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- PDB-2pzx: Structure of the methuselah ectodomain with peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 2pzx
TitleStructure of the methuselah ectodomain with peptide inhibitor
ComponentsG-protein coupled receptor Mth
KeywordsSIGNALING PROTEIN / GPCR G protein-coupled receptor ectodomain
Function / homology
Function and homology information


response to paraquat / G protein-coupled peptide receptor activity / synaptic vesicle exocytosis / response to starvation / G protein-coupled receptor activity / response to reactive oxygen species / determination of adult lifespan / peptide binding / presynapse / response to heat ...response to paraquat / G protein-coupled peptide receptor activity / synaptic vesicle exocytosis / response to starvation / G protein-coupled receptor activity / response to reactive oxygen species / determination of adult lifespan / peptide binding / presynapse / response to heat / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / membrane / plasma membrane
Similarity search - Function
Methuselah ectodomain, domain 2 / Methuselah ectodomain, domain 2 / Methuselah Ectodomain; Chain: A, domain 1 / Methuselah Ectodomain; Chain: A, domain 1 - #11 / Methuselah, N-terminal domain / Methuselah ectodomain, domain 2 / Methuselah, N-terminal domain superfamily / Methuselah ectodomain, domain 1 / Methuselah N-terminus / GPCR, family 2, secretin-like ...Methuselah ectodomain, domain 2 / Methuselah ectodomain, domain 2 / Methuselah Ectodomain; Chain: A, domain 1 / Methuselah Ectodomain; Chain: A, domain 1 - #11 / Methuselah, N-terminal domain / Methuselah ectodomain, domain 2 / Methuselah, N-terminal domain superfamily / Methuselah ectodomain, domain 1 / Methuselah N-terminus / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Beta Complex / Roll / Mainly Beta
Similarity search - Domain/homology
G-protein coupled receptor Mth
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWest Jr., A.P. / Ja, W.W. / Delker, S.L. / Bjorkman, P.J. / Benzer, S. / Roberts, R.W.
CitationJournal: Nat.Chem.Biol. / Year: 2007
Title: Extension of Drosophila melanogaster life span with a GPCR peptide inhibitor.
Authors: Ja, W.W. / West, A.P. / Delker, S.L. / Bjorkman, P.J. / Benzer, S. / Roberts, R.W.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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: G-protein coupled receptor Mth
B: G-protein coupled receptor Mth
C: G-protein coupled receptor Mth
D: G-protein coupled receptor Mth


Theoretical massNumber of molelcules
Total (without water)87,3434
Polymers87,3434
Non-polymers00
Water00
1
A: G-protein coupled receptor Mth


Theoretical massNumber of molelcules
Total (without water)21,8361
Polymers21,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: G-protein coupled receptor Mth


Theoretical massNumber of molelcules
Total (without water)21,8361
Polymers21,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: G-protein coupled receptor Mth


Theoretical massNumber of molelcules
Total (without water)21,8361
Polymers21,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: G-protein coupled receptor Mth


Theoretical massNumber of molelcules
Total (without water)21,8361
Polymers21,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.233, 94.233, 173.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
G-protein coupled receptor Mth / Protein methuselah


Mass: 21835.809 Da / Num. of mol.: 4 / Fragment: N-terminal extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mth / Production host: unidentified baculovirus / References: UniProt: O97148

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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: 4.42 Å3/Da / Density % sol: 72.15 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 1.7 M ammonium sulfate 2% w/v PEG 400 0.1 M HEPES-KOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 6.2 / Number: 66512 / Rmerge(I) obs: 0.155 / Χ2: 1.33 / D res high: 3.5 Å / D res low: 20 Å / Num. obs: 18125 / % possible obs: 95.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
7.422090.810.0591.228
5.947.4294.310.0971.206
5.215.9494.410.1171.347
4.745.2195.310.1361.342
4.44.7495.610.141.503
4.144.495.810.1651.468
3.944.1496.410.1891.335
3.773.9496.810.2581.396
3.623.7796.710.3271.343
3.53.6296.910.371.107
ReflectionResolution: 3.5→20 Å / Num. obs: 18125 / % possible obs: 95.3 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 6.2
Reflection shellResolution: 3.5→3.62 Å / Rmerge(I) obs: 0.37 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJR

1fjr


Resolution: 3.5→7.99 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1208292.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE R8-01 15-MER PEPTIDE (FPSSWLQRYYLAKRR) WAS NOT INCLUDED IN THE MODEL. THIS CRYSTAL HAS A STACKING FAULT-TYPE DISORDER, WHICH CAN ONLY BE PARTIALLY MODELED. THE OVERLAPPING NCS-RELATED ...Details: THE R8-01 15-MER PEPTIDE (FPSSWLQRYYLAKRR) WAS NOT INCLUDED IN THE MODEL. THIS CRYSTAL HAS A STACKING FAULT-TYPE DISORDER, WHICH CAN ONLY BE PARTIALLY MODELED. THE OVERLAPPING NCS-RELATED MOLECULES ARE NECESSARY TO MODEL THE DISORDER. Refinement was done with 8 strict NCS matrices as follows: matrix_1 = ( 1.000000 0.000000 0.000000 ) ( 0.000000 1.000000 0.000000 ) ( 0.000000 0.000000 1.000000 ) vector_1 = ( 0.0000 0.0000 0.0000 ) matrix_2 = ( -0.025450 -0.999672 -0.002776 ) ( -0.999629 0.025476 -0.009636 ) ( 0.009703 0.002530 -0.999950 ) vector_2 = ( 95.7336 93.6049 30.5814 ) matrix_3 = ( 0.999874 -0.015577 -0.003041 ) ( -0.015587 -0.999874 -0.003124 ) ( -0.002992 0.003171 -0.999991 ) vector_3 = ( -46.4752 48.4846 0.7945 ) matrix_4 = ( -0.030796 -0.999466 -0.010894 ) ( 0.999470 -0.030907 0.010218 ) ( -0.010550 -0.010574 0.999888 ) vector_4 = ( 48.9629 -45.9887 -29.5468 ) matrix_5 = ( -0.010011 -0.999911 -0.008770 ) ( 0.999838 -0.010141 0.014863 ) ( -0.014951 -0.008620 0.999851 ) vector_5 = ( 48.0912 -47.3711 31.8114 ) matrix_6 = ( 0.999542 -0.030236 -0.001427 ) ( -0.030235 -0.999542 0.001202 ) ( -0.001463 -0.001158 -0.999998 ) vector_6 = ( -45.5886 48.9605 61.9827 ) matrix_7 = ( 1.000000 0.000000 0.000000 ) ( 0.000000 1.000000 0.000000 ) ( 0.000000 0.000000 1.000000 ) vector_7 = ( 0.0000 0.0000 0.0000 ) matrix_8 = ( -0.025450 -0.999672 -0.002776 ) ( -0.999629 0.025476 -0.009636 ) ( 0.009703 0.002530 -0.999950 ) vector_8 = ( 95.7336 93.6049 30.5814 ). Author has stated one complication: Because of the stacking fault-type disorder, the alternate conformers in the current PDB file were assigned different chain IDs during author's refinement. The two alternate conformers of chain C were assigned chain IDs C and F, and the two conformers of chain D were assigned D and E. During the processing of deposition, alternate conformers were used because of the essential PDB format requirement. Therefore, during author's refinement, there were six chains A/B/C/D/E/F. To get the right occupancies during the refinement (1.0 on chains A/B, 0.5 on chains C/D/E/F), author set the occupancies of the starting file at 0.5, and put in two copies of the ncs matrices for the chains A and B with occupancy of 1.0. So there are 8 matrices.
RfactorNum. reflection% reflectionSelection details
Rfree0.407 822 4.9 %RANDOM
Rwork0.376 ---
obs0.376 16870 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.5771 Å2 / ksol: 0.172883 e/Å3
Displacement parametersBiso mean: 53.3 Å2
Baniso -1Baniso -2Baniso -3
1-20.83 Å20 Å20 Å2
2--20.83 Å20 Å2
3----41.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.77 Å0.69 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.87 Å
Refinement stepCycle: LAST / Resolution: 3.5→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 0 0 1529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.7 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 137 4.9 %
Rwork0.42 2667 -
obs--96.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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