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- EMDB-47801: The Structure of ApoB100 from Human Low-Density Lipoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-47801
TitleThe Structure of ApoB100 from Human Low-Density Lipoprotein
Map data
Sample
  • Complex: apolipoprotein B-100
    • Protein or peptide: Apolipoprotein B 100
Keywordsapolipoprotein / LIPID BINDING PROTEIN
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 / LDL remodeling / Scavenging by Class B Receptors / lipase binding / VLDL clearance ...mature chylomicron / Scavenging by Class H Receptors / triglyceride mobilization / positive regulation of cholesterol storage / VLDL assembly / regulation of cholesterol biosynthetic process / LDL remodeling / Scavenging by Class B Receptors / lipase binding / 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 / positive regulation of lipid storage / chylomicron / lipoprotein catabolic process / flagellated sperm motility / 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 / Scavenging by Class A Receptors / low-density lipoprotein particle receptor binding / lipoprotein transport / Scavenging by Class F Receptors / Platelet sensitization by LDL / endoplasmic reticulum exit site / smooth endoplasmic reticulum / cholesterol metabolic process / Retinoid metabolism and transport / lipid droplet / endocytic vesicle lumen / lysosomal lumen / cholesterol homeostasis / endosome lumen / post-embryonic development / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / establishment of localization in cell / clathrin-coated endocytic vesicle membrane / Heme signaling / phospholipid binding / response to virus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Cargo recognition for clathrin-mediated endocytosis / nervous system development / 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 / cytoplasm / cytosol
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsBerndsen ZT / Cassidy CK
Funding support1 items
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, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47801.png

Downloads & links

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Map

FileDownload / File: emd_47801.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 450 pix.
= 490.5 Å		1.09 Å/pix.
x 450 pix.
= 490.5 Å		1.09 Å/pix.
x 450 pix.
= 490.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.182
Minimum - Maximum-0.55990076 - 1.1475471
Average (Standard dev.)-0.00023670348 (±0.024902765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 490.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47801_msk_1.map
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Additional map: #1

Fileemd_47801_additional_1.map
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Additional map: local refinement of the apoB100 N-terminal domain

Fileemd_47801_additional_2.map
Annotationlocal refinement of the apoB100 N-terminal domain
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Half map: #2

Fileemd_47801_half_map_1.map
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Half map: #1

Fileemd_47801_half_map_2.map
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Sample components

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Entire : apolipoprotein B-100

EntireName: apolipoprotein B-100
Components
  • Complex: apolipoprotein B-100
    • Protein or peptide: Apolipoprotein B 100

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Supramolecule #1: apolipoprotein B-100

SupramoleculeName: apolipoprotein B-100 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 550 kDa/nm

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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
Recombinant expressionOrganism: Homo sapiens (human)
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 14 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 600000
Startup modelType of model: OTHER / Details: ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 52843
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsThe Molecular Dynamics Flexible Fitting protocol was applied using NAMD 3.0
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient
Output model

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

PDB-9ea7:
The Structure of ApoB100 from Human Low-Density Lipoprotein

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

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