← Back to search
2m0p

Solution structure of the tenth complement type repeat of human megalin

Method: SOLUTION NMR Dmax: 29.7 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1103–1148 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

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 2M0P Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9CWM Cryo-EM structure of human Low-density lipoprotein receptor-related protein 2 Deposited 2024-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
9QAW CryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1 Deposited 2025-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 1–4423（4423 aa）
Chain B 1–4423（4423 aa）
Not recorded 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

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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–46； UniProt 1103–1148

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 2m0p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2m0p
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2m0p
Deposition date deposition_date2012-11-01
Structure title titleSolution structure of the tenth complement type repeat of human megalin
Keywords keywordsComplement type repeat, receptor, megalin, ldl receptor family, lrp2, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodSOLUTION NMR
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.02 Å
Radius of gyration Rg (electron density) rg_electron11.19 Å
Forward intensity I(0) i0219593000.00
Molecular weight molecular_weight101150.0 kDa
Excluded volume excluded_volume116630 ų
Envelope volume envelope_volume21985 ų
Hydration-shell volume shell_volume12195 ų
Envelope diameter envelope_diameter54.1 Å
Shell Rg shell_rg21.12 Å
Envelope Rg envelope_rg16.66 Å
Shape Rg shape_rg11.23 Å
Total Rg total_rg11.41 Å
Total atoms total_atoms12720
Residues n_residues920
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax29.7 Å
Rg (real space) rg_real10.38 Å
Rg uncertainty (real space) rg_real_error0.04 Å
I(0) (real space) i0_real2.1040e+08
I(0) uncertainty (real space) i0_real_error1.3790e+06
Rg (reciprocal space) rg_reciprocal11.18 Å
I(0) (reciprocal space) i0_reciprocal219600000.0000
Solution quality estimate total_estimate0.6851
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary12.4 Å
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.421
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha4.1960
Highest regularization parameter α highest_alpha31020.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.997; Stabil: 0.974; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2m0pa_
Class classg — Small proteins
Fold Fold foldg.12 — LDL receptor-like module
Superfamily Superfamily superfamilyg.12.1 — LDL receptor-like module
Family Family familyg.12.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id2m0pA00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology400 — Low-density Lipoprotein Receptor
Homologous superfamily homologous superfamily10 — Low-density Lipoprotein Receptor
▶

8. Citations (1)

▶

9. Files and Curves (10)