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- EMDB-45787: Nanobody 4 bound to Apolipoprotein B 100 -

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Basic information

Entry
Database: EMDB / ID: EMD-45787
TitleNanobody 4 bound to Apolipoprotein B 100
Map dataMap File
Sample
  • Complex: Middle of ApoB100 bound to LDL receptor and Legobody
    • Protein or peptide: Apolipoprotein B 100
    • Protein or peptide: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
    • Protein or peptide: Legobody 8D3 Fab Heavy Chain
    • Protein or peptide: Legobody 8D3 Fab Light Chain
    • Protein or peptide: ApoB100 nanobody 4
    • Protein or peptide: Low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsApolipoprotein B 100 / ApoB100 / LDLreceptor / LIPID TRANSPORT
Function / homology
Function and homology information


mature chylomicron / Scavenging by Class H Receptors / triglyceride mobilization / positive regulation of cholesterol storage / regulation of cholesterol biosynthetic process / VLDL assembly / 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 / regulation of cholesterol biosynthetic process / VLDL assembly / 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 / VLDL clearance / negative regulation of astrocyte activation / triglyceride catabolic process / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle assembly / cholesterol import / PCSK9-LDLR complex / low-density lipoprotein particle clearance / clathrin heavy chain binding / negative regulation of receptor recycling / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / chylomicron remnant / low-density lipoprotein particle receptor activity / intermediate-density lipoprotein particle / response to caloric restriction / Chylomicron clearance / low-density lipoprotein particle binding / positive regulation of macrophage derived foam cell differentiation / amyloid-beta clearance by cellular catabolic process / Chylomicron remodeling / positive regulation of lipid storage / flagellated sperm motility / cellular response to lipoprotein particle stimulus / regulation of protein metabolic process / Chylomicron assembly / LDL clearance / Regulation of TLR by endogenous ligand / high-density lipoprotein particle clearance / chylomicron / lipoprotein catabolic process / phospholipid transport / cholesterol transfer activity / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transport / very-low-density lipoprotein particle / endolysosome membrane / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / fertilization / negative regulation of protein metabolic process / IgG binding / cholesterol efflux / Scavenging by Class F Receptors / artery morphogenesis / cellular response to fatty acid / Scavenging by Class A Receptors / lipoprotein transport / regulation of cholesterol metabolic process / low-density lipoprotein particle receptor binding / 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 / maltodextrin transmembrane transport / long-term memory / smooth endoplasmic reticulum / phagocytosis / Retinoid metabolism and transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / clathrin-coated pit / somatodendritic compartment / endocytic vesicle lumen / lysosomal lumen / receptor-mediated endocytosis / cholesterol metabolic process / lipid droplet / post-embryonic development / cholesterol homeostasis / endosome lumen / establishment of localization in cell / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / Heme signaling / response to virus / lipid metabolic process / phospholipid binding / 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 / LysM domain superfamily / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / Lysin motif / 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. / LDL-receptor class A (LDLRA) domain profile. / : / Calcium-binding EGF domain / 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 / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / EGF-type aspartate/asparagine hydroxylation site / 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 speciesHomo sapiens (human) / Escherichia coli (E. coli) / Mus musculus (house mouse) / Camelus bactrianus (Bactrian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsDearborn AD / Kumar A / Reimund M / Graziano G / Lei H / 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: 2024
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
DepositionJul 17, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45787.png

Downloads & links

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Map

FileDownload / File: emd_45787.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap File
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.36828685 - 0.7143979
Average (Standard dev.)0.0001363222 (±0.006056178)
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: #2

Fileemd_45787_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_45787_half_map_2.map
Projections & Slices
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Sample components

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Entire : Middle of ApoB100 bound to LDL receptor and Legobody

EntireName: Middle of ApoB100 bound to LDL receptor and Legobody
Components
  • Complex: Middle of ApoB100 bound to LDL receptor and Legobody
    • Protein or peptide: Apolipoprotein B 100
    • Protein or peptide: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
    • Protein or peptide: Legobody 8D3 Fab Heavy Chain
    • Protein or peptide: Legobody 8D3 Fab Light Chain
    • Protein or peptide: ApoB100 nanobody 4
    • Protein or peptide: Low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Middle of ApoB100 bound to LDL receptor and Legobody

SupramoleculeName: Middle of ApoB100 bound to LDL receptor and Legobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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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: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,I...

MacromoleculeName: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 59.233246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDQALAFAQ ILIMPNLTEE QRNGFIQSLK DDPSVSKEIL AEAK KLNEH QAPKGGSGGA GSGDQQSAFY EILNMPNLNE AQRNGFIQSL KDDPSQSTNV LGEAKKLNES QAGGGSGGGS GGSAV TTYK LVINGKTLKG ETTTKAVDAE TAEKAFKQYA NDNGVDGVWT YDDATKTFTV TEGSGHHHHH H

UniProtKB: Maltodextrin-binding protein, Immunoglobulin G-binding protein A, Immunoglobulin G-binding protein G

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Macromolecule #3: Legobody 8D3 Fab Heavy Chain

MacromoleculeName: Legobody 8D3 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.252217 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLVESGGG LVQPGKSLRL SCAASGFTFS NFGMHWVRQA PEMGLEWVAY ISSGSTTKYY GDTVKGRFTI SRDNPKNTLY LQMNSLRSE DTAMYYCARR PLYDGDYGYP MDYWGQGTSV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
DVQLVESGGG LVQPGKSLRL SCAASGFTFS NFGMHWVRQA PEMGLEWVAY ISSGSTTKYY GDTVKGRFTI SRDNPKNTLY LQMNSLRSE DTAMYYCARR PLYDGDYGYP MDYWGQGTSV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCGS HHHHHH

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Macromolecule #4: Legobody 8D3 Fab Light Chain

MacromoleculeName: Legobody 8D3 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.095852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NIMLTQSPSS LAVSAGERVT MSCKSTQSIL YNSNQKTYLA WYQQKPGQSP KLLIYWASTR ASGVPDRFTG SGSGTDFTLT INSVQPEDL AVYYCHQYLS AWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
NIMLTQSPSS LAVSAGERVT MSCKSTQSIL YNSNQKTYLA WYQQKPGQSP KLLIYWASTR ASGVPDRFTG SGSGTDFTLT INSVQPEDL AVYYCHQYLS AWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #5: ApoB100 nanobody 4

MacromoleculeName: ApoB100 nanobody 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Camelus bactrianus (Bactrian camel)
Molecular weightTheoretical: 14.322896 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCVASGYTDG AVNMGWFRQA PGKDRDWVAA ISPGGGLTYY ADSVKGRFTI SQDKAKNTVY LQMNSLKPE DTAIYYCAAA RSLAHFKLSQ YNYWGQGTQV TVSSLEHHHH HH

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Macromolecule #6: Low-density lipoprotein receptor

MacromoleculeName: Low-density lipoprotein receptor / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.327016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VTCKSGDFSC GGRVNRCIPQ FWRCDGQVDC DNGSDEQGCP PKTCSQDEFR CHDGKCISRQ FVCDSDRDCL DGSDEASCPV LTCGPASFQ CNSSTCIPQL WACDNDPDCE DGSDEWPQRC RGLYVFQGDS SPCSAFEFHC LSGECIHSSW RCDGGPDCKD K SDEENCAV ...String:
VTCKSGDFSC GGRVNRCIPQ FWRCDGQVDC DNGSDEQGCP PKTCSQDEFR CHDGKCISRQ FVCDSDRDCL DGSDEASCPV LTCGPASFQ CNSSTCIPQL WACDNDPDCE DGSDEWPQRC RGLYVFQGDS SPCSAFEFHC LSGECIHSSW RCDGGPDCKD K SDEENCAV ATCRPDEFQC SDGNCIHGSR QCDREYDCKD MSDEVGCVNV TLCEGPNKFK CHSGECITLD KVCNMARDCR DW SDEPIKE CGTNECLDNN GGCSHVCNDL KIGYECLCPD GFQLVAQRRC EDIDECQDPD TCSQLCVNLE GGYKCQCEEG FQL DPHTKA CKAVGSIAYL FFTNRHEVRK MTLDRSEYTS LIPNLRNVVA LDTEVASNRI YWSDLSQRMI CSTQLDRAHG VSSY DTVIS RDIQAPDGLA VDWIHSNIYW TDSVLGTVSV ADTKGVKRKT LFRENGSKPR AIVVDPVHGF MYWTDWGTPA KIKKG GLNG VDIYSLVTEN IQWPNGITLD LLSGRLYWVD SKLHSISSID VNGGNRKTIL EDEKRLAHPF SLAVFEDKVF WTDIIN EAI FSANRLTGSD VNLLAENLLS PEDMVLFHNL TQPRGVNWCE RTTLSNGGCQ YLCLPAPQIN PHSPKFTCAC PDGMLLA RD MRSCLTEAEA AVATQETSTV RLKVSSTAVR TQHTTTRPVP DTSRLPGATP GLTTVEIVTM SHQALGDVAG RGNEKKPS S VRALSIVLPI VLLVFLCLGV FLLWKNWRLK NINSINFDNP VYQKTTEDEV HICHNQDGYS YPSRQMVSLE DDVA

UniProtKB: Low-density lipoprotein receptor

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
VitrificationCryogen name: ETHANE

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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

Particle selectionNumber selected: 3689076 / Details: Picked with Topaz
Startup modelType of model: OTHER / Details: AlphaFold PDBID 7RXC and 1N7D
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 527598
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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