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- PDB-7ddz: The Crystal Structure of Human Neuropeptide Y Y2 Receptor with JN... -

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Basic information

Entry
Database: PDB / ID: 7ddz
TitleThe Crystal Structure of Human Neuropeptide Y Y2 Receptor with JNJ-31020028
ComponentsHuman Neuropeptide Y Y2 Receptor fusion protein
KeywordsMEMBRANE PROTEIN / neuropeptide Y Y2 receptor
Function / homology
Function and homology information


peptide YY receptor activity / neuropeptide Y receptor activity / cardiac left ventricle morphogenesis / neuropeptide binding / non-motile cilium / outflow tract morphogenesis / calcium channel regulator activity / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process ...peptide YY receptor activity / neuropeptide Y receptor activity / cardiac left ventricle morphogenesis / neuropeptide binding / non-motile cilium / outflow tract morphogenesis / calcium channel regulator activity / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process / Peptide ligand-binding receptors / locomotory behavior / cilium / cell wall macromolecule catabolic process / FMN binding / lysozyme / lysozyme activity / signaling receptor activity / G alpha (i) signalling events / host cell cytoplasm / electron transfer activity / defense response to bacterium / neuron projection / plasma membrane
Similarity search - Function
Neuropeptide Y2 receptor / Neuropeptide Y receptor family / Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Neuropeptide Y2 receptor / Neuropeptide Y receptor family / Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Serpentine type 7TM GPCR chemoreceptor Srsx / Flavoprotein-like superfamily / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-H46 / Endolysin / Flavodoxin / Neuropeptide Y receptor type 2
Similarity search - Component
Biological speciesEnterobacteria phage RB59 (virus)
Homo sapiens (human)
Desulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, T. / Han, S. / Zhao, Q. / Wu, B.
Funding support China, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31825010 China
National Science Foundation (NSF, China)81525024 China
National Science Foundation (NSF, China)31700653 China
Chinese Academy of SciencesXDB37030101 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for ligand recognition of the neuropeptide Y Y 2 receptor.
Authors: Tang, T. / Hartig, C. / Chen, Q. / Zhao, W. / Kaiser, A. / Zhang, X. / Zhang, H. / Qu, H. / Yi, C. / Ma, L. / Han, S. / Zhao, Q. / Beck-Sickinger, A.G. / Wu, B.
History
DepositionOct 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Human Neuropeptide Y Y2 Receptor fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3073
Polymers74,2851
Non-polymers1,0222
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.420, 50.863, 184.629
Angle α, β, γ (deg.)90.000, 90.667, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Human Neuropeptide Y Y2 Receptor fusion protein / Lysis protein / Lysozyme / Muramidase / NPY2-R / NPY-Y2 receptor / Y2 receptor


Mass: 74285.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB59 (virus), (gene. exp.) Homo sapiens (human), (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: e, RB59_126, NPY2R, DVU_2680 / Strain: Hildenborough / Production host: Baculovirus expression vector pUltraBac-1
References: UniProt: A0A097J809, UniProt: P49146, UniProt: P00323, lysozyme
#2: Chemical ChemComp-H46 / ~{N}-[4-[4-[(1~{S})-2-(diethylamino)-2-oxidanylidene-1-phenyl-ethyl]piperazin-1-yl]-3-fluoranyl-phenyl]-2-pyridin-3-yl-benzamide


Mass: 565.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
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: 4.66 Å3/Da / Density % sol: 73.58 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 0.1 M HEPES, pH 7.0-7.5, 250-350 mM (NH4)2SO4, and 20-30% PEG500DME, or 0.1 M MES, pH 6.0-6.5, 380-420 mM NH4 tartrate, and 24-26% PEG500DME

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 21815 / % possible obs: 98.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 63.08 Å2 / Rpim(I) all: 0.112 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.9 Å / Rpim(I) all: 0.517

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZBQ

5zbq


Resolution: 2.8→37.74 Å / SU ML: 0.3925 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.9802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2891 2020 9.26 %
Rwork0.2548 19795 -
obs0.2581 21815 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 73 0 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01083569
X-RAY DIFFRACTIONf_angle_d1.21184864
X-RAY DIFFRACTIONf_chiral_restr0.0605564
X-RAY DIFFRACTIONf_plane_restr0.0063596
X-RAY DIFFRACTIONf_dihedral_angle_d23.16591240
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.379 --
Rwork0.308 --
obs-1878 84 %
Refinement TLS params.Method: refined / Origin x: -18.9097 Å / Origin y: 7.9181 Å / Origin z: 24.4218 Å
111213212223313233
T0.3655 Å20.0307 Å2-0.0271 Å2-0.364 Å2-0.0131 Å2--0.4661 Å2
L1.0203 °20.3041 °2-0.8281 °2-1.1569 °2-0.8327 °2--6.5334 °2
S-0.0028 Å °-0.3696 Å °-0.0758 Å °0.3767 Å °-0.0691 Å °-0.0071 Å °0.1848 Å °-0.0851 Å °0.0614 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA48 - 343
2X-RAY DIFFRACTION1allA1201 - 1202

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