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- PDB-6yxf: Cryogenic human adiponectin receptor 2 (ADIPOR2) with Gd-DO3 liga... -

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Basic information

Entry
Database: PDB / ID: 6yxf
TitleCryogenic human adiponectin receptor 2 (ADIPOR2) with Gd-DO3 ligand determined by Serial Crystallography (SSX) using CrystalDirect
Components
  • Adiponectin receptor protein 2
  • V REGION HEAVY and LIGHT CHAINS
KeywordsMEMBRANE PROTEIN / Adiponectin receptor / ADIPOR2 / serial synchrotron crystallography / SSX / ligand soaking / 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
Chem-DO3 / GADOLINIUM ATOM / 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: 3.025 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: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_unobs_or_zero_occ_atoms
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 1.3Oct 16, 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 and LIGHT CHAINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,17516
Polymers58,0022
Non-polymers4,17214
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex between ADIPOR2 and anti-ADIPOR2 scFv purified by pull down and gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-66 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.640, 100.650, 111.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 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
#2: Antibody V REGION HEAVY and LIGHT CHAINS


Mass: 24904.604 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 , 6 types, 58 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H32N4O7 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution using either a Mosquito LCP robot (SPT Labtech) in CrystalDirect plate-2. The crystallisation condition is made of 42.3% PEG 400, ...Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution using either a Mosquito LCP robot (SPT Labtech) in CrystalDirect plate-2. The crystallisation condition is made of 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0. 60-120 nL of Gd-DO3 soaking solution with a final conc. of 10 - 25 mM was delivered onto LCP crystallisation drop. Crystallisation experiments were carried out at the HTX facility of EMBL Grenoble. LCP bolus were harvested automatically at cryogenic condition using CrystalDirect technology.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.72 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 31468 / % possible obs: 100 % / Redundancy: 14.98 % / CC1/2: 0.98 / Net I/σ(I): 5.06
Reflection shellResolution: 3.01→3.1 Å / Num. unique obs: 2336 / CC1/2: 0.3
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (29-NOV-2019)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LWY

5lwy


Resolution: 3.025→48.67 Å / Cor.coef. Fo:Fc: 0.826 / Cor.coef. Fo:Fc free: 0.82 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.394
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 956 5.71 %RANDOM
Rwork0.2136 ---
obs0.2163 16752 98.8 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 81.24 Å2 / Biso min: 36.47 Å2
Baniso -1Baniso -2Baniso -3
1-15.679 Å20 Å20 Å2
2--27.2272 Å20 Å2
3----42.9062 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: final / Resolution: 3.025→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4037 0 333 44 4414
Biso mean--111.36 64.64 -
Num. residues----512
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1548SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes711HARMONIC5
X-RAY DIFFRACTIONt_it4403HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion533SEMIHARMONIC5
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_contact3863SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4501HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6148HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion21.07
LS refinement shellResolution: 3.025→3.06 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4375 26 7.28 %
Rwork0.3057 331 -
obs--64.13 %

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