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- EMDB-44443: beta/alpha1 region of ApoB 100 -

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Basic information

Entry
Database: EMDB / ID: EMD-44443
Titlebeta/alpha1 region of ApoB 100
Map data
Sample
  • Complex: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
    • Complex: Low Density Lipoprotein ApoB 100
      • Protein or peptide: Apolipoprotein B-100
    • Complex: LDL receptor
    • Complex: Legobody Fab
    • Complex: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsApolipoprotien B 100 / alpha/beta 1 region / LDL / LIPID TRANSPORT
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) / Mus musculus (house mouse) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsDearborn AD / Reimund M / Graziano G / Lei H / Kumar A / Neufeld EB / Remaley AT / Marcotrigiano J
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44443.png

Downloads & links

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Map

FileDownload / File: emd_44443.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 336 pix.
= 557.76 Å		1.66 Å/pix.
x 336 pix.
= 557.76 Å		1.66 Å/pix.
x 336 pix.
= 557.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.19295265 - 0.30894253
Average (Standard dev.)0.000121065015 (±0.0040526194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 557.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44443_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44443_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Apolipoprotein B 100 on LDL with LDL receptor and Legobody

EntireName: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
Components
  • Complex: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
    • Complex: Low Density Lipoprotein ApoB 100
      • Protein or peptide: Apolipoprotein B-100
    • Complex: LDL receptor
    • Complex: Legobody Fab
    • Complex: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Apolipoprotein B 100 on LDL with LDL receptor and Legobody

SupramoleculeName: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

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Supramolecule #2: Low Density Lipoprotein ApoB 100

SupramoleculeName: Low Density Lipoprotein ApoB 100 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: LDL receptor

SupramoleculeName: LDL receptor / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Legobody Fab

SupramoleculeName: Legobody Fab / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #5: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion

SupramoleculeName: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion
type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Apolipoprotein B-100

MacromoleculeName: Apolipoprotein B-100 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 516.167469 KDa
SequenceString: MDPPRPALLA LLALPALLLL LLAGARAEEE MLENVSLVCP KDATRFKHLR KYTYNYEAES SSGVPGTADS RSATRINCKV ELEVPQLCS FILKTSQCTL KEVYGFNPEG KALLKKTKNS EEFAAAMSRY ELKLAIPEGK QVFLYPEKDE PTYILNIKRG I ISALLVPP ...String:
MDPPRPALLA LLALPALLLL LLAGARAEEE MLENVSLVCP KDATRFKHLR KYTYNYEAES SSGVPGTADS RSATRINCKV ELEVPQLCS FILKTSQCTL KEVYGFNPEG KALLKKTKNS EEFAAAMSRY ELKLAIPEGK QVFLYPEKDE PTYILNIKRG I ISALLVPP ETEEAKQVLF LDTVYGNCST HFTVKTRKGN VATEISTERD LGQCDRFKPI RTGISPLALI KGMTRPLSTL IS SSQSCQY TLDAKRKHVA EAICKEQHLF LPFSYKNKYG MVAQVTQTLK LEDTPKINSR FFGEGTKKMG LAFESTKSTS PPK QAEAVL KTLQELKKLT ISEQNIQRAN LFNKLVTELR GLSDEAVTSL LPQLIEVSSP ITLQALVQCG QPQCSTHILQ WLKR VHANP LLIDVVTYLV ALIPEPSAQQ LREIFNMARD QRSRATLYAL SHAVNNYHKT NPTGTQELLD IANYLMEQIQ DDCTG DEDY TYLILRVIGN MGQTMEQLTP ELKSSILKCV QSTKPSLMIQ KAAIQALRKM EPKDKDQEVL LQTFLDDASP GDKRLA AYL MLMRSPSQAD INKIVQILPW EQNEQVKNFV ASHIANILNS EELDIQDLKK LVKEALKESQ LPTVMDFRKF SRNYQLY KS VSLPSLDPAS AKIEGNLIFD PNNYLPKESM LKTTLTAFGF ASADLIEIGL EGKGFEPTLE ALFGKQGFFP DSVNKALY W VNGQVPDGVS KVLVDHFGYT KDDKHEQDMV NGIMLSVEKL IKDLKSKEVP EARAYLRILG EELGFASLHD LQLLGKLLL MGARTLQGIP QMIGEVIRKG SKNDFFLHYI FMENAFELPT GAGLQLQISS SGVIAPGAKA GVKLEVANMQ AELVAKPSVS VEFVTNMGI IIPDFARSGV QMNTNFFHES GLEAHVALKA GKLKFIIPSP KRPVKLLSGG NTLHLVSTTK TEVIPPLIEN R QSWSVCKQ VFPGLNYCTS GAYSNASSTD SASYYPLTGD TRLELELRPT GEIEQYSVSA TYELQREDRA LVDTLKFVTQ AE GAKQTEA TMTFKYNRQS MTLSSEVQIP DFDVDLGTIL RVNDESTEGK TSYRLTLDIQ NKKITEVALM GHLSCDTKEE RKI KGVISI PRLQAEARSE ILAHWSPAKL LLQMDSSATA YGSTVSKRVA WHYDEEKIEF EWNTGTNVDT KKMTSNFPVD LSDY PKSLH MYANRLLDHR VPQTDMTFRH VGSKLIVAMS SWLQKASGSL PYTQTLQDHL NSLKEFNLQN MGLPDFHIPE NLFLK SDGR VKYTLNKNSL KIEIPLPFGG KSSRDLKMLE TVRTPALHFK SVGFHLPSRE FQVPTFTIPK LYQLQVPLLG VLDLST NVY SNLYNWSASY SGGNTSTDHF SLRARYHMKA DSVVDLLSYN VQGSGETTYD HKNTFTLSCD GSLRHKFLDS NIKFSHV EK LGNNPVSKGL LIFDASSSWG PQMSASVHLD SKKKQHLFVK EVKIDGQFRV SSFYAKGTYG LSCQRDPNTG RLNGESNL R FNSSYLQGTN QITGRYEDGT LSLTSTSDLQ SGIIKNTASL KYENYELTLK SDTNGKYKNF ATSNKMDMTF SKQNALLRS EYQADYESLR FFSLLSGSLN SHGLELNADI LGTDKINSGA HKATLRIGQD GISTSATTNL KCSLLVLENE LNAELGLSGA SMKLTTNGR FREHNAKFSL DGKAALTELS LGSAYQAMIL GVDSKNIFNF KVSQEGLKLS NDMMGSYAEM KFDHTNSLNI A GLSLDFSS KLDNIYSSDK FYKQTVNLQL QPYSLVTTLN SDLKYNALDL TNNGKLRLEP LKLHVAGNLK GAYQNNEIKH IY AISSAAL SASYKADTVA KVQGVEFSHR LNTDIAGLAS AIDMSTNYNS DSLHFSNVFR SVMAPFTMTI DAHTNGNGKL ALW GEHTGQ LYSKFLLKAE PLAFTFSHDY KGSTSHHLVS RKSISAALEH KVSALLTPAE QTGTWKLKTQ FNNNEYSQDL DAYN TKDKI GVELTGRTLA DLTLLDSPIK VPLLLSEPIN IIDALEMRDA VEKPQEFTIV AFVKYDKNQD VHSINLPFFE TLQEY FERN RQTIIVVLEN VQRNLKHINI DQFVRKYRAA LGKLPQQAND YLNSFNWERQ VSHAKEKLTA LTKKYRITEN DIQIAL DDA KINFNEKLSQ LQTYMIQFDQ YIKDSYDLHD LKIAIANIID EIIEKLKSLD EHYHIRVNLV KTIHDLHLFI ENIDFNK SG SSTASWIQNV DTKYQIRIQI QEKLQQLKRH IQNIDIQHLA GKLKQHIEAI DVRVLLDQLG TTISFERIND ILEHVKHF V INLIGDFEVA EKINAFRAKV HELIERYEVD QQIQVLMDKL VELAHQYKLK ETIQKLSNVL QQVKIKDYFE KLVGFIDDA VKKLNELSFK TFIEDVNKFL DMLIKKLKSF DYHQFVDETN DKIREVTQRL NGEIQALELP QKAEALKLFL EETKATVAVY LESLQDTKI TLIINWLQEA LSSASLAHMK AKFRETLEDT RDRMYQMDIQ QELQRYLSLV GQVYSTLVTY ISDWWTLAAK N LTDFAEQY SIQDWAKRMK ALVEQGFTVP EIKTILGTMP AFEVSLQALQ KATFQTPDFI VPLTDLRIPS VQINFKDLKN IK IPSRFST PEFTILNTFH IPSFTIDFVE MKVKIIRTID QMLNSELQWP VPDIYLRDLK VEDIPLARIT LPDFRLPEIA IPE FIIPTL NLNDFQVPDL HIPEFQLPHI SHTIEVPTFG KLYSILKIQS PLFTLDANAD IGNGTTSANE AGIAASITAK GESK LEVLN FDFQANAQLS NPKINPLALK ESVKFSSKYL RTEHGSEMLF FGNAIEGKSN TVASLHTEKN TLELSNGVIV KINNQ LTLD SNTKYFHKLN IPKLDFSSQA DLRNEIKTLL KAGHIAWTSS GKGSWKWACP RFSDEGTHES QISFTIEGPL TSFGLS NKI NSKHLRVNQN LVYESGSLNF SKLEIQSQVD SQHVGHSVLT AKGMALFGEG KAEFTGRHDA HLNGKVIGTL KNSLFFS AQ PFEITASTNN EGNLKVRFPL RLTGKIDFLN NYALFLSPSA QQASWQVSAR FNQYKYNQNF SAGNNENIME AHVGINGE A NLDFLNIPLT IPEMRLPYTI ITTPPLKDFS LWEKTGLKEF LKTTKQSFDL SVKAQYKKNK HRHSITNPLA VLCEFISQS IKSFDRHFEK NRNNALDFVT KSYNETKIKF DKYKAEKSHD ELPRTFQIPG YTVPVVNVEV SPFTIEMSAF GYVFPKAVSM PSFSILGSD VRVPSYTLIL PSLELPVLHV PRNLKLSLPD FKELCTISHI FIPAMGNITY DFSFKSSVIT LNTNAELFNQ S DIVAHLLS SSSSVIDALQ YKLEGTTRLT RKRGLKLATA LSLSNKFVEG SHNSTVSLTT KNMEVSVATT TKAQIPILRM NF KQELNGN TKSKPTVSSS MEFKYDFNSS MLYSTAKGAV DHKLSLESLT SYFSIESSTK GDVKGSVLSR EYSGTIASEA NTY LNSKST RSSVKLQGTS KIDDIWNLEV KENFAGEATL QRIYSLWEHS TKNHLQLEGL FFTNGEHTSK ATLELSPWQM SALV QVHAS QPSSFHDFPD LGQEVALNAN TKNQKIRWKN EVRIHSGSFQ SQVELSNDQE KAHLDIAGSL EGHLRFLKNI ILPVY DKSL WDFLKLDVTT SIGRRQHLRV STAFVYTKNP NGYSFSIPVK VLADKFIIPG LKLNDLNSVL VMPTFHVPFT DLQVPS CKL DFREIQIYKK LRTSSFALNL PTLPEVKFPE VDVLTKYSQP EDSLIPFFEI TVPESQLTVS QFTLPKSVSD GIAALDL NA VANKIADFEL PTIIVPEQTI EIPSIKFSVP AGIVIPSFQA LTARFEVDSP VYNATWSASL KNKADYVETV LDSTCSST V QFLEYELNVL GTHKIEDGTL ASKTKGTFAH RDFSAEYEED GKYEGLQEWE GKAHLNIKSP AFTDLHLRYQ KDKKGISTS AASPAVGTVG MDMDEDDDFS KWNFYYSPQS SPDKKLTIFK TELRVRESDE ETQIKVNWEE EAASGLLTSL KDNVPKATGV LYDYVNKYH WEHTGLTLRE VSSKLRRNLQ NNAEWVYQGA IRQIDDIDVR FQKAASGTTG TYQEWKDKAQ NLYQELLTQE G QASFQGLK DNVFDGLVRV TQEFHMKVKH LIDSLIDFLN FPRFQFPGKP GIYTREELCT MFIREVGTVL SQVYSKVHNG SE ILFSYFQ DLVITLPFEL RKHKLIDVIS MYRELLKDLS KEAQEVFKAI QSLKTTEVLR NLQDLLQFIF QLIEDNIKQL KEM KFTYLI NYIQDEINTI FSDYIPYVFK LLKENLCLNL HKFNEFIQNE LQEASQELQQ IHQYIMALRE EYFDPSIVGW TVKY YELEE KIVSLIKNLL VALKDFHSEY IVSASNFTSQ LSSQVEQFLH RNIQEYLSIL TDPDGKGKEK IAELSATAQE IIKSQ AIAT KKIISDYHQQ FRYKLQDFSD QLSDYYEKFI AESKRLIDLS IQNYHTFLIY ITELLKKLQS TTVMNPYMKL APGELT IIL

UniProtKB: Apolipoprotein B-100

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 51.38 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Generated by AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287079
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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