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- PDB-6ks0: Crystal structure of the human adiponectin receptor 1 -

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Basic information

Entry
Database: PDB / ID: 6ks0
TitleCrystal structure of the human adiponectin receptor 1
Components
  • Adiponectin receptor protein 1
  • The heavy chain variable domain (Antibody)
  • The light chain variable domain (Antibody)
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / membrane protein / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of epithelial to mesenchymal transition / negative regulation of non-canonical NF-kappaB signal transduction / fatty acid oxidation ...adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of epithelial to mesenchymal transition / negative regulation of non-canonical NF-kappaB signal transduction / fatty acid oxidation / regulation of lipid metabolic process / regulation of glucose metabolic process / positive regulation of insulin receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of cell growth / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis / protein kinase binding / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
AdipoR/Haemolysin-III-related / Haemolysin-III related
Similarity search - Domain/homology
PHOSPHATE ION / Adiponectin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsTanabe, H. / Fujii, Y. / Nakamura, Y. / Hosaka, T. / Okada-Iwabu, M. / Iwabu, M. / Kimura-Someya, T. / Shirouzu, M. / Yamauchi, T. / Kadowaki, T. / Yokoyama, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am010108 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K18509 Japan
CitationJournal: Commun Biol / Year: 2020
Title: Human adiponectin receptor AdipoR1 assumes closed and open structures.
Authors: Tanabe, H. / Fujii, Y. / Okada-Iwabu, M. / Iwabu, M. / Kano, K. / Kawana, H. / Hato, M. / Nakamura, Y. / Terada, T. / Kimura-Someya, T. / Shirouzu, M. / Kawano, Y. / Yamamoto, M. / Aoki, J. ...Authors: Tanabe, H. / Fujii, Y. / Okada-Iwabu, M. / Iwabu, M. / Kano, K. / Kawana, H. / Hato, M. / Nakamura, Y. / Terada, T. / Kimura-Someya, T. / Shirouzu, M. / Kawano, Y. / Yamamoto, M. / Aoki, J. / Yamauchi, T. / Kadowaki, T. / Yokoyama, S.
History
DepositionAug 22, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 19, 2020ID: 3WXV
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adiponectin receptor protein 1
H: The heavy chain variable domain (Antibody)
L: The light chain variable domain (Antibody)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0105
Polymers59,8493
Non-polymers1602
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-60 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.663, 194.443, 74.384
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 35040.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADIPOR1, PAQR1, TESBP1A, CGI-45 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96A54

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Antibody , 2 types, 2 molecules HL

#2: Antibody The heavy chain variable domain (Antibody)


Mass: 13160.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody The light chain variable domain (Antibody)


Mass: 11647.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: PEG 400, magnesium sulphate, bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 17815 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 58.33 Å2 / Rmerge(I) obs: 0.171 / Χ2: 1 / Net I/σ(I): 4.5 / Num. measured all: 131713
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsΧ2Diffraction-ID% possible allRmerge(I) obs
2.75-2.857.517450.9991100
2.85-2.967.517491.0011100
2.96-3.17.517781.00311000.842
3.1-3.267.517601.00211000.579
3.26-3.467.517600.997199.90.43
3.46-3.737.417920.998199.90.303
3.73-4.117.417620.999199.90.209
4.11-4.77.417961.001199.90.118
4.7-5.917.318121199.60.102
5.91-30718611198.10.068

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E6J, 1FDL

1e6j

1fdl


Resolution: 2.79→19.94 Å / SU ML: 0.4503 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2771 824 5 %
Rwork0.221 15665 -
obs0.2238 16489 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.4 Å2
Refinement stepCycle: LAST / Resolution: 2.79→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 6 30 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184434
X-RAY DIFFRACTIONf_angle_d0.48816026
X-RAY DIFFRACTIONf_chiral_restr0.0386645
X-RAY DIFFRACTIONf_plane_restr0.0031757
X-RAY DIFFRACTIONf_dihedral_angle_d10.90192525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.960.38391280.29582452X-RAY DIFFRACTION91.98
2.96-3.190.37411400.28582650X-RAY DIFFRACTION98.62
3.19-3.510.33581380.25822635X-RAY DIFFRACTION98.33
3.51-4.010.26491400.21852647X-RAY DIFFRACTION97.62
4.01-5.040.21381390.18372635X-RAY DIFFRACTION96.55
5.04-19.940.26421390.20262646X-RAY DIFFRACTION93.17
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)
11.719688832940.607770368758-0.497317545795.305529847811.297430131151.721661196980.08652524435810.1369196613130.250264293483-0.682418895407-0.04205416560340.749380705471-0.67485597804-0.307087624486-0.1257230682330.8005501938270.236206994362-0.1553888098510.540482470234-0.01077678778090.48701544805720.193624317836.910149148-13.912193524
21.56677794361-0.6393837821730.09206615056346.218941985983.230441788983.1876418799-0.0157195855984-0.2273816618270.4544982318730.5683294789120.682711336536-0.938314892261-0.5727605881260.0994199472087-0.4405951415840.9971966530870.169493296655-0.00674234081550.609732169271-0.1246766231390.64374830610329.815695186149.2901697319-2.97976757476
30.370876657607-0.4492646206621.463381394040.596657762414-1.882456846875.86305013287-0.2940778169040.3224913035780.4338213990590.0901752633168-0.689105518843-0.427168969552-0.4077781357121.2668912625-0.3580870562840.7284611319950.0535611374383-0.08107183573360.381098550604-0.1458098393431.0005048843333.82991824931.9782034733.55711010778
40.8982360682160.4018091571330.06518032025220.329944864779-0.2982040484840.5272615228580.00822854990988-0.2822650247750.178848142277-0.55429035730.0248562204313-0.0684098349586-0.968423309834-0.157282666265-0.01866571482741.133203749640.2418142911580.1299045274010.702731824141-0.01189339841640.50946299443524.70851.3687.186
54.90830433201-2.58434818731-3.149075802175.24278757179-0.5761348291493.590401394070.8054359099410.4420389703880.208803844890.7762373431470.7663425924451.09479371616-0.76836715469-0.0302356323768-0.4232096852512.091201153620.530235191518-0.08167834301790.944966187605-0.1443015475611.0459620049612.611924965267.51046229933.62411720984
62.158428832270.141552311807-1.120665742697.24820066486-0.3952108566213.032225296910.110810779371-0.4205674950731.339668187750.9712813310250.0705048121478-0.806194641993-0.283566316231.15026370323-0.2314799650211.21051686230.2557306930110.1204637428220.753936443045-0.03067868141071.056273889513.412897961848.30713711111.91335401213
73.19551009934-0.335403870928-0.9776258931572.723035598930.8122049762093.019697185720.260651840242-0.0007655321950770.5736552759610.520516191960.01755954425990.885580218228-1.03933021138-0.137310457167-0.1054156001930.9600083409750.371039510019-0.005508456083110.743015119482-0.09847574590890.72724989922713.032226358849.8543930449-4.31615407593
81.78521347304-1.17063614658-2.414226933574.556905264570.8723337781115.41025236406-0.200239057946-0.2863256431-0.470940085652-0.1375502419990.09498723224930.448221614510.796092057496-0.1051476671060.3598355326090.628744504392-0.437740859083-0.05423232796431.008037748580.02287890055480.74852532268213.0692358059-11.2798544383-17.2094496104
90.935068143427-0.7849708074510.5877179690861.095965409070.7354065438233.77064029926-0.323356823386-0.5275595847040.0350692383215-0.069874097477-0.2788892756051.287304987890.324091824225-1.687768708930.5968188164860.418776518266-0.1304208440170.09590299620410.890256345281-0.1407006713080.8654717704489.675902488511.22890482637-12.5715645747
104.898884636820.1503612515970.2014189199746.04080864493-0.6836849178455.62262287705-0.2098102593290.6415710536770.00547006073763-1.33592118364-0.07114628518150.662584291186-0.429623609965-0.8452662477110.3514400476390.648947528471-0.0658530869555-0.218917899460.582678346695-0.1205206124760.66598570277515.19463557030.244948674122-24.6637521838
116.35846743353-5.51640458752-4.070058709488.631121791411.072942733334.11842719313-0.3335144268510.2667282176370.423889235282-0.378979904077-0.2107692185842.21754307398-0.111177807424-1.680471628750.2767028719590.378699660342-0.102836823713-0.08159059669781.06008629287-0.206506525841.043257312895.9267733753-2.62996647948-17.4933755826
123.102719292210.3782781676670.2397000160024.996721074232.012822680294.85393897922-0.161172939510.360691258930.0451813161867-1.345429956970.6291423925440.1253583907370.548730815365-0.608764583770.08923278544690.514673437905-0.236060151225-0.01012007642270.549360793092-0.01327174204340.45436222575917.1841951222-7.67493738422-24.308630329
131.799297534911.00335529988-0.6282708817354.811475527040.8654456024053.357093082880.0857285707699-0.2357802042810.009912634040270.674128207393-0.4515521755650.8983631984260.671605960562-0.5469590482330.2878074848570.384277723545-0.05081441352670.0409617981810.533404633526-0.02282514627780.47821352423719.1174221219-4.14599281466-17.0548918505
149.43814255945-5.229597600170.8053039847279.82978199314-2.737973389474.79150662767-0.1779318692371.00263364280.218886332009-1.024109175390.3496364962020.243896915428-0.911622485602-0.41193058363-0.1167347385220.8348992749290.02398251815520.03180708341650.428604242220.0312741517810.40877340336434.51964035683.84698180199-26.8364304963
153.20174266789-2.20103188422-0.151773373714.64311710257-1.425355868680.7559256831060.2212737390080.2765530592650.155921554269-0.431700408801-0.530509099869-0.859984132895-0.300160760171.121309695310.2590367299650.4001421013860.0599257284098-0.04076441282520.3931587114850.01584790205660.44300195083243.82152845050.948044443067-15.2706165427
163.53831776854-0.453930812888-0.3606849633741.125753520070.9245170736213.11158839643-0.131380395532-0.07083593531910.304676283533-0.09615241641690.05295893816490.313500789691-0.386585899955-0.5050865137470.1936890740290.2221960677230.0922698321889-0.0323677626370.224202932207-0.006644353691960.36845785672530.65249250188.91734678035-19.5471081014
173.62362576146-0.0734201292431.200982763534.962513160051.168887592174.46184112677-0.292384039277-0.360967452793-1.514385919540.88512049441-0.3572548166070.190444601551.55855120505-1.151073092960.03783037076420.514717808298-0.1135996165110.04471960821840.386851295757-0.04909930265860.60983195251928.4078673689-1.67095177586-11.1028247873
183.30031926724-1.448905103590.5344348570083.41561559237-1.782967055667.961555564320.4399402923520.058444848551-0.00223788476279-0.00273771829961-0.130198077105-0.12631459816-0.853034259460.2556804450810.551870705430.301515151407-0.0212369102609-0.1131071771710.273617850354-0.04969829435750.40741777997834.06976845569.42406981319-8.60535711052
193.53741717524-2.097944444013.148791653127.78179981516-5.544361341818.455225717720.0824743147999-0.3498856089230.0280584788815-0.105544533835-0.2063096300420.00705299507404-0.2556917698860.1451940318830.1100680615130.3288860235380.08175437224510.1500476329470.3156758065770.001437769914090.41556899078839.7718821173.0222728654-11.393396232
203.98124290415-0.3341177235140.7829324037873.82303545948-0.1179035199064.48321468456-0.02576180260740.00799560173663-0.765196988753-0.5580970880640.2150263985830.330967275947-0.248132560334-0.447274113134-0.1753104561040.3385407449610.0585256337213-0.02621760513030.35174025723-0.04356685514060.27806829376528.11802432954.95921879802-22.1741843619
214.80899904361-0.943225373136.561184132224.75394458414-1.982303556552.00515468647-0.06625134812980.116204171326-1.70077647292-0.383221976685-0.372235128084-0.1031751206461.46702090510.932388341487-0.9156358062640.195102719022-0.00397575393933-0.06109419439610.552857245846-0.1206704468510.53063745105841.9065235962-7.4361658197-13.781023256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 195 )
2X-RAY DIFFRACTION2chain 'A' and (resid 196 through 252 )
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 288 )
5X-RAY DIFFRACTION5chain 'A' and (resid 289 through 299 )
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 373 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'H' and (resid 18 through 33 )
10X-RAY DIFFRACTION10chain 'H' and (resid 34 through 73 )
11X-RAY DIFFRACTION11chain 'H' and (resid 74 through 83 )
12X-RAY DIFFRACTION12chain 'H' and (resid 84 through 99 )
13X-RAY DIFFRACTION13chain 'H' and (resid 100 through 119 )
14X-RAY DIFFRACTION14chain 'L' and (resid 1 through 9 )
15X-RAY DIFFRACTION15chain 'L' and (resid 10 through 25 )
16X-RAY DIFFRACTION16chain 'L' and (resid 26 through 38 )
17X-RAY DIFFRACTION17chain 'L' and (resid 39 through 49 )
18X-RAY DIFFRACTION18chain 'L' and (resid 50 through 67 )
19X-RAY DIFFRACTION19chain 'L' and (resid 68 through 83 )
20X-RAY DIFFRACTION20chain 'L' and (resid 84 through 101 )
21X-RAY DIFFRACTION21chain 'L' and (resid 102 through 107 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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