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- EMDB-45967: Cryo-EM structure of human Low-density lipoprotein receptor-relat... -

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Basic information

Entry
Database: EMDB / ID: EMD-45967
TitleCryo-EM structure of human Low-density lipoprotein receptor-related protein 2
Map data
Sample
  • Complex: Low-density lipoprotein receptor-related protein 2
    • Protein or peptide: Low-density lipoprotein receptor-related protein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshuman / kidney / Low-density lipoprotein receptor-related protein 2 / LRP2 / MEMBRANE PROTEIN
Function / homology
Function and homology information


Transport of RCbl within the body / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane / cobalamin transport / protein transporter activity / ventricular compact myocardium morphogenesis ...Transport of RCbl within the body / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane / cobalamin transport / protein transporter activity / ventricular compact myocardium morphogenesis / response to leptin / Vitamin D (calciferol) metabolism / low-density lipoprotein particle receptor activity / metal ion transport / transcytosis / vitamin D metabolic process / cranial skeletal system development / neuron projection arborization / coronary artery morphogenesis / insulin-like growth factor I binding / outflow tract septum morphogenesis / positive regulation of neurogenesis / cargo receptor activity / aorta development / ventricular septum development / amyloid-beta clearance / hormone binding / vagina development / negative regulation of BMP signaling pathway / forebrain development / transport across blood-brain barrier / retinoid metabolic process / Retinoid metabolism and transport / clathrin-coated pit / receptor-mediated endocytosis / endosome lumen / neural tube closure / phosphatidylinositol 3-kinase/protein kinase B signal transduction / brush border membrane / kidney development / sensory perception of sound / clathrin-coated endocytic vesicle membrane / cellular response to growth factor stimulus / SH3 domain binding / lipid metabolic process / endocytosis / male gonad development / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein transport / protein-folding chaperone binding / gene expression / lysosome / cell population proliferation / receptor complex / apical plasma membrane / axon / lysosomal membrane / external side of plasma membrane / dendrite / calcium ion binding / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / extracellular exosome / plasma membrane
Similarity search - Function
: / LRP2-like, EGF-like domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A ...: / LRP2-like, EGF-like domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Legume lectin, beta chain, Mn/Ca-binding site / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / 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 / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / 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 / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang Z / Lyu M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of human Low-density lipoprotein receptor-related protein 2
Authors: Zhang Z / Lyu M
History
DepositionJul 29, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45967.png

Downloads & links

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Map

FileDownload / File: emd_45967.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.059676185 - 1.0332347
Average (Standard dev.)0.008305931 (±0.02260741)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 547.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Low-density lipoprotein receptor-related protein 2

EntireName: Low-density lipoprotein receptor-related protein 2
Components
  • Complex: Low-density lipoprotein receptor-related protein 2
    • Protein or peptide: Low-density lipoprotein receptor-related protein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Low-density lipoprotein receptor-related protein 2

SupramoleculeName: Low-density lipoprotein receptor-related protein 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Low-density lipoprotein receptor-related protein 2

MacromoleculeName: Low-density lipoprotein receptor-related protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 522.502562 KDa
SequenceString: MDRGPAAVAC TLLLALVACL APASGQECDS AHFRCGSGHC IPADWRCDGT KDCSDDADEI GCAVVTCQQG YFKCQSEGQC IPNSWVCDQ DQDCDDGSDE RQDCSQSTCS SHQITCSNGQ CIPSEYRCDH VRDCPDGADE NDCQYPTCEQ LTCDNGACYN T SQKCDWKV ...String:
MDRGPAAVAC TLLLALVACL APASGQECDS AHFRCGSGHC IPADWRCDGT KDCSDDADEI GCAVVTCQQG YFKCQSEGQC IPNSWVCDQ DQDCDDGSDE RQDCSQSTCS SHQITCSNGQ CIPSEYRCDH VRDCPDGADE NDCQYPTCEQ LTCDNGACYN T SQKCDWKV DCRDSSDEIN CTEICLHNEF SCGNGECIPR AYVCDHDNDC QDGSDEHACN YPTCGGYQFT CPSGRCIYQN WV CDGEDDC KDNGDEDGCE SGPHDVHKCS PREWSCPESG RCISIYKVCD GILDCPGRED ENNTSTGKYC SMTLCSALNC QYQ CHETPY GGACFCPPGY IINHNDSRTC VEFDDCQIWG ICDQKCESRP GRHLCHCEEG YILERGQYCK ANDSFGEASI IFSN GRDLL IGDIHGRSFR ILVESQNRGV AVGVAFHYHL QRVFWTDTVQ NKVFSVDING LNIQEVLNVS VETPENLAVD WVNNK IYLV ETKVNRIDMV NLDGSYRVTL ITENLGHPRG IAVDPTVGYL FFSDWESLSG EPKLERAFMD GSNRKDLVKT KLGWPA GVT LDMISKRVYW VDSRFDYIET VTYDGIQRKT VVHGGSLIPH PFGVSLFEGQ VFFTDWTKMA VLKANKFTET NPQVYYQ AS LRPYGVTVYH SLRQPYATNP CKDNNGGCEQ VCVLSHRTDN DGLGFRCKCT FGFQLDTDER HCIAVQNFLI FSSQVAIR G IPFTLSTQED VMVPVSGNPS FFVGIDFDAQ DSTIFFSDMS KHMIFKQKID GTGREILAAN RVENVESLAF DWISKNLYW TDSHYKSISV MRLADKTRRT VVQYLNNPRS VVVHPFAGYL FFTDWFRPAK IMRAWSDGSH LLPVINTTLG WPNGLAIDWA ASRLYWVDA YFDKIEHSTF DGLDRRRLGH IEQMTHPFGL AIFGEHLFFT DWRLGAIIRV RKADGGEMTV IRSGIAYILH L KSYDVNIQ TGSNACNQPT HPNGDCSHFC FPVPNFQRVC GCPYGMRLAS NHLTCEGDPT NEPPTEQCGL FSFPCKNGRC VP NYYLCDG VDDCHDNSDE QLCGTLNNTC SSSAFTCGHG ECIPAHWRCD KRNDCVDGSD EHNCPTHAPA SCLDTQYTCD NHQ CISKNW VCDTDNDCGD GSDEKNCNST ETCQPSQFNC PNHRCIDLSF VCDGDKDCVD GSDEVGCVLN CTASQFKCAS GDKC IGVTN RCDGVFDCSD NSDEAGCPTR PPGMCHSDEF QCQEDGICIP NFWECDGHPD CLYGSDEHNA CVPKTCPSSY FHCDN GNCI HRAWLCDRDN DCGDMSDEKD CPTQPFRCPS WQWQCLGHNI CVNLSVVCDG IFDCPNGTDE SPLCNGNSCS DFNGGC THE CVQEPFGAKC LCPLGFLLAN DSKTCEDIDE CDILGSCSQH CYNMRGSFRC SCDTGYMLES DGRTCKVTAS ESLLLLV AS QNKIIADSVT SQVHNIYSLV ENGSYIVAVD FDSISGRIFW SDATQGKTWS AFQNGTDRRV VFDSSIILTE TIAIDWVG R NLYWTDYALE TIEVSKIDGS HRTVLISKNL TNPRGLALDP RMNEHLLFWS DWGHHPRIER ASMDGSMRTV IVQDKIFWP CGLTIDYPNR LLYFMDSYLD YMDFCDYNGH HRRQVIASDL IIRHPYALTL FEDSVYWTDR ATRRVMRANK WHGGNQSVVM YNIQWPLGI VAVHPSKQPN SVNPCAFSRC SHLCLLSSQG PHFYSCVCPS GWSLSPDLLN CLRDDQPFLI TVRQHIIFGI S LNPEVKSN DAMVPIAGIQ NGLDVEFDDA EQYIYWVENP GEIHRVKTDG TNRTVFASIS MVGPSMNLAL DWISRNLYST NP RTQSIEV LTLHGDIRYR KTLIANDGTA LGVGFPIGIT VDPARGKLYW SDQGTDSGVP AKIASANMDG TSVKTLFTGN LEH LECVTL DIEEQKLYWA VTGRGVIERG NVDGTDRMIL VHQLSHPWGI AVHDSFLYYT DEQYEVIERV DKATGANKIV LRDN VPNLR GLQVYHRRNA AESSNGCSNN MNACQQICLP VPGGLFSCAC ATGFKLNPDN RSCSPYNSFI VVSMLSAIRG FSLEL SDHS ETMVPVAGQG RNALHVDVDV SSGFIYWCDF SSSVASDNAI RRIKPDGSSL MNIVTHGIGE NGVRGIAVDW VAGNLY FTN AFVSETLIEV LRINTTYRRV LLKVTVDMPR HIVVDPKNRY LFWADYGQRP KIERSFLDCT NRTVLVSEGI VTPRGLA VD RSDGYVYWVD DSLDIIARIR INGENSEVIR YGSRYPTPYG ITVFENSIIW VDRNLKKIFQ ASKEPENTEP PTVIRDNI N WLRDVTIFDK QVQPRSPAEV NNNPCLENNG GCSHLCFALP GLHTPKCDCA FGTLQSDGKN CAISTENFLI FALSNSLRS LHLDPENHSP PFQTINVERT VMSLDYDSVS DRIYFTQNLA SGVGQISYAT LSSGIHTPTV IASGIGTADG IAFDWITRRI YYSDYLNQM INSMAEDGSN RTVIARVPKP RAIVLDPCQG YLYWADWDTH AKIERATLGG NFRVPIVNSS LVMPSGLTLD Y EEDLLYWV DASLQRIERS TLTGVDREVI VNAAVHAFGL TLYGQYIYWT DLYTQRIYRA NKYDGSGQIA MTTNLLSQPR GI NTVVKNQ KQQCNNPCEQ FNGGCSHICA PGPNGAECQC PHEGNWYLAN NRKHCIVDNG ERCGASSFTC SNGRCISEEW KCD NDNDCG DGSDEMESVC ALHTCSPTAF TCANGRCVQY SYRCDYYNDC GDGSDEAGCL FRDCNATTEF MCNNRRCIPR EFIC NGVDN CHDNNTSDEK NCPDRTCQSG YTKCHNSNIC IPRVYLCDGD NDCGDNSDEN PTYCTTHTCS SSEFQCASGR CIPQH WYCD QETDCFDASD EPASCGHSER TCLADEFKCD GGRCIPSEWI CDGDNDCGDM SDEDKRHQCQ NQNCSDSEFL CVNDRP PDR RCIPQSWVCD GDVDCTDGYD ENQNCTRRTC SENEFTCGYG LCIPKIFRCD RHNDCGDYSD ERGCLYQTCQ QNQFTCQ NG RCISKTFVCD EDNDCGDGSD ELMHLCHTPE PTCPPHEFKC DNGRCIEMMK LCNHLDDCLD NSDEKGCGIN ECHDPSIS G CDHNCTDTLT SFYCSCRPGY KLMSDKRTCV DIDECTEMPF VCSQKCENVI GSYICKCAPG YLREPDGKTC RQNSNIEPY LIFSNRYYLR NLTIDGYFYS LILEGLDNVV ALDFDRVEKR LYWIDTQRQV IERMFLNKTN KETIINHRLP AAESLAVDWV SRKLYWLDA RLDGLFVSDL NGGHRRMLAQ HCVDANNTFC FDNPRGLALH PQYGYLYWAD WGHRAYIGRV GMDGTNKSVI I STKLEWPN GITIDYTNDL LYWADAHLGY IEYSDLEGHH RHTVYDGALP HPFAITIFED TIYWTDWNTR TVEKGNKYDG SN RQTLVNT THRPFDIHVY HPYRQPIVSN PCGTNNGGCS HLCLIKPGGK GFTCECPDDF RTLQLSGSTY CMPMCSSTQF LCA NNEKCI PIWWKCDGQK DCSDGSDELA LCPQRFCRLG QFQCSDGNCT SPQTLCNAHQ NCPDGSDEDR LLCENHHCDS NEWQ CANKR CIPESWQCDT FNDCEDNSDE DSSHCASRTC RPGQFRCANG RCIPQAWKCD VDNDCGDHSD EPIEECMSSA HLCDN FTEF SCKTNYRCIP KWAVCNGVDD CRDNSDEQGC EERTCHPVGD FRCKNHHCIP LRWQCDGQND CGDNSDEENC APRECT ESE FRCVNQQCIP SRWICDHYND CGDNSDERDC EMRTCHPEYF QCTSGHCVHS ELKCDGSADC LDASDEADCP TRFPDGA YC QATMFECKNH VCIPPYWKCD GDDDCGDGSD EELHLCLDVP CNSPNRFRCD NNRCIYSHEV CNGVDDCGDG TDETEEHC R KPTPKPCTEY EYKCGNGHCI PHDNVCDDAD DCGDWSDELG CNKGKERTCA ENICEQNCTQ LNEGGFICSC TAGFETNVF DRTSCLDINE CEQFGTCPQH CRNTKGSYEC VCADGFTSMS DRPGKRCAAE GSSPLLLLPD NVRIRKYNLS SERFSEYLQD EEYIQAVDY DWDPKDIGLS VVYYTVRGEG SRFGAIKRAY IPNFESGRNN LVQEVDLKLK YVMQPDGIAV DWVGRHIYWS D VKNKRIEV AKLDGRYRKW LISTDLDQPA AIAVNPKLGL MFWTDWGKEP KIESAWMNGE DRNILVFEDL GWPTGLSIDY LN NDRIYWS DFKEDVIETI KYDGTDRRVI AKEAMNPYSL DIFEDQLYWI SKEKGEVWKQ NKFGQGKKEK TLVVNPWLTQ VRI FHQLRY NKSVPNLCKQ ICSHLCLLRP GGYSCACPQG SSFIEGSTTE CDAAIELPIN LPPPCRCMHG GNCYFDETDL PKCK CPSGY TGKYCEMAFS KGISPGTTAV AVLLTILLIV VIGALAIAGF FHYRRTGSLL PALPKLPSLS SLVKPSENGN GVTFR SGAD LNMDIGVSGF GPETAIDRSM AMSEDFVMEM GKQPIIFENP MYSARDSAVK VVQPIQVTVS ENVDNKNYGS PINPSE IVP ETNPTSPAAD GTQVTKWNLF KRKSKQTTNF ENPIYAQMEN EQKESVAATP PPSPSLPAKP KPPSRRDPTP TYSATED TF KDTANLVKED SEV

UniProtKB: Low-density lipoprotein receptor-related protein 2

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 23 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111811
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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