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- PDB-2fcw: Structure of a Complex Between the Pair of the LDL Receptor Ligan... -

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Basic information

Entry
Database: PDB / ID: 2fcw
TitleStructure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP).
Components
  • Alpha-2-macroglobulin receptor-associated protein
  • Low-density lipoprotein receptor
KeywordsLIPID TRANSPORT/ENDOCYTOSIS/CHAPERONE / protein-protein complex / RAP / LDLR / escort protein / calcium-binding / LIPID TRANSPORT-ENDOCYTOSIS-CHAPERONE COMPLEX
Function / homology
Function and homology information


extracellular negative regulation of signal transduction / regulation of receptor-mediated endocytosis / negative regulation of very-low-density lipoprotein particle clearance / receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / lipase binding / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / rough endoplasmic reticulum lumen / negative regulation of astrocyte activation ...extracellular negative regulation of signal transduction / regulation of receptor-mediated endocytosis / negative regulation of very-low-density lipoprotein particle clearance / receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / lipase binding / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / rough endoplasmic reticulum lumen / negative regulation of astrocyte activation / negative regulation of microglial cell activation / receptor antagonist activity / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / amyloid-beta clearance by transcytosis / low-density lipoprotein particle clearance / clathrin heavy chain binding / negative regulation of receptor recycling / negative regulation of amyloid-beta clearance / positive regulation of triglyceride biosynthetic process / intestinal cholesterol absorption / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle receptor activity / response to caloric restriction / Chylomicron clearance / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / LDL clearance / high-density lipoprotein particle clearance / regulation of protein metabolic process / very-low-density lipoprotein particle receptor binding / lipoprotein catabolic process / phospholipid transport / positive regulation of amyloid-beta clearance / low-density lipoprotein particle / cis-Golgi network / cholesterol transport / negative regulation of receptor internalization / endolysosome membrane / negative regulation of amyloid fibril formation / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / retinoid metabolic process / cellular response to fatty acid / low-density lipoprotein particle receptor binding / sorting endosome / endoplasmic reticulum-Golgi intermediate compartment / amyloid-beta clearance / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / Retinoid metabolism and transport / phagocytosis / clathrin-coated pit / somatodendritic compartment / negative regulation of protein binding / endomembrane system / receptor-mediated endocytosis / cholesterol metabolic process / cholesterol homeostasis / endosome lumen / clathrin-coated endocytic vesicle membrane / lipid metabolic process / Golgi lumen / positive regulation of inflammatory response / endocytosis / apical part of cell / late endosome / Cargo recognition for clathrin-mediated endocytosis / heparin binding / Clathrin-mediated endocytosis / amyloid-beta binding / virus receptor activity / protease binding / basolateral plasma membrane / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome / endosome membrane / receptor ligand activity / external side of plasma membrane / signaling receptor binding / negative regulation of gene expression / intracellular membrane-bounded organelle / calcium ion binding / positive regulation of gene expression / cell surface / Golgi apparatus / endoplasmic reticulum / signal transduction / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
RAP domain / Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / Receptor-associated Protein ...RAP domain / Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / Receptor-associated Protein / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Endoplasmic reticulum targeting sequence. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Low-density lipoprotein receptor / Alpha-2-macroglobulin receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.26 Å
AuthorsBeglova, N. / Fisher, C. / Blacklow, S.C.
CitationJournal: Mol.Cell / Year: 2006
Title: Structure of an LDLR-RAP Complex Reveals a General Mode for Ligand Recognition by Lipoprotein Receptors
Authors: Fisher, C. / Beglova, N. / Blacklow, S.C.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-2-macroglobulin receptor-associated protein
B: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,36413
Polymers21,6012
Non-polymers76311
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-60 kcal/mol
Surface area11910 Å2
MethodPISA
2
A: Alpha-2-macroglobulin receptor-associated protein
B: Low-density lipoprotein receptor
hetero molecules

A: Alpha-2-macroglobulin receptor-associated protein
B: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,72826
Polymers43,2024
Non-polymers1,52622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7080 Å2
ΔGint-132 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.523, 30.019, 58.143
Angle α, β, γ (deg.)90.00, 96.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-55-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha-2-macroglobulin receptor-associated protein / Alpha-2- MRAP / Low density lipoprotein receptor-related protein-associated protein 1 / RAP


Mass: 12791.311 Da / Num. of mol.: 1 / Fragment: Domain Three / Mutation: E215G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEST15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30533
#2: Protein Low-density lipoprotein receptor / LDL receptor


Mass: 8809.619 Da / Num. of mol.: 1 / Fragment: A Pair of Ligand-Binding Modules 3 and 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Plasmid: pMM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01130

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Non-polymers , 4 types, 190 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2005 / Details: mirrors
RadiationMonochromator: Cryogenically cooled double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 46566 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.5
Reflection shellResolution: 1.26→1.31 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3151 / % possible all: 57.1

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS
Starting model: built by ARP/WARP

Resolution: 1.26→50 Å / Num. parameters: 15302 / Num. restraintsaints: 18660 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2323 5.3 %RANDOM
Rwork0.152 ---
all0.152 44243 --
obs0.1346 34481 79.9 %-
Displacement parametersBiso mean: 18.3 Å2
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1315 / Occupancy sum non hydrogen: 1690.5
Refinement stepCycle: LAST / Resolution: 1.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 6 219 1705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0224
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.087

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