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- PDB-6tla: CRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 (C 1 2 1) -

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Basic information

Entry
Database: PDB / ID: 6tla
TitleCRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 (C 1 2 1)
ComponentsOxidized low-density lipoprotein receptor 1
KeywordsLIPID BINDING PROTEIN / LOX-1 / OLR1 / CTLD / C-TYPE LECTIN LIKE DOMAIN / SCAVENGER RECEPTOR / OXLDL BINDING
Function / homology
Function and homology information


low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex ...low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex / inflammatory response / membrane raft / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular region / nucleoplasm / membrane / identical protein binding / plasma membrane
Similarity search - Function
Ly49-like, N-terminal / Ly49-like protein, N-terminal region / Natural killer cell receptor-like, C-type lectin-like domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Oxidized low-density lipoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsNar, H. / Fiegen, D. / Schnapp, G.
CitationJournal: Commun Chem / Year: 2020
Title: A small-molecule inhibitor of lectin-like oxidized LDL receptor-1 acts by stabilizing an inactive receptor tetramer state
Authors: Nar, H. / Fiegen, D. / Schnapp, G.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidized low-density lipoprotein receptor 1
B: Oxidized low-density lipoprotein receptor 1
C: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9264
Polymers50,7313
Non-polymers1951
Water2,126118
1
A: Oxidized low-density lipoprotein receptor 1
B: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0163
Polymers33,8202
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-13 kcal/mol
Surface area14050 Å2
2
C: Oxidized low-density lipoprotein receptor 1

C: Oxidized low-density lipoprotein receptor 1


Theoretical massNumber of molelcules
Total (without water)33,8202
Polymers33,8202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1830 Å2
ΔGint-10 kcal/mol
Surface area12690 Å2
Unit cell
Length a, b, c (Å)76.83, 52.19, 109.82
Angle α, β, γ (deg.)90, 92.04, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oxidized low-density lipoprotein receptor 1 / Ox-LDL receptor 1 / C-type lectin domain family 8 member A / Lectin-like oxidized LDL receptor 1 / ...Ox-LDL receptor 1 / C-type lectin domain family 8 member A / Lectin-like oxidized LDL receptor 1 / hLOX-1 / Lectin-type oxidized LDL receptor 1


Mass: 16910.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLR1, CLEC8A, LOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P78380
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6, 20% PEG6000, 0.2 M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9101 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9101 Å / Relative weight: 1
ReflectionResolution: 2.16→109.75 Å / Num. obs: 22997 / % possible obs: 97 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.035 / Rrim(I) all: 0.035 / Net I/σ(I): 19.2
Reflection shellResolution: 2.16→2.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / Num. unique obs: 3126 / Rpim(I) all: 0.32 / Rrim(I) all: 0.552 / % possible all: 90.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (3-OCT-2019)refinement
autoPROCdata reduction
SCALAdata scaling
Cootmodel building
XDSdata processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ypu

1ypu


Resolution: 2.16→55 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.263 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.262 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1178 -RANDOM
Rwork0.2105 ---
obs0.2116 22997 96.9 %-
Displacement parametersBiso mean: 77.78 Å2
Baniso -1Baniso -2Baniso -3
1-9.1667 Å20 Å2-4.6034 Å2
2--1.6948 Å20 Å2
3----10.8615 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.16→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 12 118 3281
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083275HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914460HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1070SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes541HARMONIC5
X-RAY DIFFRACTIONt_it3275HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion404SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2426SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion15.79
LS refinement shellResolution: 2.16→2.175 Å
RfactorNum. reflection% reflection
Rfree0.2646 18 -
Rwork0.2462 --
obs--75.12 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.36771.96442.11765.9820.95134.26830.08920.3787-0.19030.37870.101-0.0036-0.1903-0.0036-0.19020.00230.04340.0249-0.26670.0313-0.101513.54186.506546.6104
24.7893-0.287-0.43147.00342.8926.5862-0.0407-0.231-0.067-0.2310.35420.1099-0.0670.1099-0.3135-0.3119-0.1613-0.0104-0.0142-0.127-0.19354.7638-12.444926.957
36.7556-0.4263-2.84379.7421.20267.32950.0090.24170.24090.2417-0.1366-0.03120.2409-0.03120.1276-0.2735-0.29660.0859-0.1169-0.2133-0.204330.1681-7.874912.0025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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