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- PDB-5lx9: CRYSTAL STRUCTURE OF HUMAN ADIPONECTIN RECEPTOR 2 IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 5lx9
TitleCRYSTAL STRUCTURE OF HUMAN ADIPONECTIN RECEPTOR 2 IN COMPLEX WITH A C18 FREE FATTY ACID AT 2.4 ANGSTROM RESOLUTION
Components
  • HUMAN ADIPONECTIN RECEPTOR 2
  • single-chain variable fragment
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 / vascular wound healing / fatty acid oxidation / hormone-mediated signaling pathway / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis ...adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / 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 / identical protein binding / metal ion 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
AuthorsVasiliauskaite-Brooks, I. / Leyrat, C. / Hoh, F. / 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 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 2.0Oct 23, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN ADIPONECTIN RECEPTOR 2
H: single-chain variable fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,48916
Polymers64,8622
Non-polymers4,62614
Water9,494527
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-45 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.578, 101.128, 111.577
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 / Antibody , 2 types, 2 molecules AH

#1: Protein HUMAN ADIPONECTIN RECEPTOR 2


Mass: 35020.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86V24*PLUS
#2: Antibody single-chain variable fragment


Mass: 29841.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly)

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Non-polymers , 4 types, 541 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical
ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30-45% PEG 400, 0.1 M HEPES pH 7.0, and 50-100 mM potassium citrate, 0.01 mM AdipoRon

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.4→101.13 Å / Num. obs: 33584 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 41.55 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.527 / Net I/σ(I): 5.5
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 10.2 % / Rmerge(I) obs: 5.681 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.489 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→101.13 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.294 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1626 4.84 %RANDOM
Rwork0.181 ---
obs0.183 33584 99.6 %-
Displacement parametersBiso mean: 50.14 Å2
Baniso -1Baniso -2Baniso -3
1-12.8977 Å20 Å20 Å2
2--16.3833 Å20 Å2
3----29.281 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→101.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4037 0 283 527 4847
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094472HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055976HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1608SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes645HARMONIC5
X-RAY DIFFRACTIONt_it4472HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion25.95
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_contact5316SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.247 132 4.76 %
Rwork0.229 2640 -
all0.23 2772 -
obs--96.16 %
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)
10.9026-0.46230.0220.626-0.44360-0.00570.01210.0302-0.0025-0.00320.00820.0258-0.0010.0089-0.04530.0071-0.0303-0.05470.02740.0315.5085-5.5816-28.3396
20.0250.01830.086500.074800.0001-0.0023-0.00080.0025-0.00020.0001-0.0005-0.00210.0001-0.0049-0.0023-0.00130.00030.00040.000219.9879-0.3092-23.8411
30.40670.00760.17780.6833-0.42420.4196-0.0028-0.0262-0.0033-0.01580.008-0.00170.0230.0098-0.00520.0026-0.0051-0.0167-0.002-0.019-0.024426.4586-49.0436-20.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }
3X-RAY DIFFRACTION3{ H|* }

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