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2fyl

Haddock model of the complex between double module of LRP, CR56, and first domain of receptor associated protein, RAP-d1.

Method: SOLUTION NMR Dmax: 63.9 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 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 51–131 Fragment：Rapd1 Low-density lipoprotein receptor-related protein 1 × 1 （Q07954） 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

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 2FYL 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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
2P01 The structure of receptor-associated protein(RAP) Deposited 2007-02-28 Different construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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

Low-density lipoprotein receptor-related protein 1

Homo sapiens

UniProt Q07954

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 932–1013 Fragment：CR56 Alpha-2-macroglobulin receptor-associated protein × 1 （P30533） 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

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 2FYL 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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
1J8E Crystal structure of ligand-binding repeat CR7 from LRP Deposited 2001-05-21 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 1011–1054（44 aa） 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
2FYJ NMR Solution structure of calcium-loaded LRP double module Deposited 2006-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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
2KNX Solution Structure of complement repeat CR17 from LRP-1 Deposited 2009-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 2
Chains and sequence ranges Author chain B； PDBConstruct 1–82； UniProt 932–1013

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 2fyl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2fyl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2fyl
Deposition date deposition_date2006-02-08
Structure title titleHaddock model of the complex between double module of LRP, CR56, and first domain of receptor associated protein, RAP-d1.
Keywords keywordsComplex, shift-mapping, haddock, interface, SURFACE ACTIVE PROTEIN; SURFACE ACTIVE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.95 Å
Radius of gyration Rg (electron density) rg_electron17.03 Å
Forward intensity I(0) i07638220.00
Molecular weight molecular_weight18511.0 kDa
Excluded volume excluded_volume22451 ų
Envelope volume envelope_volume27812 ų
Hydration-shell volume shell_volume14301 ų
Envelope diameter envelope_diameter63.6 Å
Shell Rg shell_rg22.33 Å
Envelope Rg envelope_rg17.03 Å
Shape Rg shape_rg17.01 Å
Total Rg total_rg17.95 Å
Total atoms total_atoms2504
Residues n_residues163
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 dmax63.9 Å
Rg (real space) rg_real17.88 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real7.6380e+06
I(0) uncertainty (real space) i0_real_error9.8710e+04
Rg (reciprocal space) rg_reciprocal17.89 Å
I(0) (reciprocal space) i0_reciprocal7638000.0000
Solution quality estimate total_estimate0.8526
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.189
Angular range angular_range— – 0.4450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha896800.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2fyla1
Class classa — All alpha proteins
Fold Fold folda.13 — RAP domain-like
Superfamily Superfamily superfamilya.13.1 — RAP domain-like
Family Family familya.13.1.1 — RAP domain

CATH v4.4 (1 domains)

Domain ID domain_id2fylA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology81 — Receptor-associated Protein
Homologous superfamily homologous superfamily10 — RAP domain
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8. Citations (1)

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9. Files and Curves (10)