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- PDB-6yxd: Room temperature structure of human adiponectin receptor 2 (ADIPO... -

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Basic information

Entry
Database: PDB / ID: 6yxd
TitleRoom temperature structure of human adiponectin receptor 2 (ADIPOR2) at 2.9 A resolution determined by Serial Crystallography (SSX) using CrystalDirect
Components
  • Adiponectin receptor protein 2
  • V REGION HEAVY CHAIN
  • V REGION LIGHT CHAIN
KeywordsMEMBRANE PROTEIN / Adiponectin receptor / ADIPOR / serial synchrotron crystallography / SSX / CrystalDirect / LCP crystallization / in meso / Membrane proteins
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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionMay 1, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)60,12911
Polymers57,9063
Non-polymers2,2238
Water99155
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 area4830 Å2
ΔGint-56 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.46, 100.76, 114.92
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


Mass: 13160.635 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


Mass: 11647.850 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, 63 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


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


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.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: CrystalDirect-2 plates (MiTeGen) in 30 or 50 nL bolus overlaid with 600 nl precipitant solution. 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0 for ADIPOR2.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.988 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 15292 / % possible obs: 100 % / Redundancy: 130.57 % / CC1/2: 0.98 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→2.98 Å / Num. unique obs: 1971 / CC1/2: 0.737
Serial crystallography sample deliveryDescription: CrystalDirect-2 plate / Method: fixed target
Serial crystallography data reductionCrystal hits: 28949 / Frames indexed: 25297 / Frames total: 382552

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
CrystFEL0.8.0data reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LWY

5lwy


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.825 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.419
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 760 -RANDOM
Rwork0.1987 ---
obs0.2013 15176 75.7 %-
Displacement parametersBiso mean: 48.56 Å2
Baniso -1Baniso -2Baniso -3
1-3.8134 Å20 Å20 Å2
2--14.4021 Å20 Å2
3----18.2155 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 152 55 4251
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0064316HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.825816HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1467SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes701HARMONIC5
X-RAY DIFFRACTIONt_it4316HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion531SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3223SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion20
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.3932 20 -
Rwork0.234 --
obs0.2407 400 12.11 %
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)
11.4180.0646-0.08884.3986-0.08860.3916-0.0679-0.0612-0.0037-0.06120.0410.0135-0.00370.01350.0269-0.08290.0053-0.0479-0.0362-0.00760.113416.4808-5.2889-28.4349
22.5706-1.0447-0.02210.21870.83382.8863-0.014-0.33590.1333-0.3359-0.06640.0450.13330.0450.0804-0.07080.0047-0.0209-0.0804-0.02540.000224.5847-54.2392-29.1462
34.5846-0.23652.33614.6667-1.12676.19120.01360.3060.1470.306-0.0261-0.0590.147-0.0590.0125-0.1314-0.00440.0002-0.1082-0.04540.010230.182-43.0071-10.7702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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