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- PDB-7rt9: Crystal structures of human PYY and NPY -

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Basic information

Entry
Database: PDB / ID: 7rt9
TitleCrystal structures of human PYY and NPY
Components
  • 4A3B2-A Fab heavy chain
  • 4A3B2-A Fab light chain
  • Peptide YY
KeywordsHORMONE/IMMUNE SYSTEM / peptide hormone C-terminal amidation helix antibody / HORMONE / HORMONE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


neuropeptide Y receptor binding / intestinal epithelial cell differentiation / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor binding / hormone activity / G alpha (i) signalling events / 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: 1.9 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

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Assembly

Deposited unit
A: 4A3B2-A Fab heavy chain
B: 4A3B2-A Fab light chain
C: 4A3B2-A Fab heavy chain
D: 4A3B2-A Fab light chain
Y: Peptide YY
Z: Peptide YY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9148
Polymers103,7296
Non-polymers1842
Water10,196566
1
A: 4A3B2-A Fab heavy chain
B: 4A3B2-A Fab light chain
Y: Peptide YY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0495
Polymers51,8653
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-29 kcal/mol
Surface area20420 Å2
MethodPISA
2
C: 4A3B2-A Fab heavy chain
D: 4A3B2-A Fab light chain
Z: Peptide YY


Theoretical massNumber of molelcules
Total (without water)51,8653
Polymers51,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-28 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.980, 103.300, 138.350
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: Antibody 4A3B2-A Fab heavy chain


Mass: 23954.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 4A3B2-A Fab light chain


Mass: 23595.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Peptide YY / / PYY / PYY-I / Peptide tyrosine tyrosine


Mass: 4314.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10082
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.55 Å3/Da / Density % sol: 51.7 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.65
Details: Fab-PYY (~5.5 mg/mL with respect to Fab, 2.4:1 molar ratio of PYY:Fab, in 25 mM Tris (pH 7.5), 100 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 200 mM citrate ...Details: Fab-PYY (~5.5 mg/mL with respect to Fab, 2.4:1 molar ratio of PYY:Fab, in 25 mM Tris (pH 7.5), 100 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 200 mM citrate (pH 6.65) and 13% (w/v) PEG1500.

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→42.11 Å / Num. obs: 87134 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Rrim(I) all: 0.13 / Net I/σ(I): 8.8 / Num. measured all: 571023 / Scaling rejects: 92
Reflection shell

Diffraction-ID: 1 / % possible all: 98.3

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.9-1.935.80.52493843370.8620.2180.5482.2
10.23-42.116.40.0441846530.9990.0160.04417

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.61 Å42.11 Å
Translation5.61 Å42.11 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimless0.5.17data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic Fab

Resolution: 1.9→42.11 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2058 / WRfactor Rwork: 0.1732 / FOM work R set: 0.8546 / SU B: 3.148 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1299 / SU Rfree: 0.1232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 4393 5 %RANDOM
Rwork0.1793 ---
obs0.1809 82663 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.33 Å2 / Biso mean: 21.313 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.54 Å2
Refinement stepCycle: final / Resolution: 1.9→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6836 0 14 566 7416
Biso mean--33.01 28.24 -
Num. residues----907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137033
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176092
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.6469599
X-RAY DIFFRACTIONr_angle_other_deg1.4161.56714143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8125899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62922.508319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.628151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1351531
X-RAY DIFFRACTIONr_chiral_restr0.0720.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021491
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 311 -
Rwork0.239 5989 -
all-6300 -
obs--98.36 %

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