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- PDB-6ks1: Crystal structure of the human adiponectin receptor 2 -

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Basic information

Entry
Database: PDB / ID: 6ks1
TitleCrystal structure of the human adiponectin receptor 2
Components
  • Adiponectin receptor protein 2
  • 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 / adiponectin-activated signaling pathway / adipokinetic hormone receptor activity / 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 / adiponectin-activated signaling pathway / adipokinetic hormone receptor activity / 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
Similarity search - Domain/homology
Chem-LPX / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-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
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)JP17am0101081 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: 3WXW
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
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: The heavy chain variable domain (Antibody)
L: The light chain variable domain (Antibody)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,84712
Polymers57,9063
Non-polymers2,9419
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-55 kcal/mol
Surface area24060 Å2
Unit cell
Length a, b, c (Å)74.580, 101.030, 108.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)

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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: Trichoplusia ni (cabbage looper) / References: UniProt: Q86V24

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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 , 6 types, 210 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#6: 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
#7: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H44NO7P
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 400, potassium citrate, sodium citrate

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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: Dec 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→19.5162 Å / Num. obs: 32174 / % possible obs: 98.1 % / Redundancy: 4.512 % / Biso Wilson estimate: 48.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.13 / Χ2: 0.987 / Net I/σ(I): 8.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.54.5451.2581.2336870.5251.43299.4
2.5-2.64.5320.9171.631420.6551.04399.1
2.6-2.74.5350.7042.1126930.710.80299.2
2.7-2.84.5560.5372.6723490.8330.6198.9
2.8-2.94.5380.4013.4519990.9170.45499.3
2.9-34.5260.3224.1617900.9420.36599
3-3.54.5420.1856.9460640.9770.20998.4
3.5-44.4790.0913.1434260.9930.10297.7
4-54.5140.05619.634210.9970.06397.5
5-64.460.04721.5615320.9980.05297.4
6-84.4170.04322.9612180.9980.04996.4
8-204.1510.03228.368530.9980.03692.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXV

3wxv
PDB Unreleased entry


Resolution: 2.4→19.5162 Å / SU ML: 0.4291 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.059
RfactorNum. reflection% reflection
Rfree0.2671 2952 4.99 %
Rwork0.2287 --
obs0.2306 32174 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.21 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.5162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 201 201 4455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244407
X-RAY DIFFRACTIONf_angle_d0.5315933
X-RAY DIFFRACTIONf_chiral_restr0.0397615
X-RAY DIFFRACTIONf_plane_restr0.0035735
X-RAY DIFFRACTIONf_dihedral_angle_d7.3723049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.48461290.38242429X-RAY DIFFRACTION86.45
2.44-2.480.35551360.35762535X-RAY DIFFRACTION91.13
2.48-2.530.40421380.36382606X-RAY DIFFRACTION93.02
2.53-2.570.38091440.37592655X-RAY DIFFRACTION95.73
2.57-2.630.38631430.36552683X-RAY DIFFRACTION96.42
2.63-2.680.37511450.32982756X-RAY DIFFRACTION97.32
2.68-2.750.41861390.32862716X-RAY DIFFRACTION97.21
2.75-2.810.34381430.31572728X-RAY DIFFRACTION97.42
2.81-2.890.34841410.31682707X-RAY DIFFRACTION97.17
2.89-2.980.35631410.28262763X-RAY DIFFRACTION97.32
2.98-3.070.31271410.27092712X-RAY DIFFRACTION97.17
3.07-3.180.34041400.25242709X-RAY DIFFRACTION96.94
3.18-3.310.34381480.24922697X-RAY DIFFRACTION96.8
3.31-3.460.25571480.23712724X-RAY DIFFRACTION96.83
3.46-3.640.25351380.21092673X-RAY DIFFRACTION95.78
3.64-3.860.21221470.19162682X-RAY DIFFRACTION95.96
3.86-4.160.19191350.18492699X-RAY DIFFRACTION95.68
4.16-4.570.21951370.16542689X-RAY DIFFRACTION96.02
4.57-5.220.21521390.17112692X-RAY DIFFRACTION96
5.22-6.540.21141410.19182698X-RAY DIFFRACTION96.14
6.54-19.520.21751390.19212638X-RAY DIFFRACTION94.2
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)
11.147281356730.4900565412310.06307418312191.618483879550.302299336740.5584374940520.08692291865250.3984179322780.755017468056-0.380109032849-0.0351257602992-0.0965960003579-0.1789438633560.159614260034-0.001753378452070.228191924002-0.1773183865690.1108948292270.321719862370.1771560268622.0565594759721.443648755332.956164303123.8047985744
21.72685664944-1.33017893411-0.2777579524311.082603361550.4731603768670.793843500257-0.273451723218-0.2206954758790.8711551709960.50350690033-0.1797425909-0.387149773656-0.182329079758-0.254502822199-0.3269896169070.4459059076050.234682241011-0.3418781921630.1126345966160.04548391504122.2969324066213.905379349851.472276771732.5792966908
32.04467341265-0.162297800251-0.6484910220823.83916281415-0.9846919744152.530655671420.3521729950140.4398268132750.5581618993370.11789752649-0.3972279657930.698557029673-0.403680169181-0.07126012035240.09904203958360.462565257637-0.00728391378506-0.05743161619790.5257280739360.04122589605251.561538290324.5785268946240.411395294821.4390665144
40.3943424768851.62156211290.1039178435216.82617781751-0.1104715340041.683628440110.1437506869250.4246210283471.1102962914-0.487248342462-0.461638326732-0.278860140643-0.543148278271-0.09100195685930.3227198252720.5412096469510.0383427174796-0.1024673504170.4737910227530.2614440097462.1540233767914.125886642858.612722744820.2221718418
54.329910533560.457446703861.397189014545.33680498127-2.25216483321.92434321803-0.0922041808821-0.138659878235-0.7915591698490.2528194857250.1486736637030.8460961706210.638053924525-0.115655748874-0.02938154388820.38994173425-0.0947459564564-0.01391775201620.461381031303-0.0006212005696081.2765598131119.6677797575-11.451700723928.0915144235
64.51921119651-2.70865674670.8705972045762.21406396593-1.170465863370.8807866791210.1180470841440.441883803409-0.192111406829-0.222033091430.1921959459551.098438359230.147133944656-0.140912898015-0.2256626292920.5248869862040.0223005344904-0.1238140774450.385516548966-0.07797667797261.7201688043714.52156314040.76357566634124.1021935552
72.7547418834-1.429013684852.33842193028.4703610513-2.113231403558.02955549334-0.310784818108-0.0646934968563-0.277469568737-0.218154893801-0.195375704820.417662957340.125022254208-0.09171676484860.3610326454980.4399239540370.04346405558130.04023699404980.331423748459-0.01960289069211.321238953826.0857137937-2.5257101942829.4643730435
83.31522650611.82615363799-1.999220046892.157640085110.3055377246122.907920955830.375940271008-0.03975787059110.135702535082-0.0632563991080.307050572829-0.1331200889990.3574907692670.816613447849-0.2756088170510.3406808575410.108896634143-0.1310681671280.485842916014-0.1818846185351.5557116919930.1172557933-1.3414548805329.9618747662
97.68813035936-1.488651372592.584811536492.01478540147-1.131848943256.363974169630.5117624757920.786501124493-0.267529737389-1.00548087417-0.300539092978-0.107887488790.2494859322540.251081999295-0.2208392749960.5699527904380.01625130848330.06166486766240.399650044908-0.1030922572581.2094225911427.06779743150.0099816008419118.7712534601
101.99978959275-1.664677579264.256895440351.71268669005-1.646025497692.426336064380.0210919521150.680726141315-0.136362285689-1.082596109020.03454378953221.025368013970.106034234366-0.0963205987815-0.1357131968460.539896776426-0.0758585048075-0.3493081826390.386643068487-0.1340384010851.5552585885417.0585126287-4.3099034399219.6358535104
110.601133957423-0.7232064489851.151309164263.26949751872-0.4097947737843.070350608230.3443295659220.2347545703760.111442772677-0.2330676362130.114447521661-0.5854935146220.6101774130090.572563585437-0.3674914597520.4489875996640.0106737104092-0.0009842334985470.306238334387-0.03660047522571.5799807077628.6958991446-9.3832352353327.6433411555
120.00966535208426-0.02302985368420.1183093661321.80198108014-0.1570183127281.440011329030.2216379683890.317646219173-0.2299061304590.147620770708-0.04329045483970.506080585882-0.0353884334033-0.450106317271-0.07914249353350.2535656204170.08666039835620.0880549370660.334346133065-0.01912967345441.466838724820.08290669665.4275261062832.5071866667
133.77328586051-4.50603212406-1.825421942299.134468064873.619276051174.98366897693-0.299450876581-0.0847236548644-0.2040287861060.1895542198440.211857968547-0.13592288810.5860912806430.219904240236-0.01430701833960.4642219205080.06065383785460.04205584271930.3156716752860.1024176033421.5526467870927.5468441439-18.561702365129.8961101597
142.60173136438-2.169948117983.561749063912.82365615436-3.583029214145.2439439101-0.00114782438920.3791109725650.137312339229-0.337833462979-0.350567960217-0.7173520587360.452409690721.19032882150.3962988393060.4600743410850.03056498278810.115701852260.559191070433-0.01961267721831.6411335658338.89601696956.1151615520238.9402842194
151.55695777999-0.7012652411282.201121969021.98661659562-0.9307957636993.18636827010.124651055483-0.4529580656820.1918772330890.118289309173-0.216140240963-0.330503974509-0.1006206437610.589454746877-0.03384700884530.402749310683-0.027890451383-0.01779776910420.376644042751-0.0007513511695661.306443091533.38585964486.2176291925552.6366679804
161.289552411580.3143674590690.6736405475151.99490370830.5545179833220.4379378962670.06727631560620.04462084636980.03022836226070.216586715349-0.169010928365-0.252178034673-0.1340683128550.1667597370350.1150484391680.274239570834-0.167988767284-0.06119853525020.1864700169840.08237807321751.5271401440830.706423362511.282462664537.6014147647
176.233699626681.835723861151.482021033852.341574104561.476632176913.782849331480.143279515535-0.317682764066-0.9472213346090.1669543545120.111731617630.6757347635211.06607533904-0.24485616939-0.3880299331370.466708473325-0.0320368921054-0.09931659683150.3415158985520.02027272907741.0256012606321.9585257254-0.20155534649942.6217470292
185.818777040251.98230945583-4.35803912186.10753848934-5.899522212829.44748863345-0.190082119903-0.3681289041120.8526800205780.3576943495460.3088035766710.627150725651-0.0959943054514-0.559807980116-0.1543023901010.3745205586540.0498651440540.03065078013260.363877548841-0.08451165808261.197238633420.554538643813.313708721244.5521000158
199.17062061717.85906612628-7.497597953428.03826873392-6.902982729146.299304519090.181003701078-0.3797193781660.9088443709320.339664238438-0.264997842298-0.264806829198-0.3658594987790.558712864501-0.02880154420540.3706084879840.0119692557002-0.04629944466840.4385317763450.0177600388661.252918797831.57195523914.294818603145.8428279482
209.666996524345.655001671370.5441504407488.71329032834-1.732758217817.203589986350.30669222785-0.3792822977660.1753951087820.1511477947030.06932219504360.8107608035850.175363396481-1.11356392755-0.3323535709660.556903422789-0.08941973955250.0441187232860.6767991902490.007336729476671.3800813062522.76683819473.1179577426155.6822583877
211.589344504330.05118151590661.123266433781.37662544058-0.02757814127794.08211834070.01480298160540.235920101530.342102695123-0.0820025748686-0.0639623746719-0.5975274660790.3093374172630.519773126513-0.03837388350840.2473326413720.005375057722830.007995854143770.331708399327-0.004821006150181.2684601132131.69104881276.5625966409235.1554181629
224.703089497032.82443254096-6.24212970612.85590080691-3.58509873388.30751823105-0.260872981506-0.638450192577-0.9884223186970.205626554789-0.291651161229-0.1911157051871.234250178890.5705389328790.4678933386370.536436086830.00873689526231-0.04722012016980.470973611664-0.02820585853581.2135230687630.4135723809-2.0142241347153.7047550347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 176 )
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 309 )
3X-RAY DIFFRACTION3chain 'A' and (resid 310 through 346 )
4X-RAY DIFFRACTION4chain 'A' and (resid 347 through 383 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 17 )
6X-RAY DIFFRACTION6chain 'H' and (resid 18 through 33 )
7X-RAY DIFFRACTION7chain 'H' and (resid 34 through 40 )
8X-RAY DIFFRACTION8chain 'H' and (resid 41 through 51 )
9X-RAY DIFFRACTION9chain 'H' and (resid 52 through 73 )
10X-RAY DIFFRACTION10chain 'H' and (resid 74 through 83 )
11X-RAY DIFFRACTION11chain 'H' and (resid 84 through 98 )
12X-RAY DIFFRACTION12chain 'H' and (resid 99 through 111 )
13X-RAY DIFFRACTION13chain 'H' and (resid 112 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 48 )
18X-RAY DIFFRACTION18chain 'L' and (resid 49 through 61 )
19X-RAY DIFFRACTION19chain 'L' and (resid 62 through 75 )
20X-RAY DIFFRACTION20chain 'L' and (resid 76 through 83 )
21X-RAY DIFFRACTION21chain 'L' and (resid 84 through 101 )
22X-RAY DIFFRACTION22chain 'L' and (resid 102 through 107 )

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