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- PDB-6tl9: CRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 6tl9
TitleCRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 IN COMPLEX WITH BI-0115
ComponentsOxidized low-density lipoprotein receptor 1
KeywordsLIPID BINDING PROTEIN / LOX-1 / OLR1 / CTLD / C-TYPE LECTIN LIKE DOMAIN / SCAVENGER RECEPTOR / OXLDL BINDING / PPI STABILIZATION / INHIBITOR
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
Chem-NJT / Oxidized low-density lipoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.734 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
D: Oxidized low-density lipoprotein receptor 1
E: Oxidized low-density lipoprotein receptor 1
F: Oxidized low-density lipoprotein receptor 1
G: Oxidized low-density lipoprotein receptor 1
H: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,27913
Polymers123,0368
Non-polymers1,2435
Water3,423190
1
A: Oxidized low-density lipoprotein receptor 1
B: Oxidized low-density lipoprotein receptor 1
C: Oxidized low-density lipoprotein receptor 1
D: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1857
Polymers61,5184
Non-polymers6683
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Oxidized low-density lipoprotein receptor 1
F: Oxidized low-density lipoprotein receptor 1
G: Oxidized low-density lipoprotein receptor 1
H: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0936
Polymers61,5184
Non-polymers5752
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.816, 62.211, 116.331
Angle α, β, γ (deg.)90, 93.99, 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: 15379.451 Da / Num. of mol.: 8
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NJT / 9-chloranyl-5-propyl-11~{H}-pyrido[2,3-b][1,4]benzodiazepin-6-one


Mass: 287.744 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14ClN3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 7.5, 30% PEG MME 2000 and 0.15 M KBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.734→75.225 Å / Num. obs: 27991 / % possible obs: 97.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.046 / Rrim(I) all: 0.084 / Net I/σ(I): 12.5
Reflection shellResolution: 2.734→2.743 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 305 / Rpim(I) all: 0.216 / Rrim(I) all: 0.388 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (3-OCT-2019)refinement
autoPROCdata reduction
XDSMarch 1, 20data reduction
autoPROC1.1.6data scaling
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ypu

1ypu


Resolution: 2.734→39 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.368
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1424 -RANDOM
Rwork0.2218 ---
obs0.2231 27986 97.1 %-
Displacement parametersBiso mean: 64.77 Å2
Baniso -1Baniso -2Baniso -3
1-11.9211 Å20 Å21.4334 Å2
2--7.6788 Å20 Å2
3----19.5999 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.734→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8352 0 86 190 8628
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0068749HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7511907HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2856SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1446HARMONIC5
X-RAY DIFFRACTIONt_it8749HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1062SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6174SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion16.24
LS refinement shellResolution: 2.734→2.752 Å
RfactorNum. reflection% reflection
Rfree0.3967 22 -
Rwork0.2888 --
obs--99.82 %
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)
19.19271.1054-0.5497.0138-2.56848.7134-0.0167-0.0217-0.5688-0.02170.12520.4338-0.56880.4338-0.1085-0.3478-0.1544-0.0293-0.283-0.0281-0.085625.5455-31.7258-44.8195
22.4036-1.6939-1.82118.7517-0.75132.9868-0.08860.02670.58570.02670.070.13350.58570.13350.0186-0.092-0.0307-0.0739-0.33020.12810.208214.5908-58.0961-39.3009
38.3628-2.14161.37497.44981.75585.57680.0320.0576-0.38080.0576-0.0577-0.2028-0.3808-0.20280.0257-0.1946-0.05930.00310.0188-0.0006-0.3055-7.5793-37.264-39.9985
47.47561.5312-0.20035.66461.4467.09380.04580.0630.57340.0630.1298-0.33320.5734-0.3332-0.1755-0.2374-0.2203-0.1185-0.34890.06430.2317-18.2631-63.4599-46.4737
58.23930.8536-1.40855.34383.47787.88550.0151-0.018-0.5959-0.018-0.0708-0.5347-0.5959-0.53470.0557-0.3355-0.0458-0.0060.35810.078-0.3419-63.7513-59.8623-11.5638
66.9732-0.5842-0.56256.79010.55853.19810.01450.13440.26070.13440.0373-0.01730.2607-0.0173-0.0518-0.2789-0.0784-0.08450.25350.0648-0.3032-37.7534-70.9366-18.0474
75.4253-1.39381.62977.2913-0.30993.714-0.0443-0.1912-0.1869-0.19120.0579-0.1909-0.1869-0.1909-0.0136-0.19730.0361-0.03570.12890.0577-0.222-36.8285-40.2856-18.5466
88.75431.79792.14454.0672-2.52958.31320.0246-0.30.4738-0.30.06830.19670.47380.1967-0.0929-0.344-0.0487-0.01990.2004-0.0391-0.2957-10.5095-51.2083-13.0136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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