SAXSdb — 1lre

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

RECEPTOR-ASSOCIATED PROTEIN

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 51–131	Fragment：N-TERMINAL DOMAIN, DOMAIN 1, RESIDUES 17 - 97	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.4；298 K	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 1LRE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NRE RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-05-08	Parsed fields agree	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 experimental conditions	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 experimental conditions	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 experimental conditions	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 oligomeric state Different ligand/ion Different experimental conditions	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 experimental conditions	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 experimental conditions	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
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 K 35–357（323 aa） Chain L 35–357（323 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

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 A； PDBConstruct 1–81； UniProt 51–131

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	1lre
Deposition date deposition_date	1997-05-08
Structure title title	RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, 20 STRUCTURES
Keywords keywords	;ALPHA2-MACROGLOBULIN RECEPTOR ASSOCIATED PROTEIN, LOW DENSITY LIPOPROTEIN RECEPTOR FAMILY ASSOCIATED PROTEIN, LDLR FAMILY ASSOCIATED PROTEIN, HELIX BUNDLE, CELL SURFACE PROTEIN ;; CELL SURFACE PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	13.97 Å
Radius of gyration Rg (electron density) rg_electron	13.60 Å
Forward intensity I(0) i0	497321000.00
Molecular weight molecular_weight	190340.0 kDa
Excluded volume excluded_volume	239650 Å³
Envelope volume envelope_volume	24746 Å³
Hydration-shell volume shell_volume	13177 Å³
Envelope diameter envelope_diameter	55.2 Å
Shell Rg shell_rg	21.70 Å
Envelope Rg envelope_rg	17.13 Å
Shape Rg shape_rg	13.59 Å
Total Rg total_rg	13.83 Å
Total atoms total_atoms	27300
Residues n_residues	1620
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	49.9 Å
Rg (real space) rg_real	14.02 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.9730e+08
I(0) uncertainty (real space) i0_real_error	6.2900e+06
Rg (reciprocal space) rg_reciprocal	14.02 Å
I(0) (reciprocal space) i0_reciprocal	497300000.0000
Solution quality estimate total_estimate	0.8435
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.2 Å
Skewness Skewness skewness	0.386
Kurtosis Kurtosis kurtosis	-0.253
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	113300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1lrea_
Class class	a — All alpha proteins
Fold Fold fold	a.13 — RAP domain-like
Superfamily Superfamily superfamily	a.13.1 — RAP domain-like
Family Family family	a.13.1.1 — RAP domain

CATH v4.4 (1 domains)

Domain ID domain_id	1lreA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	81 — Receptor-associated Protein
Homologous superfamily homologous superfamily	10 — RAP domain

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8. Citations (3)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	RECEPTOR-ASSOCIATED PROTEIN
Molecular weight formula_weight	9536.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	27300

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

RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, 20 STRUCTURES

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

RECEPTOR-ASSOCIATED PROTEIN

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/lr/1lre/1lre.fit
pddf	/app/data/pr_computation/lr/1lre/1lre.pr.out
profile	/app/data/saxs_computation/lr/1lre/1lre.dat