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- PDB-5zbq: The Crystal Structure of human neuropeptide Y Y1 receptor with UR... -

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Basic information

Entry
Database: PDB / ID: 5zbq
TitleThe Crystal Structure of human neuropeptide Y Y1 receptor with UR-MK299
ComponentsNeuropeptide Y receptor type 1,T4 Lysozyme
KeywordsSIGNALING PROTEIN / G Protein-Coupled Receptor / Receptor Inhibitor / Complex structure
Function / homology
Function and homology information


pancreatic polypeptide receptor activity / peptide YY receptor activity / neuropeptide Y receptor activity / neuropeptide receptor activity / feeding behavior / neuropeptide binding / outflow tract morphogenesis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of multicellular organism growth / viral release from host cell by cytolysis ...pancreatic polypeptide receptor activity / peptide YY receptor activity / neuropeptide Y receptor activity / neuropeptide receptor activity / feeding behavior / neuropeptide binding / outflow tract morphogenesis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of multicellular organism growth / viral release from host cell by cytolysis / sensory perception of pain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process / Peptide ligand-binding receptors / locomotory behavior / regulation of blood pressure / glucose metabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / host cell cytoplasm / defense response to bacterium / neuron projection / plasma membrane
Similarity search - Function
Neuropeptide Y1 receptor / Neuropeptide Y receptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Neuropeptide Y1 receptor / Neuropeptide Y receptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain 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
Chem-9AO / Endolysin / Neuropeptide Y receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB55 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYang, Z. / Han, S. / Zhao, Q. / Wu, B.
CitationJournal: Nature / Year: 2018
Title: Structural basis of ligand binding modes at the neuropeptide Y Y1receptor
Authors: Yang, Z. / Han, S. / Keller, M. / Kaiser, A. / Bender, B.J. / Bosse, M. / Burkert, K. / Kogler, L.M. / Wifling, D. / Bernhardt, G. / Plank, N. / Littmann, T. / Schmidt, P. / Yi, C. / Li, B. ...Authors: Yang, Z. / Han, S. / Keller, M. / Kaiser, A. / Bender, B.J. / Bosse, M. / Burkert, K. / Kogler, L.M. / Wifling, D. / Bernhardt, G. / Plank, N. / Littmann, T. / Schmidt, P. / Yi, C. / Li, B. / Ye, S. / Zhang, R. / Xu, B. / Larhammar, D. / Stevens, R.C. / Huster, D. / Meiler, J. / Zhao, Q. / Beck-Sickinger, A.G. / Buschauer, A. / Wu, B.
History
DepositionFeb 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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
Revision 1.4Oct 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

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Assembly

Deposited unit
A: Neuropeptide Y receptor type 1,T4 Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2112
Polymers60,5951
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.840, 100.680, 83.160
Angle α, β, γ (deg.)90.00, 98.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS NUKNOWN

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Components

#1: Protein Neuropeptide Y receptor type 1,T4 Lysozyme / NPY1-R / Lysis protein / Lysozyme / Muramidase


Mass: 60595.223 Da / Num. of mol.: 1 / Fragment: UNP residues 2-358,UNP residues 2-161 / Mutation: F129W,C1053T, C1096A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB55 (virus)
Gene: NPY1R, NPYR, NPYY1, e, RB55_p125 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25929, UniProt: A0A097J792, lysozyme
#2: Chemical ChemComp-9AO / N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide


Mass: 615.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H41N7O5
Has protein modificationY
Sequence detailsAuthors state that the site (359-366) is the prescission protease site connected to the C terminal ...Authors state that the site (359-366) is the prescission protease site connected to the C terminal of the receptor.

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.4
Details: 0.1 M Tris, pH 7.4-8.0, 30-40% (v/v) PEG400, 50-150 mM sodium tartrate and 100 uM UR-MK299
PH range: 7.4-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 16689 / % possible obs: 97.3 % / Redundancy: 3.97 % / Biso Wilson estimate: 78.39 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.166 / Net I/σ(I): 4.78
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 1 / Num. unique obs: 2119 / CC1/2: 0.633 / % possible all: 96.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GRV, 1C5P

4grv

1c5p


Resolution: 2.7→29.38 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.876 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.974 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.745 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.32
RfactorNum. reflection% reflectionSelection details
Rfree0.247 790 4.78 %RANDOM
Rwork0.225 ---
obs0.226 16520 97.5 %-
Displacement parametersBiso mean: 87.93 Å2
Baniso -1Baniso -2Baniso -3
1-14.1321 Å20 Å2-1.1398 Å2
2---31.8253 Å20 Å2
3---17.6932 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: 1 / Resolution: 2.7→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 45 0 3760
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013850HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.045229HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1308SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes557HARMONIC5
X-RAY DIFFRACTIONt_it3850HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion19.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion512SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4577SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.264 131 4.44 %
Rwork0.224 2818 -
all0.226 2949 -
obs--96.4 %
Refinement TLS params.Method: refined / Origin x: -50.2552 Å / Origin y: -14.9395 Å / Origin z: 95.5975 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °
Refinement TLS groupSelection details: { A|* }

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