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- PDB-9qaw: CryoEM structure of the human LRP2 receptor ectodomain in complex... -

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Basic information

Entry
Database: PDB / ID: 9qaw
TitleCryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1
Components
  • (Unidentified peptide ...) x 5
  • Alpha-2-macroglobulin receptor-associated protein
  • Low-density lipoprotein receptor-related protein 2
KeywordsENDOCYTOSIS / Megalin / LRP2 / LDL receptor
Function / homology
Function and homology information


extracellular negative regulation of signal transduction / regulation of receptor-mediated endocytosis / Transport of RCbl within the body / negative regulation of very-low-density lipoprotein particle clearance / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / rough endoplasmic reticulum lumen / lipase binding ...extracellular negative regulation of signal transduction / regulation of receptor-mediated endocytosis / Transport of RCbl within the body / negative regulation of very-low-density lipoprotein particle clearance / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / rough endoplasmic reticulum lumen / lipase binding / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane / cobalamin transport / receptor antagonist activity / amyloid-beta clearance by transcytosis / negative regulation of amyloid-beta clearance / ventricular compact myocardium morphogenesis / response to leptin / protein transporter activity / Vitamin D (calciferol) metabolism / low-density lipoprotein particle receptor activity / metal ion transport / transcytosis / vitamin D metabolic process / very-low-density lipoprotein particle receptor binding / cranial skeletal system development / positive regulation of amyloid-beta clearance / neuron projection arborization / coronary artery morphogenesis / cis-Golgi network / insulin-like growth factor I binding / negative regulation of receptor internalization / outflow tract septum morphogenesis / cargo receptor activity / positive regulation of neurogenesis / ventricular septum development / aorta development / low-density lipoprotein particle receptor binding / endoplasmic reticulum-Golgi intermediate compartment / forebrain development / vagina development / hormone binding / amyloid-beta clearance / negative regulation of BMP signaling pathway / negative regulation of protein binding / retinoid metabolic process / transport across blood-brain barrier / Retinoid metabolism and transport / endomembrane system / clathrin-coated pit / receptor-mediated endocytosis / endosome lumen / lipid metabolic process / kidney development / neural tube closure / phosphatidylinositol 3-kinase/protein kinase B signal transduction / brush border membrane / clathrin-coated endocytic vesicle membrane / sensory perception of sound / SH3 domain binding / Golgi lumen / cellular response to growth factor stimulus / male gonad development / endocytosis / Cargo recognition for clathrin-mediated endocytosis / heparin binding / protein transport / amyloid-beta binding / Clathrin-mediated endocytosis / protein-folding chaperone binding / gene expression / lysosome / cell population proliferation / signaling receptor complex / endosome / apical plasma membrane / receptor ligand activity / signaling receptor binding / external side of plasma membrane / axon / lysosomal membrane / calcium ion binding / dendrite / negative regulation of apoptotic process / cell surface / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / : / LRP2-like, EGF-like domain ...Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / : / 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 / Endoplasmic reticulum targeting sequence. / 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
beta-D-mannopyranose / 2-acetamido-2-deoxy-beta-D-galactopyranose / NICKEL (II) ION / Alpha-2-macroglobulin receptor-associated protein / Low-density lipoprotein receptor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsRamanadane, K. / Coscia, F.
Funding supportEuropean Union, Switzerland, France, 3items
OrganizationGrant numberCountry
European Research Council (ERC)101041298European Union
Swiss National Science FoundationP500PB_217862 Switzerland
Human Frontier Science Program (HFSP)LT0024/2024-L France
CitationJournal: To Be Published
Title: CryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1
Authors: Ramanadane, K. / Coscia, F.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Alpha-2-macroglobulin receptor-associated protein
A: Low-density lipoprotein receptor-related protein 2
B: Low-density lipoprotein receptor-related protein 2
D: Unidentified peptide 1
C: Unidentified peptide 2
F: Unidentified peptide 2
E: Unidentified peptide 1
H: Unidentified peptide 3
I: Unidentified peptide 4
G: Unidentified peptide 5
J: Unidentified peptide 2
K: Alpha-2-macroglobulin receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,106,85283
Polymers1,091,69612
Non-polymers15,15671
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules LKAB

#1: Protein Alpha-2-macroglobulin receptor-associated protein / Alpha-2-MRAP / Low density lipoprotein receptor-related protein-associated protein 1 / RAP


Mass: 40404.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRPAP1, A2MRAP / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P30533
#2: Protein Low-density lipoprotein receptor-related protein 2 / LRP-2 / Glycoprotein 330 / gp330 / Megalin


Mass: 502222.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP2 / Production host: Homo sapiens (human) / References: UniProt: P98164

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Unidentified peptide ... , 5 types, 8 molecules DECFJHIG

#3: Protein/peptide Unidentified peptide 1


Mass: 869.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Protein/peptide Unidentified peptide 2


Mass: 613.749 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#5: Protein/peptide Unidentified peptide 3


Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#6: Protein/peptide Unidentified peptide 4


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#7: Protein/peptide Unidentified peptide 5


Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Sugars , 5 types, 44 molecules

#8: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#10: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#11: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#12: Sugar
ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 27 molecules

#13: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Ca
#14: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human LRP2 ectodomain in complex with unidentified endogenous ligands and LRPAP1COMPLEX#1-#70RECOMBINANT
2LRPAP1COMPLEX#11RECOMBINANT
3Human LRP2 ectodomain in complex with unidentified endogenous ligandsCOMPLEX#2-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Escherichia coli (E. coli)562
43Homo sapiens (human)9606
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
140 mMsodium chlorideNaCl1
220 mMHEPESHEPES1
30.2 %OGOG1
40.0075 %Tween-20Tween-201
53 mMcalcium chlorideCaCl21
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 318131
Details: Composite map (please refer to related focused map and initial consensus map)
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 107.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005164944
ELECTRON MICROSCOPYf_angle_d0.767788189
ELECTRON MICROSCOPYf_chiral_restr0.0939535
ELECTRON MICROSCOPYf_plane_restr0.004311622
ELECTRON MICROSCOPYf_dihedral_angle_d6.330110054

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