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- PDB-5lwy: Revised crystal structure of the human adiponectin receptor 2 in ... -

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Basic information

Entry
Database: PDB / ID: 5lwy
TitleRevised crystal structure of the human adiponectin receptor 2 in complex with a C18 free fatty acid
Components
  • Adiponectin receptor protein 2
  • 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 / adiponectin-activated signaling pathway / adipokinetic hormone receptor activity / AMPK inhibits chREBP transcriptional activation activity / vascular wound healing / fatty acid oxidation / hormone-mediated signaling pathway / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis ...adiponectin binding / adiponectin-activated signaling pathway / adipokinetic hormone receptor activity / AMPK inhibits chREBP transcriptional activation activity / vascular wound healing / fatty acid oxidation / hormone-mediated signaling pathway / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
AdipoR/Haemolysin-III-related / Haemolysin-III related / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Adiponectin receptor protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 19, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionMar 22, 2017ID: 3WXW
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Apr 19, 2017Group: Atomic model / Structure summary
Revision 1.4Feb 7, 2018Group: Advisory / Author supporting evidence / Database references
Category: pdbx_audit_support / pdbx_related_exp_data_set / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 5, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _entity.src_method / _entity_name_com.name / _struct_ref.db_code
Revision 1.6Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.7Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Oct 23, 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 2
H: V REGION HEAVY CHAIN
L: V REGION LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,19914
Polymers57,9063
Non-polymers3,29211
Water5,657314
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-54 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.580, 101.030, 108.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adiponectin receptor protein 2 / Progestin and adipoQ receptor family member 2 / Progestin and adipoQ receptor family member II


Mass: 33097.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADIPOR2, PAQR2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86V24

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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 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#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 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)

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Non-polymers , 5 types, 325 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100mM Na-Citrate, 400mM K-Citrate, 30% PEG400, pH 6.0, 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: Dec 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→101.03 Å / Num. obs: 32174 / % possible obs: 98.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 52.25 Å2 / Net I/σ(I): 8.55

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Processing

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

3wxw
PDB Unreleased entry


Resolution: 2.4→19.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.294 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1609 5 %RANDOM
Rwork0.198 ---
obs0.199 32174 98.3 %-
Displacement parametersBiso mean: 80.12 Å2
Baniso -1Baniso -2Baniso -3
1-3.4084 Å20 Å20 Å2
2--7.9477 Å20 Å2
3----11.3561 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 221 314 4579
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084422HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025943HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1538SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes643HARMONIC5
X-RAY DIFFRACTIONt_it4422HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion23.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion536SEMIHARMONIC5
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_contact4988SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.276 148 4.99 %
Rwork0.231 2815 -
all0.233 2963 -
obs--99.3 %
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)
13.1124-1.96340.33545.806-0.28260.6134-0.17040.11680.83550.0091-0.118-0.6248-0.2304-0.02130.2884-0.4259-0.0171-0.0938-0.39970.07070.675314.9251-5.2766-27.2531
23.83351.5363-2.10065.80141.70550.763-0.0081-0.0219-0.07430.00860.0111-0.0636-0.284-0.2394-0.003-0.0456-0.0432-0.03520.2701-0.05280.13721.02130.5561-23.8804
32.7481-0.42490.38275.35520.06641.49370.11270.238-0.2158-0.36310.00030.26630.2379-0.0069-0.113-0.50950.0159-0.0349-0.5133-0.01420.386123.2636-54.29-28.3298
42.06380.04671.10861.1441-0.67452.3670.0978-0.14410.21340.13770.0029-0.06440.1297-0.0188-0.1007-0.5652-0.0098-0.0083-0.554-0.00810.332729.3286-43.0653-10.3451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }
3X-RAY DIFFRACTION3{ H|* }
4X-RAY DIFFRACTION4{ L|* }

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