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- PDB-7rta: Crystal structures of human PYY and NPY -

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Basic information

Entry
Database: PDB / ID: 7rta
TitleCrystal structures of human PYY and NPY
Components
  • 4A3B2-B Fab heavy chain
  • 4A3B2-B Fab light chain
  • Neuropeptide Y
KeywordsHORMONE/IMMUNE SYSTEM / peptide hormone C-terminal amidation helix antibody / HORMONE / HORMONE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


synaptic signaling via neuropeptide / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / positive regulation of appetite / adult feeding behavior / neuropeptide hormone activity / feeding behavior / central nervous system neuron development / neuronal dense core vesicle / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger ...synaptic signaling via neuropeptide / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / positive regulation of appetite / adult feeding behavior / neuropeptide hormone activity / feeding behavior / central nervous system neuron development / neuronal dense core vesicle / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / calcium channel regulator activity / GABA-ergic synapse / neuropeptide signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Peptide ligand-binding receptors / G protein-coupled receptor activity / cerebral cortex development / regulation of blood pressure / neuron projection development / G alpha (i) signalling events / chemical synaptic transmission / signaling receptor binding / Golgi apparatus / extracellular space / extracellular region
Similarity search - Function
Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Neuropeptides / Year: 2022
Title: Crystal structures of human neuropeptide Y (NPY) and peptide YY (PYY).
Authors: Langley, D.B. / Schofield, P. / Jackson, J. / Herzog, H. / Christ, D.
History
DepositionAug 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 4A3B2-B Fab heavy chain
L: 4A3B2-B Fab light chain
N: Neuropeptide Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1197
Polymers51,7353
Non-polymers3844
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron density clearly shows the antibody Fab bound to the peptide
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-59 kcal/mol
Surface area20540 Å2
Unit cell
Length a, b, c (Å)136.830, 136.830, 116.985
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Antibody 4A3B2-B Fab heavy chain


Mass: 23862.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi-293 / Production host: Homo sapiens (human)
#2: Antibody 4A3B2-B Fab light chain


Mass: 23595.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi-293 / Production host: Homo sapiens (human)
#3: Protein/peptide Neuropeptide Y / Neuropeptide tyrosine / NPY


Mass: 4276.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01303
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 58 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein complex (~4 mg/mL with respect to Fab, NPY:Fab at molar ratio of 1.4:1, all dissolved in 25 mM Tris (pH 7.5), 100 mM NaCl) was combined to an equal volume (2 uL) of well solution ...Details: Protein complex (~4 mg/mL with respect to Fab, NPY:Fab at molar ratio of 1.4:1, all dissolved in 25 mM Tris (pH 7.5), 100 mM NaCl) was combined to an equal volume (2 uL) of well solution comprising 200 mM Li2SO4, 100 mM sodium acetate (pH 4.5), 22% (w/v) PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→44.79 Å / Num. obs: 20402 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.043 / Rrim(I) all: 0.15 / Net I/σ(I): 13 / Num. measured all: 249910
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.7212.71.4513066224090.720.421.512299.5
9.01-44.7910.30.04259315780.9990.0140.04440.699.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.17 Å44.79 Å
Translation4.17 Å44.79 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic Fab

Resolution: 2.6→44.79 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.827 / SU B: 23.547 / SU ML: 0.233 / SU R Cruickshank DPI: 0.4227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.423 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 1024 5 %RANDOM
Rwork0.2171 ---
obs0.2198 19349 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.22 Å2 / Biso mean: 59.707 Å2 / Biso min: 12.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 2.6→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 21 17 3296
Biso mean--106.81 40.08 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133375
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172899
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6454617
X-RAY DIFFRACTIONr_angle_other_deg1.241.5676710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2895439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65622.246138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44515465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8631513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02717
LS refinement shellResolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 71 -
Rwork0.313 1383 -
all-1454 -
obs--99.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4003-0.0806-0.14533.3516-0.77450.8474-0.1252-0.03850.1104-0.1995-0.0505-0.0037-0.1983-0.060.17560.25830.1171-0.17620.14-0.07010.1288-17.282640.5879-27.6481
20.94180.28240.04091.2214-0.50770.832-0.0811-0.27790.22770.3806-0.1703-0.1747-0.4857-0.00530.25150.37610.0659-0.21120.1687-0.0990.1615-8.662446.0402-13.2504
38.2699-7.659-5.103411.34383.52423.50330.3409-0.0266-0.4254-0.8687-0.57450.3599-0.10430.16980.23360.16040.0878-0.01630.08610.0290.15090.50615.9181-23.9586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 213
2X-RAY DIFFRACTION2L1 - 212
3X-RAY DIFFRACTION3N13 - 37

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