001091, BF481_003801, BG944_002391, BGM66_004246, BJI68_06200, BJJ90_24825, BK292_00970, BTB68_002078, BTQ06_17300, BvCmsKKP061_03224, BvCmsSIP010_04050, C0P57_003867, C1Q91_002164, C2R31_001890, C3F40_15210, C9E67_28370, CA593_05740, CF22_001770, CG692_11710, CG704_16590, CG831_003746, CIG67_12040, CQ986_003892, CR538_23895, CR539_01985, CTR35_003815, CV83915_02005, D4M65_12865, DIV22_28370, DNX30_07695, DS732_01860, DTL43_19585, E4K51_08355, E5H86_20640, E6D34_15030, EAI46_20350, EC95NR1_03574, ECs5017, EIZ93_13775, EN85_000970, EPS97_17355, ExPECSC038_04540, F9407_08085, F9461_21760, FIJ20_18085, FJQ40_13885, FOI11_015465, FOI11_20215, FPS11_04610, FV293_00135, FWK02_22115, G3V95_18070, G4A38_02205, G4A47_04495, G9448_13225, GAI89_05080, GAJ12_13200, GJ11_25475, GKF66_19285, GNW61_17855, GOP25_18965, GP965_07770, GP975_07695, GP979_10140, GQA06_09595, GQM04_22095, GQM21_08325, GRW05_14255, GRW24_12940, GRW56_08975, GRW57_10345, GUC01_08260, H0O72_20100, HEP30_015080, HHH44_003952, HLX92_13085, HMV95_14740, HV109_22180, HV209_20940, HVW43_14700, HVY77_23840, HX086_10250, HX136_23390, I6H00_16895, I6H02_15990, J0541_001933, J5U05_001620, JNP96_01525, KV259_002584, KV317_002918, KV371_002846, KV406_003109, KV449_002737, KV455_002759, KV463_002918, KV469_002607, KV499_002898, KV500_002927, NCTC10418_07064, NCTC10429_00012, NCTC10865_05806, NCTC11126_02082, NCTC11181_01902, NCTC12950_05149, NCTC13148_04480, NCTC4450_01671, NCTC8009_08341, NCTC8179_05034, NCTC8333_05503, NCTC8500_05253, NCTC8622_01707, NCTC8960_02276, NCTC8985_03950, NCTC9706_01951, NCTC9962_03706, NEP60_16880, O5851_07355, RG28_25590, SAMEA3752557_02201, TUM18780_41180, WR15_07725, spa, SA0107, spg
Production host: Escherichia coli (E. coli)
References: UniProt: C3SHQ8, UniProt: P99134, UniProt: P06654
#6: 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 , 2 types, 5 molecules

#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: 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.: 4
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

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Non-polymers , 1 types, 7 molecules

#9: 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: Apoliprotein B 100 from LDL bound to LDL receptor and Legobody
Type: COMPLEX / Entity ID: #2-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
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

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3689076 / Details: Selected with Topaz
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 527598 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00239667
ELECTRON MICROSCOPYf_angle_d0.60953804
ELECTRON MICROSCOPYf_dihedral_angle_d5.1735352
ELECTRON MICROSCOPYf_chiral_restr0.0456159
ELECTRON MICROSCOPYf_plane_restr0.0046926

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