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- PDB-8s79: Lotus japonicus NFR5 intracellular domain in complex with Nanobody 200 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8s79
TitleLotus japonicus NFR5 intracellular domain in complex with Nanobody 200
Components
  • Nanobody 200
  • Nod-factor receptor 5
KeywordsPLANT PROTEIN / Receptor kinase / protein kinase / pseudokinase / nanobody / complex
Function / homology
Function and homology information


protein kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / LysM domain / LysM domain profile. / LysM domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / Nod-factor receptor 5
Similarity search - Component
Biological speciesLotus japonicus (plant)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHansen, S.B. / Gysel, K. / Andersen, K.R.
Funding support Denmark, United States, 4items
OrganizationGrant numberCountry
Danish Council for Independent Research9040-00175B Denmark
Danish Council for Independent Research3103-00137B Denmark
Bill & Melinda Gates FoundationINV-57461 United States
Bill & Melinda Gates FoundationINV-55767 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A conserved juxtamembrane motif in plant NFR5 receptors is essential for root nodule symbiosis.
Authors: Hansen, S.B. / Luu, T.B. / Gysel, K. / Lironi, D. / Kronauer, C. / Rubsam, H. / Jensen, I.B. / Tsitsikli, M. / Birkefeldt, T.G. / Trgovcevic, A. / Stougaard, J. / Radutoiu, S. / Andersen, K.R.
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nod-factor receptor 5
B: Nod-factor receptor 5
C: Nanobody 200
D: Nanobody 200
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,03521
Polymers91,7584
Non-polymers1,27717
Water1,892105
1
A: Nod-factor receptor 5
D: Nanobody 200
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,87315
Polymers45,8792
Non-polymers99413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-5 kcal/mol
Surface area18850 Å2
MethodPISA
2
B: Nod-factor receptor 5
C: Nanobody 200
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1626
Polymers45,8792
Non-polymers2834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-10 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.755, 126.755, 137.875
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-725-

HOH

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein Nod-factor receptor 5


Mass: 32175.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: nfr5 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta II / References: UniProt: Q70KR1
#2: Antibody Nanobody 200


Mass: 13703.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 122 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 1.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.29→46.66 Å / Num. obs: 32844 / % possible obs: 56.4 % / Redundancy: 9.8 % / Biso Wilson estimate: 65.25 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.091 / Net I/σ(I): 16.8
Reflection shellResolution: 2.29→2.58 Å / Redundancy: 9 % / Mean I/σ(I) obs: 7.11 / Num. unique obs: 1642 / CC1/2: 0.58 / Rrim(I) all: 1.486

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→41.49 Å / SU ML: 0.2827 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 1740 5.3 %
Rwork0.1957 31100 -
obs0.1976 32840 56.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.66 Å2
Refinement stepCycle: LAST / Resolution: 2.29→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 83 105 6196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00486227
X-RAY DIFFRACTIONf_angle_d0.67358399
X-RAY DIFFRACTIONf_chiral_restr0.0449933
X-RAY DIFFRACTIONf_plane_restr0.0051078
X-RAY DIFFRACTIONf_dihedral_angle_d10.94012292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.444110.5334108X-RAY DIFFRACTION2.28
2.35-2.430.4576120.5035369X-RAY DIFFRACTION7.99
2.43-2.520.5577440.436558X-RAY DIFFRACTION12.61
2.52-2.620.4109490.4035835X-RAY DIFFRACTION18.49
2.62-2.740.3321540.3441182X-RAY DIFFRACTION25.81
2.74-2.880.35091010.32311830X-RAY DIFFRACTION39.68
2.88-3.060.34441750.29593011X-RAY DIFFRACTION66.43
3.06-3.30.31332590.27624539X-RAY DIFFRACTION99.13
3.3-3.630.27272520.21754592X-RAY DIFFRACTION99.84
3.63-4.150.2282600.17854612X-RAY DIFFRACTION99.88
4.15-5.230.17742570.1514667X-RAY DIFFRACTION99.92
5.23-41.490.19872760.17274797X-RAY DIFFRACTION99.67
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)
16.97476147524-1.71110390758-2.174491023120.7224192522470.8717156365051.46412525493-0.305023318826-0.1027604386490.685436806857-0.0604012487853-0.224507036560.929464008482-1.34446426858-0.818132551-0.6249976106210.7121733030650.2320464701070.1211870795550.485438500971-0.07700326678660.71468767021924.454370902941.308536436913.2338604511
21.40592038275-0.849619565633-1.943490640996.140030407352.654580534743.37998251216-0.584916945094-0.802847412617-0.6985531747371.144534324110.2211397021040.4332554054640.505886395455-0.5155903476680.5859425299360.9746360738350.1424782373450.3608401311920.8373606821050.155108241960.6313934286167.0670019406639.517326560129.7678068774
31.28169637215-0.472041009897-0.2445988274243.735949403271.018871201532.92847009942-0.272238859585-0.157096502287-0.3531217723950.64825764966-0.0419276294137-0.08245290314620.140180160693-0.09751108263320.2908691050660.5479935528520.1414466296950.1019243180060.4209572432840.04524740196690.2676437636348.9738939429555.942523965421.9969382019
43.18694557029-1.0476174209-0.4271673460554.116768802512.001722032765.883466502520.04336840471680.06254060040920.392048170280.357033972934-0.1073841763130.361896694852-0.763795806926-1.018154733480.1585095855980.6840719670660.22072604650.06059216577220.4334269372540.01297039950920.272715805780.73335797479975.529733035920.5181704451
58.536243087421.39849982022-1.34016363434.58850446717-0.6402642442773.30875859737-0.180068465420.963659605245-0.3224455422310.212028299143-0.02357270410032.114244958160.732273501644-1.844903542670.1114935320721.03166692988-0.463330911260.2321577744691.33067867176-0.1483072129861.5871945424-10.491967662918.4965552034-1.01672452225
65.294961934423.67234359445-0.1875340827615.63752667515-2.690911776853.609673114690.111573250742-0.76681707675-0.06757755788990.9404261467570.1786287322582.24111941204-0.230800737937-1.98900336046-0.1725296503660.508327489233-0.08327319196470.250650263220.922048452347-0.07568652999180.857507597694-5.7935616220440.52703848981.94811629787
73.46001694497-0.415716779167-0.1841432998634.17131003139-2.025963477133.828745815-0.0227554965480.334356096682-0.75969895507-0.2213203777060.02429651250370.7227620178950.543289776309-0.429901495981-0.02442604914910.178662571552-0.1108559925640.070627502380.458971383734-0.1471696310460.4021055497884.6408099916835.165913486-10.1361683532
82.70231562532-1.397374494430.2594041322465.74760637217-0.5325010858773.3556893158-0.2204608093250.0740400964808-0.1056615367260.2308098126560.000515674983839-0.307444630189-0.1411419333220.1876260100930.1815236211180.20821708223-0.0477300911420.06259353532460.459099066661-0.04947734251650.29741873552912.261967547946.9456872942-9.11574239176
94.08076961915-1.89168056512-0.3091700522324.858099467590.2917560842796.240588434710.7022628348871.331847066510.19079207926-0.516532646244-0.842920237320.3657427013440.888366812947-0.145565583051-0.0953754074610.9981420559570.194613049985-0.140235082841.52719409655-0.3513594378690.5039762111791.785519341444.2108556617-42.4273304622
105.392004204487.827501872816.840131205772.000136712049.927916987838.67605122193-0.6143341887363.970951005541.60574787573-3.479136241890.227428025384-0.0968306839807-2.786164002750.9371035937180.1883057704211.17318696720.1750679654140.2517191314481.606365194960.4516518079860.98209404467913.88900653657.5811967515-33.1767914748
114.08690811067-0.3077008974272.097849943225.77145111062-1.264412794033.861614060460.2012324004450.960802888256-0.393324748653-0.547781596379-0.1648250665891.00989606580.331849197211-0.689067068946-0.04055280848610.39309881906-0.0185135243677-0.005033262818991.07676510935-0.2083616535910.443092386752-0.93680227128545.9030636543-29.8654210384
125.07645470927-2.08934783206-1.102120766545.31321392985-0.5309580394740.7663572162950.2719778595281.61187002563-0.0293206029659-1.17112968991-0.0360981153342-0.4695500621570.3620405593830.4047023614380.5526996074270.4373406762980.03933785770080.0535241122171.62934666968-0.3247089534830.43297664016811.459222658145.4726309245-34.7365755273
132.212515043472.232238046682.511477556488.87635463488-0.2213657656484.03579734366-0.3016246622991.75843386977-0.750205769861-1.096667261530.4520705090280.6976632996871.30778104488-0.948111096549-0.1615342992420.7798676278110.109716577137-0.1054084368551.85490340191-0.4549857490990.79944244021-1.1311800746739.1151775294-37.1086263837
143.139182120643.515314989960.3091808571227.625607510543.667520130497.675607436670.2688204251972.64079843266-0.361605131745-1.56255771109-0.369256701223-0.1376731182470.05835055581010.00547547589060.2586725374830.713325012660.4468435980660.0150773008941.458118322020.03995794016550.369561881479-0.17202974655654.5068002952-35.3372906699
154.009089391071.09686220495-4.583264532032.67997861444-3.899417120578.18154482092-0.2365119829690.702116492099-1.63801913013-0.480670182258-0.247286751430.5233970378720.454330388269-0.7118901026740.3291097370631.010820496110.0335754750007-0.4206079295681.30259096205-0.4308473118411.01285926842-7.6650245285140.5710030873-43.7877688005
169.562251180513.4437354475-0.9326173745171.90001534649-2.377264792299.37364199239-0.1112770321342.61340581246-0.7993530508590.5403815942890.8505503165721.29175502889-0.241577672502-1.20787782812-1.51966125051.088567524790.5595255010240.02280095560262.263315945290.006173356514191.35307091392-24.957339079374.8584235437-1.25434144213
174.932788714212.67495535863-0.9545881865879.9309118071-6.557782465389.353146194160.3224506707852.37384758744-0.730344164501-0.5604552472251.447491198820.4011969352371.03765465144-1.09217210933-0.6692673860161.114699719760.147260305955-0.122178034992.46639972625-0.2689580028850.417942202452-19.256997826572.4974700918-2.25335823214
185.51876550954-4.88802803051.306483643894.90685226471-3.115622231237.607051047580.9192277281230.369902443362.410475719330.5610633365390.1568828322430.389801380112-0.798154885246-0.416864639888-0.8073101148141.834905386270.3242917589450.4802080410361.276516951510.2561830282661.15061944072-12.248495072290.8470416379.15293327444
197.710919584335.18487684801-2.449488005763.84258267405-1.088258482283.207381946110.5988667630260.3011214882281.327400947121.20198700333-0.1333422701831.624980166440.266877779037-1.2665451823-0.8921705134240.7068085037550.2152706239380.4488251469082.59055294102-0.2603378898931.00728302449-25.023027094973.124010512211.5629848579
207.618629596820.83292950769-0.9421068926876.013121147691.585675625772.752892216330.05273521444070.203031787812-0.01998158249030.278510049312-0.1455908868190.309398629970.13270887986-1.93618188780.1437002301720.8941605655330.1497159735440.04230302030291.30645448268-0.2267490581720.432691165425-11.471208901573.17730451638.28627559163
212.00849118797-1.714677495032.826096903061.884585369191.809321968215.0046570414-0.7930247026881.00923502620.922540648668-0.331461167381-0.6721196027290.55147242586-1.25396662233-2.34440703185-0.1310030059821.03282419480.5456311227520.1107774594112.068421778060.1901685774060.723118801489-13.572961767180.1442793422-0.186298858459
227.756118778442.933124794431.245884049821.146351443870.4401688596110.2274543346930.435154046275-0.258332023002-0.02507062687380.496884822480.2217308283130.8985936634320.14931364742-0.843875377331-1.308468056131.10067081901-0.6807663004460.04291000294482.33138435229-0.0428359189051.27781836717-21.974250818662.66516241533.05385761665
233.71262984966-1.450266753881.71652726018.332478759554.310649048084.04767591872-0.686817322310.9381745995960.4434069513591.087444824880.9911164696981.17491474202-0.769881427466-1.25594580495-0.5366650215541.413089885310.4702654714040.2624343001972.2748001866-0.01748575775010.969897478824-24.169551172177.24464205447.52363444452
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 280 through 299 )AA280 - 2991 - 20
22chain 'A' and (resid 300 through 342 )AA300 - 34221 - 63
33chain 'A' and (resid 343 through 462 )AA343 - 46264 - 183
44chain 'A' and (resid 463 through 563 )AA463 - 563184 - 284
55chain 'B' and (resid 300 through 380 )BG300 - 3801 - 79
66chain 'B' and (resid 381 through 403 )BG381 - 40380 - 100
77chain 'B' and (resid 404 through 505 )BG404 - 505101 - 202
88chain 'B' and (resid 506 through 563 )BG506 - 563203 - 260
99chain 'C' and (resid 3 through 24 )CI3 - 241 - 22
1010chain 'C' and (resid 25 through 34 )CI25 - 3423 - 32
1111chain 'C' and (resid 35 through 68 )CI35 - 6833 - 66
1212chain 'C' and (resid 69 through 78 )CI69 - 7867 - 76
1313chain 'C' and (resid 79 through 92 )CI79 - 9277 - 90
1414chain 'C' and (resid 93 through 109 )CI93 - 10991 - 107
1515chain 'C' and (resid 110 through 116 )CI110 - 116108 - 114
1616chain 'D' and (resid 5 through 14 )DJ5 - 141 - 10
1717chain 'D' and (resid 15 through 24 )DJ15 - 2411 - 20
1818chain 'D' and (resid 25 through 34 )DJ25 - 3421 - 28
1919chain 'D' and (resid 35 through 46 )DJ35 - 4629 - 40
2020chain 'D' and (resid 47 through 74 )DJ47 - 7441 - 68
2121chain 'D' and (resid 75 through 84 )DJ75 - 8469 - 78
2222chain 'D' and (resid 85 through 92 )DJ85 - 9279 - 86
2323chain 'D' and (resid 93 through 116 )DJ93 - 11687 - 110

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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