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- PDB-6yx9: Cryogenic human adiponectin receptor 2 (ADIPOR2) at 2.4 A resolut... -

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Basic information

Entry
Database: PDB / ID: 6yx9
TitleCryogenic human adiponectin receptor 2 (ADIPOR2) at 2.4 A resolution determined by Serial Crystallography (SSX) using CrystalDirect
Components
  • Adiponectin receptor protein 2
  • V REGION HEAVY CHAINAntibody
  • V REGION LIGHT CHAINAntibody
KeywordsMEMBRANE PROTEIN / Adiponectin receptor / ADIPOR2 / serial synchrotron crystallography / SSX / CrystalDirect / LCP crystallization / in meso
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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsHealey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
European Research Council (ERC)647687European Union
European Commission653706European Union
European Commission871037European Union
CitationJournal: Cell Rep Methods / Year: 2021
Title: An automated platform for structural analysis of membrane proteins through serial crystallography.
Authors: Healey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Cong, X. / Golebiowski, J. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)60,33011
Polymers58,1073
Non-polymers2,2238
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex between ADIPOR2 and anti-ADIPOR scFv purified by pulldown and gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-54 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.72, 100.58, 109.69
Angle α, β, γ (deg.)90, 90, 90
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: Drosophila melanogaster (fruit fly) / References: UniProt: Q86V24

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Antibody , 2 types, 2 molecules HL

#2: Antibody V REGION HEAVY CHAIN / Antibody


Mass: 13274.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody V REGION LIGHT CHAIN / Antibody


Mass: 11734.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)

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Non-polymers , 5 types, 107 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


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


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


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.59 Å3/Da / Density % sol: 65.7 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0. Crystallisation experiments were carried out at the HTX facility of EMBL-Grenoble. Automated crystal harvesting under cryogenic ...Details: 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0. Crystallisation experiments were carried out at the HTX facility of EMBL-Grenoble. Automated crystal harvesting under cryogenic condition was done by CrystalDirect technology

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30556 / % possible obs: 100 % / Redundancy: 37.12 % / CC1/2: 0.991 / Net I/σ(I): 8.3
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2326 / CC1/2: 0.561
Serial crystallography sample deliveryDescription: CrystalDirect pins / Method: fixed target

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LWY

5lwy


Resolution: 2.404→22 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.263 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.216
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 1632 -RANDOM
Rwork0.2069 ---
obs0.209 32613 99.4 %-
Displacement parametersBiso mean: 80.52 Å2
Baniso -1Baniso -2Baniso -3
1-10.8597 Å20 Å20 Å2
2--21.5877 Å20 Å2
3----32.4474 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.404→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 152 99 4309
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014330HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075834HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1471SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes704HARMONIC5
X-RAY DIFFRACTIONt_it4330HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion532SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3521SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion21.23
LS refinement shellResolution: 2.404→2.49 Å
RfactorNum. reflection% reflection
Rfree0.4056 32 -
Rwork0.3801 --
obs--80.07 %
Refinement TLS params.

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)
11.24990.2474-0.11552.6283-0.05930.1763-0.0782-0.0514-0.0341-0.05140.036-0.028-0.0341-0.0280.0422-0.14940.0095-0.0426-0.20160.00820.082515.4581-5.3635-27.8535
22.7416-1.0989-0.00476.6762-0.09721.283-0.0056-0.23710.1597-0.23710.01230.02410.15970.0241-0.0067-0.1254-0.0136-0.0234-0.1963-0.02120.072823.4113-54.173-28.2026
33.36410.2530.59722.9149-0.51633.15210.06280.03640.16150.0364-0.05650.00550.16150.0055-0.0064-0.1378-0.0078-0.0384-0.181-0.04110.079529.5414-42.8121-10.4664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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