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- PDB-6lw5: Crystal structure of the human formyl peptide receptor 2 in compl... -

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Basic information

Entry
Database: PDB / ID: 6lw5
TitleCrystal structure of the human formyl peptide receptor 2 in complex with WKYMVm
Components
  • Soluble cytochrome b562,N-formyl peptide receptor 2
  • TRP-LYS-TYR-MET-VAL-QXV
KeywordsMEMBRANE PROTEIN / Formyl peptide receptor / G protein-coupled receptor / Complex / Peptide agonist
Function / homology
Function and homology information


N-formyl peptide receptor activity / complement receptor activity / immune response-regulating cell surface receptor signaling pathway / scavenger receptor binding / complement receptor mediated signaling pathway / positive regulation of monocyte chemotaxis / Formyl peptide receptors bind formyl peptides and many other ligands / positive regulation of innate immune response / cargo receptor activity / positive chemotaxis ...N-formyl peptide receptor activity / complement receptor activity / immune response-regulating cell surface receptor signaling pathway / scavenger receptor binding / complement receptor mediated signaling pathway / positive regulation of monocyte chemotaxis / Formyl peptide receptors bind formyl peptides and many other ligands / positive regulation of innate immune response / cargo receptor activity / positive chemotaxis / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / positive regulation of phagocytosis / receptor-mediated endocytosis / positive regulation of superoxide anion generation / astrocyte activation / microglial cell activation / calcium-mediated signaling / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / cellular response to amyloid-beta / chemotaxis / signaling receptor activity / amyloid-beta binding / positive regulation of cytosolic calcium ion concentration / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / electron transfer activity / cell surface receptor signaling pathway / periplasmic space / cell adhesion / defense response to bacterium / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / heme binding / Neutrophil degranulation / membrane / plasma membrane / cytoplasm
Similarity search - Function
Formyl peptide receptor-related / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. ...Formyl peptide receptor-related / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / Soluble cytochrome b562 / N-formyl peptide receptor 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, T. / Zong, X. / Zhang, H. / Wang, M. / Zhao, Q. / Wu, B.
Funding support China, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31825010 China
Ministry of Science and Technology (MoST, China)2018YFA0507000 China
National Science Foundation (NSF, China)31730027 China
National Science Foundation (NSF, China)81525024 China
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of ligand binding modes at the human formyl peptide receptor 2.
Authors: Chen, T. / Xiong, M. / Zong, X. / Ge, Y. / Zhang, H. / Wang, M. / Won Han, G. / Yi, C. / Ma, L. / Ye, R.D. / Xu, Y. / Zhao, Q. / Wu, B.
History
DepositionFeb 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Soluble cytochrome b562,N-formyl peptide receptor 2
B: TRP-LYS-TYR-MET-VAL-QXV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3244
Polymers48,5512
Non-polymers7732
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.280, 66.280, 244.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Soluble cytochrome b562,N-formyl peptide receptor 2 / Cytochrome b-562 / FMLP-related receptor I / FMLP-R-I / Formyl peptide receptor-like 1 / HM63 / ...Cytochrome b-562 / FMLP-related receptor I / FMLP-R-I / Formyl peptide receptor-like 1 / HM63 / Lipoxin A4 receptor / LXA4 receptor / RFP


Mass: 47694.016 Da / Num. of mol.: 1 / Mutation: M1007W, H1102I, R1106L, S211L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, FPR2, FPRH1, FPRL1, LXA4R
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: P0ABE7, UniProt: P25090
#2: Protein/peptide TRP-LYS-TYR-MET-VAL-QXV


Mass: 857.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M Tris, pH 7.5, 35% PEG500 DME, 3% PPG400, 100 mM CH3COOLi

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 15644 / % possible obs: 96.5 % / Redundancy: 7.9 % / CC1/2: 0.99 / Net I/σ(I): 6.8
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 767 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIXV1.18refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C1M, 1M6T

5c1m

1m6t


Resolution: 2.8→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.289 782 -
Rwork0.258 --
obs-15644 96.5 %
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 49 1 3446
LS refinement shellResolution: 2.8→2.97 Å
RfactorNum. reflection% reflection
Rfree0.3851 --
Rwork0.3491 --
obs-2406 96 %

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