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- EMDB-28241: Cryo-EM structure of LRP2 at pH 5.2 -

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Basic information

Entry
Database: EMDB / ID: EMD-28241
TitleCryo-EM structure of LRP2 at pH 5.2
Map data
Sample
  • Complex: LRP2 at endosomal pH
    • Protein or peptide: Low-density lipoprotein receptor-related protein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-galactopyranose
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


Transport of RCbl within the body / endocytic hemoglobin import into cell / diol metabolic process / chemoattraction of axon / positive regulation of lipoprotein transport / Retinoid metabolism and transport / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of oligodendrocyte progenitor proliferation / folate import across plasma membrane ...Transport of RCbl within the body / endocytic hemoglobin import into cell / diol metabolic process / chemoattraction of axon / positive regulation of lipoprotein transport / Retinoid metabolism and transport / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of oligodendrocyte progenitor proliferation / folate import across plasma membrane / metal ion transport / response to leptin / ventricular compact myocardium morphogenesis / protein transporter activity / hormone binding / Cargo recognition for clathrin-mediated endocytosis / vitamin D metabolic process / neuron projection arborization / Clathrin-mediated endocytosis / hormone secretion / coronary artery morphogenesis / outflow tract septum morphogenesis / insulin-like growth factor I binding / transcytosis / protein import / coronary vasculature development / cargo receptor activity / aorta development / positive regulation of neurogenesis / ventricular septum development / endosomal transport / low-density lipoprotein particle receptor binding / hemoglobin binding / amyloid-beta clearance / positive regulation of endocytosis / vagina development / brush border / negative regulation of BMP signaling pathway / endocytic vesicle / response to X-ray / axonal growth cone / forebrain development / clathrin-coated pit / receptor-mediated endocytosis / kidney development / neural tube closure / PDZ domain binding / endosome lumen / nuclear receptor binding / brush border membrane / sensory perception of sound / cellular response to growth factor stimulus / SH3 domain binding / endocytosis / male gonad development / protein transport / apical part of cell / heart development / protein-folding chaperone binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome / membrane raft / apical plasma membrane / axon / external side of plasma membrane / dendrite / calcium ion binding / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
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 / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. ...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 / 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 / Six-bladed beta-propeller, TolB-like / 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 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse) / house mouse (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsBeenken A / Cerutti G / Fitzpatrick AW / Barasch J / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK124667 United States
CitationJournal: Cell / Year: 2023
Title: Structures of LRP2 reveal a molecular machine for endocytosis.
Authors: Andrew Beenken / Gabriele Cerutti / Julia Brasch / Yicheng Guo / Zizhang Sheng / Hediye Erdjument-Bromage / Zainab Aziz / Shelief Y Robbins-Juarez / Estefania Y Chavez / Goran Ahlsen / ...Authors: Andrew Beenken / Gabriele Cerutti / Julia Brasch / Yicheng Guo / Zizhang Sheng / Hediye Erdjument-Bromage / Zainab Aziz / Shelief Y Robbins-Juarez / Estefania Y Chavez / Goran Ahlsen / Phinikoula S Katsamba / Thomas A Neubert / Anthony W P Fitzpatrick / Jonathan Barasch / Lawrence Shapiro /
Abstract: The low-density lipoprotein (LDL) receptor-related protein 2 (LRP2 or megalin) is representative of the phylogenetically conserved subfamily of giant LDL receptor-related proteins, which function in ...The low-density lipoprotein (LDL) receptor-related protein 2 (LRP2 or megalin) is representative of the phylogenetically conserved subfamily of giant LDL receptor-related proteins, which function in endocytosis and are implicated in diseases of the kidney and brain. Here, we report high-resolution cryoelectron microscopy structures of LRP2 isolated from mouse kidney, at extracellular and endosomal pH. The structures reveal LRP2 to be a molecular machine that adopts a conformation for ligand binding at the cell surface and for ligand shedding in the endosome. LRP2 forms a homodimer, the conformational transformation of which is governed by pH-sensitive sites at both homodimer and intra-protomer interfaces. A subset of LRP2 deleterious missense variants in humans appears to impair homodimer assembly. These observations lay the foundation for further understanding the function and mechanism of LDL receptors and implicate homodimerization as a conserved feature of the LRP receptor subfamily.
History
DepositionSep 27, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateMar 8, 2023-
Current statusMar 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28241.png

Downloads & links

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Map

FileDownload / File: emd_28241.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.46168488 - 1.4269
Average (Standard dev.)0.00073808606 (±0.044584215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite of unsharpened local refinement maps

Fileemd_28241_additional_1.map
AnnotationComposite of unsharpened local refinement maps
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Composite of global map with deepEMhancer density-modified local...

Fileemd_28241_additional_2.map
AnnotationComposite of global map with deepEMhancer density-modified local refinements
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28241_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_28241_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : LRP2 at endosomal pH

EntireName: LRP2 at endosomal pH
Components
  • Complex: LRP2 at endosomal pH
    • Protein or peptide: Low-density lipoprotein receptor-related protein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-galactopyranose
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: LRP2 at endosomal pH

SupramoleculeName: LRP2 at endosomal pH / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 / Details: Endogenously purified from mouse kidney
Source (natural)Organism: Mus musculus (house mouse)

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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: house mouse (house mouse)
Molecular weightTheoretical: 519.7465 KDa
SequenceString: MERGAAAAAW MLLLAIAACL APVSGQECGS GNFRCDNGYC IPASWRCDGT RDCLDDTDEI GCPPRSCGSG FFLCPAEGTC IPSSWVCDQ DKDCSDGADE QQNCPGTTCS SQQLTCSNGQ CVPIEYRCDH VSDCPDGSDE RNCYYPTCDQ LTCANGACYN T SQKCDHKV ...String:
MERGAAAAAW MLLLAIAACL APVSGQECGS GNFRCDNGYC IPASWRCDGT RDCLDDTDEI GCPPRSCGSG FFLCPAEGTC IPSSWVCDQ DKDCSDGADE QQNCPGTTCS SQQLTCSNGQ CVPIEYRCDH VSDCPDGSDE RNCYYPTCDQ LTCANGACYN T SQKCDHKV DCRDSSDEAN CTTLCSQKEF QCGSGECILR AYVCDHDNDC EDNSDEHNCN YDTCGGHQFT CSNGQCINQN WV CDGDDDC QDSGDEDGCE SNQRHHTCYP REWACPGSGR CISMDKVCDG VPDCPEGEDE NNATSGRYCG TGLCSILNCE YQC HQTPYG GECFCPPGHI INSNDSRTCI DFDDCQIWGI CDQKCESRQG RHQCLCEEGY ILERGQHCKS NDSFSAASII FSNG RDLLV GDLHGRNFRI LAESKNRGIV MGVDFHYQKH RVFWTDPMQA KVFSTDINGL NTQEILNVSI DAPENLAVDW INNKL YLVE TRVNRIDVVN LEGNQRVTLI TENLGHPRGI ALDPTVGYLF FSDWGSLSGQ PKVERAFMDG SNRKDLVTTK LGWPAG ITL DLVSKRVYWV DSRYDYIETV TYDGIQRKTV ARGGSLVPHP FGISLFEEHV FFTDWTKMAV MKANKFTDTN PQVYHQS SL TPFGVTVYHA LRQPNATNPC GNNNGGCAQI CVLSHRTDNG GLGYRCKCEF GFELDADEHH CVAVKNFLLF SSQTAVRG I PFTLSTQEDV MVPVTGSPSF FVGIDFDAQH STIFYSDLSK NIIYQQKIDG TGKEVITANR LQNVECLSFD WISRNLYWT DGGSKSVTVM KLADKSRRQI ISNLNNPRSI VVHPAAGYMF LSDWFRPAKI MRAWSDGSHL MPIVNTSLGW PNGLAIDWST SRLYWVDAF FDKIEHSNLD GLDRKRLGHV DQMTHPFGLT VFKDNVFLTD WRLGAIIRVR KSDGGDMTVV RRGISSIMHV K AYDADLQT GTNYCSQTTH PNGDCSHFCF PVPNFQRVCG CPYGMKLQRD QMTCEGDPAR EPPTQQCGSS SFPCNNGKCV PS IFRCDGV DDCHDNSDEH QCGALNNTCS SSAFTCVHGG QCIPGQWRCD KQNDCLDGSD EQNCPTRSPS STCPPTSFTC DNH MCIPKE WVCDTDNDCS DGSDEKNCQA SGTCHPTQFR CPDHRCISPL YVCDGDKDCV DGSDEAGCVL NCTSSQFKCA DGSS CINSR YRCDGVYDCK DNSDEAGCPT RPPGMCHPDE FQCQGDGTCI PNTWECDGHP DCIQGSDEHN GCVPKTCSPS HFLCD NGNC IYNSWVCDGD NDCRDMSDEK DCPTQPFHCP SSQWQCPGYS ICVNLSALCD GVFDCPNGTD ESPLCNQDSC LHFNGG CTH RCIQGPFGAT CVCPIGYQLA NDTKTCEDVN ECDIPGFCSQ HCVNMRGSFR CACDPEYTLE SDGRTCKVTA SENLLLV VA SRDKIIMDNI TAHTHNIYSL VQDVSFVVAL DFDSVTGRVF WSDLLEGKTW SAFQNGTDKR VVHDSGLSLT EMIAVDWI G RNIYWTDYTL ETIEVSKIDG SHRTVLISKN VTKPRGLALD PRMGDNVMFW SDWGHHPRIE RASMDGTMRT VIVQEKIYW PCGLSIDYPN RLIYFMDAYL DYIEFCDYDG QNRRQVIASD LVLHHPHALT LFEDSVFWTD RGTHQVMQAN KWHGRNQSVV MYSVPQPLG IIAIHPSRQP SSPNPCASAT CSHLCLLSAQ EPRHYSCACP SGWNLSDDSV NCVRGDQPFL ISVRENVIFG I SLDPEVKS NDAMVPISGI QHGYDVEFDD SEQFIYWVEN PGEIHRVKTD GSNRTAFAPL SLLGSSLGLA LDWVSRNIYY TT PASRSIE VLTLRGDTRY GKTLITNDGT PLGVGFPVGI AVDPARGKLY WSDHGTDSGV PAKIASANMD GTSLKILFTG NME HLEVVT LDIQEQKLYW AVTSRGVIER GNVDGTERMI LVHHLAHPWG LVVHGSFLYY SDEQYEVIER VDKSSGSNKV VFRD NIPYL RGLRVYHHRN AADSSNGCSN NPNACQQICL PVPGGMFSCA CASGFKLSPD GRSCSPYNSF IVVSMLPAVR GFSLE LSDH SEAMVPVAGQ GRNVLHADVD VANGFIYWCD FSSSVRSSNG IRRIKPNGSN FTNIVTYGIG ANGIRGVAVD WVAGNL YFT NAFVYETLIE VIRINTTYRR VLLKVSVDMP RHIVVDPKHR YLFWADYGQK PKIERSFLDC TNRTVLVSEG IVTPRGL AV DHDTGYIYWV DDSLDIIARI HRDGGESQVV RYGSRYPTPY GITVFGESII WVDRNLRKVF QASKQPGNTD PPTVIRDS I NLLRDVTIFD EHVQPLSPAE LNNNPCLQSN GGCSHFCFAL PELPTPKCGC AFGTLEDDGK NCATSREDFL IYSLNNSLR SLHFDPQDHN LPFQAISVEG MAIALDYDRR NNRIFFTQKL NPIRGQISYV NLYSGASSPT ILLSNIGVTD GIAFDWINRR IYYSDFSNQ TINSMAEDGS NRAVIARVSK PRAIVLDPCR GYMYWTDWGT NAKIERATLG GNFRVPIVNT SLVWPNGLTL D LETDLLYW ADASLQKIER STLTGSNREV VISTAFHSFG LTVYGQYIYW TDFYTKKIYR ANKYDGSDLI AMTTRLPTQP SG ISTVVKT QQQQCSNPCD QFNGGCSHIC APGPNGAECQ CPHEGSWYLA NDNKYCVVDT GARCNQFQFT CLNGRCISQD WKC DNDNDC GDGSDELPTV CAFHTCRSTA FTCANGRCVP YHYRCDFYND CGDNSDEAGC LFRSCNSTTE FTCSNGRCIP LSYV CNGIN NCHDNDTSDE KNCPPITCQP DFAKCQTTNI CVPRAFLCDG DNDCGDGSDE NPIYCASHTC RSNEFQCVSP HRCIP SYWF CDGEADCVDS SDEPDTCGHS LNSCSANQFH CDNGRCISSS WVCDGDNDCG DMSDEDQRHH CELQNCSSTE FTCINS RPP NRRCIPQHWV CDGDADCADA LDELQNCTMR ACSTGEFSCA NGRCIRQSFR CDRRNDCGDY SDERGCSYPP CRDDQFT CQ NGQCITKLYV CDEDNDCGDG SDEQEHLCHT PEPTCPPHQF RCDNGHCIEM GTVCNHVDDC SDNSDEKGCG INECQDSS I SHCDHNCTDT ITSFYCSCLP GYKLMSDKRT CVDIDECKET PQLCSQKCEN VIGSYICKCA PGYIREPDGK SCRQNSNIE PYLVFSNRYY IRNLTIDGTS YSLILQGLGN VVALDFDRVE ERLYWIDAEK QIIERMFLNK TNQETIISHR LRRAESLAVD WVSRKLYWL DAILDCLFVS DLEGRQRKML AQHCVDANNT FCFENPRGIV LHPQRGYVYW ADWGDHAYIA RIGMDGTNKT V IISTKIEW PNAITIDYTN DLLYWADAHL GYIEFSDLEG HHRHTVYDGT LPHPFALTIF EDTVFWTDWN TRTVEKGNKY DG SGRVVLV NTTHKPFDIH VLHPYRQPIM SNPCATNNGG CSHLCLIKAG GRGFTCECPD DFQTVQLRDR TLCMPMCSST QFL CGNNEK CIPIWWKCDG QKDCSDGSDE SDLCPHRFCR LGQFQCRDGN CTSPQALCNA RQDCADGSDE DRVLCEHHRC EANE WQCAN KRCIPEYWQC DSVDDCLDNS DEDPSHCASR TCRPGQFKCN NGRCIPQSWK CDVDNDCGDY SDEPIHECMT AAYNC DNHT EFSCKTNYRC IPQWAVCNGF DDCRDNSDEQ GCESVPCHPS GDFRCGNHHC IPLRWKCDGI DDCGDNSDEE SCVPRE CTE SEFRCADQQC IPSRWVCDQE NDCGDNSDER DCEMKTCHPE HFQCTSGHCV PKALACDGRA DCLDASDESA CPTRFPN GT YCPAAMFECK NHVCIQSFWI CDGENDCVDG SDEEIHLCFN VPCESPQRFR CDNSRCIYGH QLCNGVDDCG DGSDEKEE H CRKPTHKPCT DTEYKCSNGN CVSQHYVCDN VDDCGDLSDE TGCNLGENRT CAEKICEQNC TQLSNGGFIC SCRPGFKPS TLDKNSCQDI NECEEFGICP QSCRNSKGSY ECFCVDGFKS MSTHYGERCA ADGSPPLLLL PENVRIRKYN ISSEKFSEYL EEEEHIQAI DYDWDPEGIG LSVVYYTVLS QGSQFGAIKR AYLPDFESGS NNPVREVDLG LKYLMQPDGL AVDWVGRHIY W SDAKSQRI EVATLDGRYR KWLITTQLDQ PAAIAVNPKL GLMFWTDQGK QPKIESAWMN GEHRSVLASA NLGWPNGLSI DY LNGDRIY WSDSKEDVIE SIKYDGTDRR LIINDAMKPF SLDIFEDQLY WVAKEKGEVW RQNKFGKGNK EKLLVVNPWL TQV RIFHQL RYNQSVSNPC KQVCSHLCLL RPGGYSCACP QGSDFVTGST VECDAASELP ITMPSPCRCM HGGSCYFDEN DLPK CKCSS GYSGEYCEIG LSRGIPPGTT MALLLTFAMV IIVGALVLVG FFHYRKTGSL LPSLPKLPSL SSLAKPSENG NGVTF RSGA DVNMDIGVSP FGPETIIDRS MAMNEQFVME VGKQPVIFEN PMYAAKDSTS KVGLAVQGPS VSSQVTVPEN VENQNY GRS IDPSEIVPEP KPASPGADET QGTKWNIFKR KPKQTTNFEN PIYAEMDTEQ KEAVAVAPPP SPSLPAKASK RSSTPGY TA TEDTFKDTAN LVKEDSDV

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 78 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-galactopyranose / type: ligand / ID: 4 / Number of copies: 44 / Formula: NGA
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NGA:
2-acetamido-2-deoxy-beta-D-galactopyranose / N-Acetylgalactosamine

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 88 / 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

Concentration2 mg/mL
BufferpH: 5.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.06 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1n7d

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 209932
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8em7:
Cryo-EM structure of LRP2 at pH 5.2

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