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9qaw

CryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1

Method: ELECTRON MICROSCOPY Dmax: 363.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-2-macroglobulin receptor-associated protein

Homo sapiens

UniProt P30533

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 12 其他Polymer 16 PDB declaration: 12-meric（12） Consistent with protein copy count Chain K； UniProt 35–357 Chain L； UniProt 35–357 Not recorded Low-density lipoprotein receptor-related protein 2 × 2 （P98164） Unidentified peptide 1 × 2 Unidentified peptide 2 × 3 Unidentified peptide 3 × 1 Unidentified peptide 4 × 1 Unidentified peptide 5 × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 7 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 BMA beta-D-mannopyranose × 2 NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 7 CA CALCIUM ION × 25 NI NICKEL (II) ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.34 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9QAW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LRE RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, 20 STRUCTURES Deposited 1997-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 51–131（81 aa） Fragment：N-TERMINAL DOMAIN, DOMAIN 1, RESIDUES 17 - 97
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K
Resolution not provided
1NRE RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 51–131（81 aa） Fragment：N-TERMINAL DOMAIN, DOMAIN 1, RESIDUES 17 - 97
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K
Resolution not provided
1OP1 Solution NMR structure of domain 1 of receptor associated protein Deposited 2003-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 51–132（82 aa） Fragment：Domain 1 of receptor associated protein
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303.5 K；Ionic strength (raw mmCIF value) 50 mM NaCl, 75 mM NaPi；Pressure ambient
NMR sample composition ~1.2 mM 15N/13C isotope labeled D1 of RAP in a 50 mM NaCl, 75 mM NaPi, pH 6.5 | 95% H2O and 5% D2O
NMR sample composition ~1.2 mM 15N/13C isotpe-labeled D1 of RAP in a 50 mM NaCl, 75 mM NaPi, pH 6.5 | 99.99% D2O
Resolution not provided
1OV2 Ensemble of the solution structures of domain one of receptor associated protein Deposited 2003-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–133（99 aa） Fragment：domain 1 of receptor associated protein
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303.5 K；Ionic strength (raw mmCIF value) 50 mM NaCl, 75 mM NaPi；Pressure ambient
NMR sample composition ~1.2 mM of 13C/15N isotope labeled domain 1 of receptor associated protein | 50 mM NaCl, 75 mM NaPi, pH 6.5
Resolution not provided
2FCW Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP). Deposited 2005-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 249–357（109 aa） Fragment：Domain Three
Mutation：E215G NA SODIUM ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.26 Å R-free 0.200
2FCW Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP). Deposited 2005-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 249–357（109 aa） Fragment：Domain Three
Mutation：E215G NA SODIUM ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.26 Å R-free 0.200
2FTU solution structure of domain 3 of RAP Deposited 2006-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 240–357（118 aa） Fragment：residues 240-357
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions Pressure AMBIENT
Resolution not provided
2FYL Haddock model of the complex between double module of LRP, CR56, and first domain of receptor associated protein, RAP-d1. Deposited 2006-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 51–131（81 aa） Fragment：Rapd1
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure ambient
NMR sample composition 0.1mM [U-99% 15N]-CR56; 0.1mM RAPd1; H2O/D2O (90:10) | H2O/D2O (90:10)
NMR sample composition 0.5mM [U-99% 15N]-RAPd1; 0.5mM CR56; H2O/D2O (90:10) | H2O/D2O (90:10)
NMR sample composition 0.08 mM [U-99% 15N, U-99% 13C]-CR56; 0.08 mM [U-99% 15N, U-99% 13C]-RAPd1; H2O/D2O (90:10) | H2O/D2O (90:10)
Resolution not provided
2P01 The structure of receptor-associated protein(RAP) Deposited 2007-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–357（323 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.25；303 K；Ionic strength (raw mmCIF value) 75 mM NaPi 50 mM NaCl；Pressure AMBIENT
Resolution not provided
2P03 The structure of receptor-associated protein(RAP) Deposited 2007-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–357（323 aa） Fragment：Residues 35-357
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.25；303 K；Ionic strength (raw mmCIF value) 75 mM NaPi 50 mM NaCl；Pressure AMBIENT
Resolution not provided

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMRP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain K； PDBConstruct 3–325； UniProt 35–357 Author chain L； PDBConstruct 3–325； UniProt 35–357

Low-density lipoprotein receptor-related protein 2

Homo sapiens

UniProt P98164

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 12 其他Polymer 16 PDB declaration: 12-meric（12） Consistent with protein copy count Chain A； UniProt 1–4423 Chain B； UniProt 1–4423 Not recorded Alpha-2-macroglobulin receptor-associated protein × 2 （P30533） Unidentified peptide 1 × 2 Unidentified peptide 2 × 3 Unidentified peptide 3 × 1 Unidentified peptide 4 × 1 Unidentified peptide 5 × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 7 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 BMA beta-D-mannopyranose × 2 NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 7 CA CALCIUM ION × 25 NI NICKEL (II) ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.34 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9QAW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2M0P Solution structure of the tenth complement type repeat of human megalin Deposited 2012-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1103–1148（46 aa）
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] CR10, 100 mM sodium chloride, 50 mM calcium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] CR10, 50 mM calcium chloride, 100 mM sodium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
9CWM Cryo-EM structure of human Low-density lipoprotein receptor-related protein 2 Deposited 2024-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–4655（4655 aa）
Chain B 1–4655（4655 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9I3V Cryo-EM structure of the human LRP2 ectodomain Deposited 2025-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–4423（4423 aa）
Chain B 1–4423（4423 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 9 CA CALCIUM ION × 25 NI NICKEL (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LRP2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–4423； UniProt 1–4423 Author chain B； PDBConstruct 1–4423； UniProt 1–4423

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9qaw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qaw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9qaw
Deposition date deposition_date2025-02-28
Structure title titleCryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1
Keywords keywordsMegalin, LRP2, LDL receptor, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier96.66 Å
Radius of gyration Rg (electron density) rg_electron96.65 Å
Forward intensity I(0) i012834300000.00
Molecular weight molecular_weight906930.0 kDa
Excluded volume excluded_volume1109100 ų
Envelope volume envelope_volume2294600 ų
Hydration-shell volume shell_volume203330 ų
Envelope diameter envelope_diameter289.6 Å
Shell Rg shell_rg87.50 Å
Envelope Rg envelope_rg90.02 Å
Shape Rg shape_rg96.64 Å
Total Rg total_rg96.61 Å
Total atoms total_atoms119966
Residues n_residues7952
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax363.6 Å
Rg (real space) rg_real102.60 Å
Rg uncertainty (real space) rg_real_error3.12 Å
I(0) (real space) i0_real1.2970e+10
I(0) uncertainty (real space) i0_real_error2.9550e+08
Rg (reciprocal space) rg_reciprocal96.55 Å
I(0) (reciprocal space) i0_reciprocal12830000000.0000
Solution quality estimate total_estimate0.8875
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary113.6 Å
Skewness Skewness skewness0.460
Kurtosis Kurtosis kurtosis0.007
Angular range angular_range— – 0.0800 Å−1
Current regularization parameter α current_alpha0.9079
Highest regularization parameter α highest_alpha470800000.0000
Real-space data points n_real_points17
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 0.822; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.649
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (14)

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8. Citations (1)

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9. Files and Curves (10)