SAXSdb — 1j8e

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

LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1

Homo sapiens

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 1011–1054	Fragment：COMPLEMENT-LIKE REPEAT 7 (CR7), LDL-RECEPTOR CLASS A 7 Mutation：C1G	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.8；292 K；0.02M Na-acetate, 0.1M CaCl2, 0.3M NaCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.85 Å R-free 0.222

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 1J8E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CR8 LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN COMPLEMENT REPEAT 8 Deposited 1998-12-14	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1059–1100（42 aa） Fragment：COMPLEMENT REPEAT 8	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1	Resolution not provided
1D2L NMR SOLUTION STRUCTURE OF COMPLEMENT-LIKE REPEAT CR3 FROM THE LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN (LRP). EVIDENCE FOR SPECIFIC BINDING TO THE RECEPTOR BINDING DOMAIN OF HUMAN ALPHA-2 MACROGLOBULIN Deposited 1999-09-24	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 851–893（43 aa） Fragment：COMPLEMENT-LIKE REPEAT 3 (CR3)	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 20 mM NA-D3-ACETATE, 10 mM CACL2；Pressure AMBIENT NMR sample composition 2 MM CR3 U-15N,13C 20 MM NA-D3-ACETATE PH 5.5 10 MM CACL 90% H2O, 10% D2O	Resolution not provided
2FYJ NMR Solution structure of calcium-loaded LRP double module Deposited 2006-02-08	Different construct Different mutation/modification 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 932–1013（82 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure ambient NMR measurement conditions pH 7；298 K；Pressure ambient NMR sample composition 0.5mM [U-99% 15N]-CR56 \| 298 K, pH 7.0, no salt NMR sample composition 0.5mM CR56 \| 298 K, pH 7.0, no salt	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 B 932–1013（82 aa） Fragment：CR56	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
2KNX Solution Structure of complement repeat CR17 from LRP-1 Deposited 2009-09-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2770–2817（48 aa） Fragment：residues 2770-2817	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7.45；307 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 150 mM sodium chloride, 20 mM [U-99% 2H] HEPES, 0.7 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 3 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KNY Fusion construct of CR17 from LRP-1 and ApoE residues 130-149 Deposited 2009-09-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2770–2817（48 aa） Fragment：Fusion of LRP UNP residues 2770-2817 and Apo-E UNP residues 147-167	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 20 mM [U-99% 2H] HEPES-1, 50 mM sodium chloride-2, 3 mM sodium azide-3, 5 mM CALCIUM ION-4, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-6, 50 mM sodium chloride-7, 3 mM sodium azide-8, 5 mM CALCIUM ION-9, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-10, 100% D2O \| 100% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-11, 50 mM sodium chloride-12, 3 mM sodium azide-13, 5 mM CALCIUM ION-14, 0.8 mM [U-99% 15N] entity_1-15, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-16, 150 mM sodium chloride-17, 3 mM sodium azide-18, 2 mM [U-99% 2H] EDTA-19, 0.5 mM [U-99% 15N] entity_2-20, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-21, 150 mM sodium chloride-22, 3 mM sodium azide-23, 2 mM [U-99% 2H] EDTA-24, 0.5 mM [U-99% 13C; U-99% 15N] entity_2-25, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LRP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–44； UniProt 1011–1054

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1j8e
Deposition date deposition_date	2001-05-21
Structure title title	Crystal structure of ligand-binding repeat CR7 from LRP
Keywords keywords	ligand binding, calcium binding, complement-like repeat, LRP receptor, signaling protein; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	11.08 Å
Radius of gyration Rg (electron density) rg_electron	9.99 Å
Forward intensity I(0) i0	832428.00
Molecular weight molecular_weight	4847.0 kDa
Excluded volume excluded_volume	5526 Å³
Envelope volume envelope_volume	6370 Å³
Hydration-shell volume shell_volume	5941 Å³
Envelope diameter envelope_diameter	37.0 Å
Shell Rg shell_rg	14.57 Å
Envelope Rg envelope_rg	10.53 Å
Shape Rg shape_rg	10.01 Å
Total Rg total_rg	11.13 Å
Total atoms total_atoms	333
Residues n_residues	44
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	38.9 Å
Rg (real space) rg_real	11.08 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	8.3240e+05
I(0) uncertainty (real space) i0_real_error	8.1410e+03
Rg (reciprocal space) rg_reciprocal	11.08 Å
I(0) (reciprocal space) i0_reciprocal	832400.0000
Solution quality estimate total_estimate	0.7183
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.3 Å
Skewness Skewness skewness	0.355
Kurtosis Kurtosis kurtosis	-0.167
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	73590.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.910; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1
Molecular weight formula_weight	4817.0 kDa
Mutation mutation	C1G
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	364

GSHSCSSTQFKCNSGRCIPEHWTCDGDNDCGDYSDETHANCTNQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1j8ea_
Class class	g — Small proteins
Fold Fold fold	g.12 — LDL receptor-like module
Superfamily Superfamily superfamily	g.12.1 — LDL receptor-like module
Family Family family	g.12.1.1 — LDL receptor-like module

CATH v4.4 (1 domains)

Domain ID domain_id	1j8eA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	400 — Low-density Lipoprotein Receptor
Homologous superfamily homologous superfamily	10 — Low-density Lipoprotein Receptor

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8. Citations (1)

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Unit-cell length a length_a	27.588 Å
Unit-cell length b length_b	35.359 Å
Unit-cell length c length_c	36.288 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	21.960 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	0.2220

fit	/app/data/saxs_computation/j8/1j8e/1j8e.fit
pddf	/app/data/pr_computation/j8/1j8e/1j8e.pr.out
profile	/app/data/saxs_computation/j8/1j8e/1j8e.dat

Crystal structure of ligand-binding repeat CR7 from LRP

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

LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction