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- PDB-1fjr: CRYSTAL STRUCTURE OF THE ECTODOMAIN OF METHUSELAH -

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Basic information

Entry
Database: PDB / ID: 1fjr
TitleCRYSTAL STRUCTURE OF THE ECTODOMAIN OF METHUSELAH
ComponentsMETHUSELAH ECTODOMAIN
KeywordsSIGNALING PROTEIN / GPCR / G PROTEIN-COUPLED RECEPTOR / ECTODOMAIN
Function / homology
Function and homology information


response to paraquat / G protein-coupled peptide receptor activity / response to starvation / synaptic vesicle exocytosis / response to reactive oxygen species / G protein-coupled receptor activity / determination of adult lifespan / peptide binding / presynapse / response to heat ...response to paraquat / G protein-coupled peptide receptor activity / response to starvation / synaptic vesicle exocytosis / response to reactive oxygen species / G protein-coupled receptor activity / 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
LEAD (II) ION / : / G-protein coupled receptor Mth
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsWest Jr., A.P. / Llamas, L.L. / Snow, P.M. / Benzer, S. / Bjorkman, P.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the ectodomain of Methuselah, a Drosophila G protein-coupled receptor associated with extended lifespan.
Authors: West Jr., A.P. / Llamas, L.L. / Snow, P.M. / Benzer, S. / Bjorkman, P.J.
#1: Journal: Science / Year: 1998
Title: Extended Life-Span and Stress Resistance in the Drosophila Mutant methuselah
Authors: Lin, Y.-J. / Seroude, L. / Benzer, S.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHUSELAH ECTODOMAIN
B: METHUSELAH ECTODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,59214
Polymers45,0412
Non-polymers2,55112
Water3,621201
1
A: METHUSELAH ECTODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8987
Polymers22,5211
Non-polymers1,3776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METHUSELAH ECTODOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6957
Polymers22,5211
Non-polymers1,1746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.937, 73.000, 115.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein METHUSELAH ECTODOMAIN


Mass: 22520.549 Da / Num. of mol.: 2 / Fragment: N-TERMINAL EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: unidentified baculovirus / References: GenBank: AAD16981, UniProt: O97148*PLUS

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Sugars , 2 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 207 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.4
Details: drop consists of 4 micro litter of protein solution and 2 micro litter of precipitant
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
31.6 M1reservoirprecipitantLiSO4
40.1 MHEPES1reservoirprecipitant

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.949
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 26305 / Num. obs: 26305 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.338 / Num. unique all: 2591 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98.6 % / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementResolution: 2.3→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1448164.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1283 4.9 %RANDOM
Rwork0.212 ---
all-26430 --
obs-26305 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.97 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2--6.21 Å20 Å2
3----7.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 112 201 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.421.5
X-RAY DIFFRACTIONc_mcangle_it3.822
X-RAY DIFFRACTIONc_scbond_it3.662
X-RAY DIFFRACTIONc_scangle_it5.132.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.309 126 4.9 %
Rwork0.261 2455 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PCARBOHYDRATE.TOP
X-RAY DIFFRACTION5PB.PARAMPB.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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