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- PDB-5lxg: Revised crystal structure of the human adiponectin receptor 1 in ... -

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Basic information

Entry
Database: PDB / ID: 5lxg
TitleRevised crystal structure of the human adiponectin receptor 1 in an open conformation
Components
  • Adiponectin receptor protein 1
  • V REGION HEAVY CHAIN
  • V REGION LIGHT CHAIN
KeywordsMEMBRANE PROTEIN / PROGESTIN AND ADIPOQ RECEPTOR FAMILY / INTEGRAL MEMBRANE PROTEIN / 7TM / CERAMIDASE
Function / homology
Function and homology information


adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of epithelial to mesenchymal transition / fatty acid oxidation ...adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of non-canonical NF-kappaB signal transduction / negative regulation of epithelial to mesenchymal transition / fatty acid oxidation / regulation of lipid metabolic process / regulation of glucose metabolic process / positive regulation of insulin receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of cell growth / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis / protein kinase binding / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
AdipoR/Haemolysin-III-related / Haemolysin-III related / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adiponectin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsLeyrat, C. / Vasiliauskaite-Brooks, I. / Granier, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council647687 France
CitationJournal: Nature / Year: 2017
Title: Structural insights into adiponectin receptors suggest ceramidase activity.
Authors: Vasiliauskaite-Brooks, I. / Sounier, R. / Rochaix, P. / Bellot, G. / Fortier, M. / Hoh, F. / De Colibus, L. / Bechara, C. / Saied, E.M. / Arenz, C. / Leyrat, C. / Granier, S.
History
DepositionSep 21, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionMar 22, 2017ID: 3WXV
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Jan 31, 2018Group: Advisory / Author supporting evidence / Database references
Category: pdbx_audit_support / pdbx_related_exp_data_set ...pdbx_audit_support / pdbx_related_exp_data_set / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adiponectin receptor protein 1
H: V REGION HEAVY CHAIN
L: V REGION LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1076
Polymers59,8493
Non-polymers2583
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-82 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.310, 194.110, 74.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adiponectin receptor protein 1 / Progestin and adipoQ receptor family member I


Mass: 35040.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADIPOR1, PAQR1, TESBP1A, CGI-45 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96A54

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Antibody , 2 types, 2 molecules HL

#2: Antibody V REGION HEAVY CHAIN


Mass: 13160.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: E.COLI CELL-FREE PROTEIN SYNTHESIS / Production host: Escherichia coli (E. coli)
#3: Antibody V REGION LIGHT CHAIN


Mass: 11647.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: E.COLI CELL-FREE PROTEIN SYNTHESIS / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 172 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100mM Bicine, 100mM MgCl2, 30% PEG400, pH 8.0, Lipidic mesophase method, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 23, 2013
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→97.06 Å / Num. obs: 17815 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 52.37 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.934

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXV

3wxv
PDB Unreleased entry


Resolution: 2.73→26.66 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.115 / SU Rfree Blow DPI: 0.312 / SU Rfree Cruickshank DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.234 890 5 %RANDOM
Rwork0.225 ---
obs0.225 17798 98.1 %-
Displacement parametersBiso mean: 74.57 Å2
Baniso -1Baniso -2Baniso -3
1--17.6039 Å20 Å20 Å2
2--13.1054 Å20 Å2
3---4.4985 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: 1 / Resolution: 2.73→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3985 0 11 169 4165
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084167HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975660HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1347SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes616HARMONIC5
X-RAY DIFFRACTIONt_it4167HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion16.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion521SEMIHARMONIC5
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_contact5171SEMIHARMONIC4
LS refinement shellResolution: 2.73→2.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.265 129 4.99 %
Rwork0.25 2454 -
all0.251 2583 -
obs--89.45 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4843-0.1315-0.47135.68081.33970.75660.07840.00730.0549-0.0368-0.01650.138-0.3042-0.0735-0.06190.15320.2381-0.0627-0.0857-0.0389-0.150521.09643.9982-5.9642
22.36721.86850.36532.14450.12141.6984-0.0402-0.08520.0372-0.17340.03040.14470.1507-0.30990.0097-0.0804-0.07-0.07590.0328-0.0421-0.061414.221-3.2063-20.165
31.8567-0.4116-0.05621.5727-0.04992.9459-0.0172-0.0033-0.0925-0.1164-0.07550.0308-0.0262-0.05040.09270.0058-0.0125-0.0061-0.073-0.0117-0.014734.51653.7607-15.8313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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