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- PDB-7r8u: LOX-1 - Structural and Functional Studies of a Receptor Implicate... -

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Basic information

Entry
Database: PDB / ID: 7r8u
TitleLOX-1 - Structural and Functional Studies of a Receptor Implicated in Atherosclerosis
Components
  • Antibody light chain, kappa
  • Antigen binding fragment, Vh and Ch1
  • Oxidized low-density lipoprotein receptor 1
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Low Density Lipoprotein Receptor Antibody complex LOX-1 Scavenger receptor Atherogenesis-Atherosclerosis Macrophage Cardiovascular disease / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / tertiary granule membrane / specific granule membrane / immune system process / 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 / tertiary granule membrane / specific granule membrane / immune system process / 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 / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / 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: 1.901 Å
AuthorsOganesyan, V. / van Dyk, N.
CitationJournal: Commun Med / Year: 2023
Title: Structural and functional studies of a monoclonal antibody blocking LOX-1
Authors: Ongstad, E.L. / Gaddipati, R. / Belkhodja, M. / van Dyk, N. / Levy, S. / Sagar, D. / Cariuk, P. / Wolny, M. / Hanna, R.N. / Borrok, M.J. / Buchanan, A. / Oganesyan, V. / Gupta, R.
History
DepositionJun 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.title / _citation.year
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Oxidized low-density lipoprotein receptor 1
BBB: Oxidized low-density lipoprotein receptor 1
HHH: Antigen binding fragment, Vh and Ch1
LLL: Antibody light chain, kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9819
Polymers77,5214
Non-polymers4605
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-52 kcal/mol
Surface area30200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.908, 89.901, 110.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / LOX-1 / Lectin-like oxLDL receptor 1 / hLOX-1 / Lectin-type oxidized LDL receptor 1


Mass: 15028.069 Da / Num. of mol.: 2 / Fragment: Extracellular fragment (UNP residues 140-271)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLR1, CLEC8A, LOX1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P78380
#2: Antibody Antigen binding fragment, Vh and Ch1


Mass: 24764.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Antibody light chain, kappa


Mass: 22700.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1 M Tris base, BICINE, pH 8.5, 50% v/v precipitant mix (25% v/v ...Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1 M Tris base, BICINE, pH 8.5, 50% v/v precipitant mix (25% v/v MPD, 25% PEG1000, 25% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 1.9→39.492 Å / Num. obs: 57364 / % possible obs: 96.9 % / Redundancy: 6.5 % / CC1/2: 0.995 / Net I/σ(I): 1.6
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 3538 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YPU

1ypu


Resolution: 1.901→39.492 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.399 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2181 1175 2.062 %
Rwork0.1861 55817 -
all0.187 --
obs-56992 99.509 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 36.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.083 Å2-0 Å2-0 Å2
2---2.628 Å20 Å2
3---2.711 Å2
Refinement stepCycle: LAST / Resolution: 1.901→39.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5407 0 30 436 5873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135754
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175078
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.647869
X-RAY DIFFRACTIONr_angle_other_deg1.3411.5711897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56823.16250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62415901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.461520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021192
X-RAY DIFFRACTIONr_nbd_refined0.2020.2943
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.24569
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22684
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2401
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.215
X-RAY DIFFRACTIONr_nbd_other0.2270.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.216
X-RAY DIFFRACTIONr_mcbond_it3.1873.7382885
X-RAY DIFFRACTIONr_mcbond_other3.1863.7362884
X-RAY DIFFRACTIONr_mcangle_it4.3955.5823620
X-RAY DIFFRACTIONr_mcangle_other4.3945.5843621
X-RAY DIFFRACTIONr_scbond_it3.9144.0912869
X-RAY DIFFRACTIONr_scbond_other3.9134.0922870
X-RAY DIFFRACTIONr_scangle_it5.7135.974237
X-RAY DIFFRACTIONr_scangle_other5.7135.974238
X-RAY DIFFRACTIONr_lrange_it7.36343.0576363
X-RAY DIFFRACTIONr_lrange_other7.36243.0616364
X-RAY DIFFRACTIONr_ncsr_local_group_10.1360.054038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.950.322710.3513994X-RAY DIFFRACTION96.6247
1.95-2.0040.333680.2823957X-RAY DIFFRACTION99.5056
2.004-2.0620.2851040.2553828X-RAY DIFFRACTION99.873
2.062-2.1250.259710.2283773X-RAY DIFFRACTION99.7923
2.125-2.1940.244630.2133667X-RAY DIFFRACTION99.6261
2.194-2.2710.279860.2433510X-RAY DIFFRACTION99.695
2.271-2.3560.256780.2153412X-RAY DIFFRACTION99.8284
2.356-2.4520.238650.193309X-RAY DIFFRACTION99.8816
2.452-2.5610.217690.1793147X-RAY DIFFRACTION99.8758
2.561-2.6850.225700.1863018X-RAY DIFFRACTION99.9029
2.685-2.830.296690.1982874X-RAY DIFFRACTION99.8643
2.83-3.0010.26540.1842751X-RAY DIFFRACTION99.4328
3.001-3.2070.221500.182573X-RAY DIFFRACTION99.7718
3.207-3.4620.244480.1882424X-RAY DIFFRACTION99.9192
3.462-3.7890.201450.1732234X-RAY DIFFRACTION100
3.789-4.2320.151440.1512033X-RAY DIFFRACTION100
4.232-4.8770.172370.1381802X-RAY DIFFRACTION100
4.877-5.9510.188370.1561533X-RAY DIFFRACTION98.3709
5.951-8.3250.191250.1481228X-RAY DIFFRACTION99.9203
8.325-39.4920.174210.126750X-RAY DIFFRACTION100

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