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- PDB-1n7d: Extracellular domain of the LDL receptor -

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Basic information

Entry
Database: PDB / ID: 1n7d
TitleExtracellular domain of the LDL receptor
ComponentsLow-density lipoprotein receptor
KeywordsLIPID TRANSPORT / LDL-Receptor / familial hypercholesterolemia / LDL / cholesterol metabolism
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / PCSK9-LDLR complex / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of receptor recycling / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / negative regulation of low-density lipoprotein particle clearance ...receptor-mediated endocytosis involved in cholesterol transport / PCSK9-LDLR complex / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of receptor recycling / negative regulation of astrocyte activation / very-low-density lipoprotein particle receptor activity / negative regulation of microglial cell activation / negative regulation of low-density lipoprotein particle clearance / cholesterol import / low-density lipoprotein particle clearance / clathrin heavy chain binding / low-density lipoprotein particle binding / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / low-density lipoprotein particle receptor activity / LDL clearance / Chylomicron clearance / response to caloric restriction / amyloid-beta clearance by cellular catabolic process / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / endolysosome membrane / cholesterol transport / low-density lipoprotein particle / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / sorting endosome / lipoprotein particle binding / amyloid-beta clearance / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / positive regulation of inflammatory response / endocytosis / late endosome / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / lysosome / early endosome / receptor complex / endosome membrane / external side of plasma membrane / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / identical protein binding / membrane / plasma membrane
Similarity search - Function
Knottins (small inhibitors, toxins, lectins) / EGF-type module / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / : / Complement Clr-like EGF-like / TolB, C-terminal domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat ...Knottins (small inhibitors, toxins, lectins) / EGF-type module / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / : / Complement Clr-like EGF-like / TolB, C-terminal domain / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / : / Calcium-binding EGF domain / 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 / Laminin / Laminin / Coagulation Factor Xa inhibitory site / 6 Propeller / Neuraminidase / 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 / Ribbon / Few Secondary Structures / Irregular / Mainly Beta
Similarity search - Domain/homology
12-TUNGSTOPHOSPHATE / Low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å
AuthorsRudenko, G. / Henry, L. / Henderson, K. / Ichtchenko, K. / Brown, M.S. / Goldstein, J.L. / Deisenhofer, J.
CitationJournal: Science / Year: 2002
Title: Structure of the LDL receptor extracellular domain at endosomal pH
Authors: Rudenko, G. / Henry, L. / Henderson, K. / Ichtchenko, K. / Brown, M.S. / Goldstein, J.L. / Deisenhofer, J.
History
DepositionNov 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS BELIEVE THE BIOLOGICAL UNIT IS A MONOMER.
Remark 600HETEROGEN THE ATOMS W1 AND W2 OF THE LIGAND KEG 6003 ARE ON A TWO-FOLD AXIS. COORDINATES FOR THE ...HETEROGEN THE ATOMS W1 AND W2 OF THE LIGAND KEG 6003 ARE ON A TWO-FOLD AXIS. COORDINATES FOR THE HALF OF THE CLUSTER KEG 6003 IN THE ASYMMETRIC UNIT ARE INCLUDED IN THIS ENTRY. THE SECOND HALF OF THE CLUSTER CAN BE GENERATED USING SYMMETRY OPERATION Y,X,1-Z.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,31514
Polymers77,7041
Non-polymers10,61113
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.290, 185.290, 85.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-6003-

KEG

21A-6003-

KEG

31A-6003-

KEG

41A-6003-

KEG

51A-6003-

KEG

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Components

#1: Protein Low-density lipoprotein receptor / LDL receptor


Mass: 77703.617 Da / Num. of mol.: 1 / Fragment: extracellular domain, RESIDUES 1-699 / Mutation: N494Q, N636Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01130
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-KEG / 12-TUNGSTOPHOSPHATE


Mass: 2877.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O40PW12

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 5.43 Å3/Da / Density % sol: 77.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: acetate buffer pH 5.3, 1,2-hexanediol, 0.5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 74 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMsodium phosphate11pH8.
2150 mM11NaCl
350 mMsodium acetate12pH5.3
43 %1,2-hexanediol12
50.5 mM12CaCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211.21363, 1.21423, 1.10696, 1.23985
SYNCHROTRONALS 8.2.12
SYNCHROTRONAPS 19-ID3
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 20, 2001
ADSC QUANTUM 2102CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.213631
21.214231
31.106961
41.239851
ReflectionResolution: 3.7→45.3 Å / Num. obs: 17303 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 74.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 3.7→3.83 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.7 / % possible all: 64.5
Reflection
*PLUS
Lowest resolution: 33.7 Å / Num. measured all: 64801 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 3.7 Å / % possible obs: 64.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5

1ajj

1d2j

1i0u

1ijq

1fx5


Resolution: 3.7→45.3 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The sugars have not been refined, just manually placed in the density. The exact identity of the sugars in these N-linked glycosylation sites is not known. At this resolution positional ...Details: The sugars have not been refined, just manually placed in the density. The exact identity of the sugars in these N-linked glycosylation sites is not known. At this resolution positional refinement is of limited use. Harmonic restraints were used on most core residues. No simulated annealing was used. The resolution of the MAD data used in the structure determination is 3.7 Ang and the B-factors were high. This means that the positions of the side chains are not well determined in the model. The authors urge users to exercize caution and restraint interpreting this model. The authors are available for questions. The clusters were included in the positional refinement (regularization of the model). The carbohydrates were not included in the positional refinement (regularization of the model) but fitted manually. The carbohydrates were modelled as the N-linked high mannose type.
RfactorNum. reflection% reflectionSelection details
Rfree0.382 1119 7 %RANDOM
Rwork0.381 ---
all-17303 --
obs-16008 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.156563 e/Å3
Displacement parametersBiso mean: 124.7 Å2
Baniso -1Baniso -2Baniso -3
1-20.49 Å29.97 Å20 Å2
2--20.49 Å20 Å2
3----40.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.19 Å1.1 Å
Luzzati d res low-50 Å
Luzzati sigma a1.11 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 3.7→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 254 0 4956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.031
X-RAY DIFFRACTIONc_angle_deg4.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d2.52
LS refinement shellResolution: 3.7→3.87 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.512 68 8.2 %
Rwork0.455 757 -
obs--36.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMKEG_12JUL02.TOP
X-RAY DIFFRACTION4KEG_18JAN02.PARCARBOHYDRATE.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 3.7 Å / Lowest resolution: 33.1 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.392 / Rfactor Rwork: 0.388
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.03
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.52

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