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- PDB-6x02: Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 -

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Basic information

Entry
Database: PDB / ID: 6x02
TitleNup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8
Components
  • Nucleoporin NUP133
  • Nucleoporin NUP84
  • VHH-SAN8
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / Nanobody
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / tRNA export from nucleus ...mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / tRNA export from nucleus / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / subtelomeric heterochromatin formation / mRNA export from nucleus / nuclear pore / protein import into nucleus / double-strand break repair / nuclear envelope / cellular response to heat / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nucleoporin NUP133 / Nucleoporin NUP84
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 6.38 Å
AuthorsNordeen, S.A. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077537 United States
CitationJournal: Nat Commun / Year: 2020
Title: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif.
Authors: Nordeen, S.A. / Turman, D.L. / Schwartz, T.U.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NUP84
B: Nucleoporin NUP133
C: VHH-SAN8


Theoretical massNumber of molelcules
Total (without water)172,8813
Polymers172,8813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.257, 287.650, 297.375
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Nucleoporin NUP84 / Nuclear pore protein NUP84


Mass: 83718.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / References: UniProt: P52891
#2: Protein Nucleoporin NUP133 / Nuclear pore protein NUP133


Mass: 75010.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP133, RAT3, YKR082W, YKR402 / Production host: Escherichia coli (E. coli) / References: UniProt: P36161
#3: Antibody VHH-SAN8


Mass: 14150.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 6% PEG 8,000, 30% ethylene glycol, 0.1M imidazole titrated with MES pH 6.5, 15mM sodium nitrate, 15mM sodium phosphate dibasic, 15mM ammonium sulfate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9791
SYNCHROTRONAPS 24-ID-C21.2141
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELAug 8, 2019
PSI PILATUS 6M2PIXELOct 15, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21.21411
Reflection

Entry-ID: 6X02

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rpim(I) allDiffraction-IDNet I/σ(I)
6.4-103.41353999.824.1614.510.022155.3
7.8-147.8753399.912.310.042213.8
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID
6.38-6.63113220.5820.8131
7.8-8.72.120670.8910.3052

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 6.38→103.38 Å / SU ML: 1.3001 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.8123
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3242 1350 10.03 %
Rwork0.3138 12103 -
obs0.3149 13453 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 574.65 Å2
Refinement stepCycle: LAST / Resolution: 6.38→103.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6667 0 0 0 6667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286653
X-RAY DIFFRACTIONf_angle_d0.84039266
X-RAY DIFFRACTIONf_chiral_restr0.0481299
X-RAY DIFFRACTIONf_plane_restr0.00381328
X-RAY DIFFRACTIONf_dihedral_angle_d4.31391328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.38-6.610.48151200.46791070X-RAY DIFFRACTION89.01
6.61-6.870.4471370.43211174X-RAY DIFFRACTION99.92
6.87-7.190.42861310.42231227X-RAY DIFFRACTION99.93
7.19-7.570.45231310.40681174X-RAY DIFFRACTION99.92
7.57-8.040.40811360.38131240X-RAY DIFFRACTION99.93
8.04-8.660.35041350.3191192X-RAY DIFFRACTION99.92
8.66-9.530.31411350.25631222X-RAY DIFFRACTION99.63
9.53-10.910.24311350.23591231X-RAY DIFFRACTION99.35
10.91-13.730.28511390.26891236X-RAY DIFFRACTION98.64
13.74-103.380.34061510.35691337X-RAY DIFFRACTION99.07
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)
10.111042100896-0.1160578481230.04305037779590.144283570193-0.02711136523360.03295251093230.0760368820315-0.606930872247-0.454358136649-0.484707647653-0.1517305337690.07974406903280.325225278162-0.3825853866-0.1324076183886.972880335552.05715492974-1.946037169786.07311257883-4.1998150199910.066944711321.674647921610.564976521440.6574520216
2-0.003784555142890.00765108824762-0.03582492188710.451576011067-0.5401623440540.8065555131610.1748209848340.828065208914-0.12290879995-0.420565936596-0.7377147354830.367570820728-0.1091023843530.0601668048662-0.39046953692.514322502782.1017609922-2.331203456894.09707933296-0.4820624338666.4101844428117.97767420742.7336330019653.4818288035
31.02860919143-0.167415988170.4872875717382.277992935990.6776008760010.6694683950191.19534478853-1.47916785853-0.0136618635452-4.92348495256-1.76109477665-1.02436068141-1.007747110373.391901842741.4920729095.31859457009-1.941613012120.6718422121857.83991772976-4.054698067976.9181444923520.217263847735.319873535453.2309838589
42.85449191702-0.924424837927-1.132791717272.13496696917-1.193806364941.68269267284-0.880522876275-2.0120444150.8900078139030.160276785233-0.5344884238831.50178678025-1.360491911951.2927198958-3.580157394027.955872669512.0991969289-3.934308857669.03375172764-5.625053493525.887104375747.9891900424646.816885182861.6962047033
50.0126241958646-0.00349473014023-0.01277904418620.01066872327470.01217985359150.0169456241345-0.5354955263180.268950196280.683295450027-0.132372115578-0.1246124614340.379356797682-0.1473816025440.0568343863432-0.34940407536113.608089437-0.2077358004081.2963730484713.5567785761-0.302261364357.11187246203-2.5121427628250.542125644775.59316342
60.057407121999-0.1513449559160.1534924633271.880426854840.09831712208670.9240325022420.150678201347-0.4293183836040.02134505167771.25033905144-0.1436620246280.547990875018-2.282050053080.4961492122880.4039254152096.72267926391-1.711358376131.956557162693.74423051602-1.5566611784611.5212105691-5.5902853826741.781180125361.5879600857
71.46224492536-0.406817135183-0.06902786770322.158734585710.3258333726490.05413344434540.3763226501971.06954572871.0188367725-2.66756965648-2.25852892217-2.0402265837-0.3601961272950.73217758294-0.09317836246456.345513887991.39613982863-2.15271248735.567197637051.317231979363.599302017910.71434158110136.167917844.6878147188
81.71960342131-0.25180204857-0.6014907510850.157121325890.007299182924150.2638636034860.4015481858420.05019255297690.1913028815720.1770988694040.204338191377-0.172732830507-0.0284979041935-0.1760320619620.2207701838539.641408133690.859175066467-1.020776746723.283504272322.78886979898.322237707136.9999145077427.933235340441.2058673394
90.940231715453-0.204181584704-0.2109864551610.0722891589210.03760170261010.0426466381651-0.400849661773-0.308536918470.0539590491610.1862814389040.08687452303850.0210679040789-0.104079641414-0.36302049029-1.653857862524.684931748190.5642994212351.389635713314.46129772793-4.448850166936.896795544571.7897171959723.585904336149.6480342507
101.105484994620.682463893951-0.28755001261.44455659279-1.13541260160.9983145289240.134003203865-0.2873450574510.798541515468-2.18983698281-0.2120581177831.150521226-0.307468845149-0.7223505887370.6792642538585.435554190525.01585286547-1.702598152365.499239767422.435694869298.43931974148-1.8166222238518.005523166535.4000837057
110.552864744225-0.6678362661950.5679330178410.777473392805-0.695708532610.6528050551954.01680372337-0.68221666962-4.06970805254-3.965250147360.0436104163972.775049186111.16497761483-3.643815828772.31973789267.03650483206-1.987698532963.918042893458.93324250232-3.319239115459.528388262024.221629415619.6958400792244.6053730407
120.0572205261618-0.1650655292050.05565747541470.3671770894490.02152885613580.1915267394544.34557949143-0.173655709523-0.4885208875870.4301761570855.091135946762.76208571942-2.98832521414-0.449262767828-1.25629028043E-54.32510173923-0.4084457704450.01697286431135.22710025256-0.07833202106516.809492305658.16440748734-1.9830361606840.1624335621
130.2875244976790.6363087132780.0758692783290.881340638328-0.04009826495210.395807349895-1.56331598888-3.01349363601-0.5197186326011.63474218203-0.962180795169-2.08430235769-0.304914660561.07809164258-0.05657905426825.625128111581.92383763044-0.05397960945755.02072902961-1.080330496142.584661817349.4805629961-12.481338483734.0874543425
143.32065339119-3.71570016279-2.314060609744.677023398342.481129738591.668966900581.225352664442.70172298108-0.390073063937-0.722707836647-0.5018996279713.26721910955-0.9657820452-1.18577432192-4.574668446246.587447183251.45368186793-3.119171412472.820255904022.842725508796.219882120257.92758845322-17.382181347215.2106372798
156.04814768373-0.5381225751962.880357520412.348779156525.090098400312.02919526629-0.222658274975-6.04647251602-3.539994680292.98302708538-2.71531325936-3.144169912342.58826787403-7.03945763893-0.6546497012984.008176831852.60723771751-1.827145786872.63601884286-0.122074206636.0060204007912.6734455651-29.706539167927.7809295599
161.494468825582.59346001036-2.169775063464.20827647734-3.044720847532.29210994438-2.189092684122.167046344633.081026690110.4952143768921.4488375536-1.88516923092-1.660884185941.44253214407-2.057103540261.729184612980.0023617577106-0.8763969292735.562108270321.24833700966.8837195833114.9199419892-41.001932673914.1315270139
171.274547626831.235334079320.8152047683780.6198117334490.4999906933690.625657808034-1.64817961745-0.248572210068-0.788041667298-0.5963404257332.2302393131.263848885060.3380348412254.17417120140.001401592945762.72956883770.637434501904-1.131995694092.95737931201-1.159483660344.473717230311.9790839486-44.22714021271.37768455705
180.0678924409585-0.6209889617510.1576182537624.90268831488-0.7630354875190.224940653306-1.366388374111.12037150196-2.47285038122-0.8834021923441.572218846582.01073638798-2.960447188833.89298411812.159010093477.131670089531.914607490435.682385609489.37293188592.375969543891.8843240626915.9112770544-57.4228983587-70.3453274002
191.72639573219-0.155109249753-0.4512041788390.009536617003140.08020202162480.12335453351-2.40627792412-1.24067486896-4.244728448280.9802884095671.410586586631.258369274822.380910212073.131381352380.07791255827518.489589456121.80849673405-0.4685266842473.418066853982.596677481873.2491507161633.362859994-71.4011383031-60.2462699862
202.28302118846-1.01169221632-3.043789757762.751823795282.274856991464.43275791399-2.432166188482.36731860091-2.36895311516-4.63714070974-1.662948595060.9409856484052.31531212898-1.34179294051-1.9717039995.30081443316-0.8415827077092.04742346966-1.83184678032-2.456309992562.7327161599528.7303324112-73.9982519823-55.9919024583
211.832748424970.8230504327591.527564695381.20168059926-0.7484431128190.698504516453.19098335554-2.29050788093-4.59722089841-7.29097517706-0.335440832048-4.217229427222.677185855430.400731399993-0.05844982149497.34234548261-1.502947312010.3650349633960.0205965473682-1.991379012183.077121513122.0414318512-59.1679491569-54.5745512795
222.01006708605-5.01852642599-3.487860569293.586630985294.859052031649.34988617824-1.08922260229-3.735981950314.8733617166-0.1450840764770.537731322724-0.5811538941290.5990242041745.539971463080.2712733042529.528833119390.0235158036718-0.0951708350094.039102952980.6421856357753.9368857447925.222333797-58.9395738611-43.2664632881
23-0.2866845548614.91802745146-2.185152470246.1940530249-3.554682529412.0451187431.64891683323-0.691284554646-0.403845376950.635814251934-1.84089572030.2837777614330.3737329737080.856616605436-0.02023266887452.51678083245-0.5241669610610.06154212341573.743914776330.36057694174.640494297486.08417586049-66.7990752575-7.01279009652
241.292707813740.3868513392513.932242760420.2205386097950.9394268627681.94409372459-2.55298467696-3.408191388110.2219401385880.848500095797-3.792161837410.332509317612-4.2431715729-3.27805824042-27.98942492833.09315198534-1.50971768451.108956529328.76896213365.63492053362-0.529977227387-9.16716789275-83.398223773223.9420550366
252.505900700531.89808690607-2.50090221491.57938082984-2.034446655132.740029716761.60912711113-3.40705728896-4.84704263217-0.494936913432-1.34864500453-6.940180116940.931485077399-1.255405399664.895437005197.999511631394.45684350236-2.0361939079610.1893128621-0.741110043965.960691136331.459665981521.486658958364.9910420387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 16 )AA7 - 161 - 10
22chain 'A' and (resid 17 through 26 )AA17 - 2611 - 20
33chain 'A' and (resid 34 through 205 )AA34 - 20521 - 154
44chain 'A' and (resid 206 through 305 )AA206 - 305155 - 241
55chain 'A' and (resid 306 through 315 )AA306 - 315242 - 251
66chain 'A' and (resid 316 through 323 )AA316 - 323252 - 259
77chain 'A' and (resid 324 through 339 )AA324 - 339260 - 275
88chain 'A' and (resid 340 through 344 )AA340 - 344276 - 280
99chain 'A' and (resid 345 through 352 )AA345 - 352281 - 288
1010chain 'A' and (resid 353 through 368 )AA353 - 368289 - 304
1111chain 'A' and (resid 381 through 419 )AA381 - 419305 - 343
1212chain 'A' and (resid 420 through 450 )AA420 - 450344 - 374
1313chain 'A' and (resid 451 through 491 )AA451 - 491375 - 415
1414chain 'A' and (resid 492 through 511 )AA492 - 511416 - 435
1515chain 'A' and (resid 512 through 603 )AA512 - 603436 - 527
1616chain 'A' and (resid 604 through 657 )AA604 - 657528 - 581
1717chain 'A' and (resid 658 through 726 )AA658 - 726582 - 650
1818chain 'B' and (resid 549 through 593 )BB549 - 59331 - 75
1919chain 'B' and (resid 594 through 626 )BB594 - 62676 - 108
2020chain 'B' and (resid 627 through 661 )BB627 - 661109 - 143
2121chain 'B' and (resid 662 through 715 )BB662 - 715144 - 180
2222chain 'B' and (resid 716 through 768 )BB716 - 768181 - 233
2323chain 'B' and (resid 769 through 1123 )BB769 - 1123234 - 568
2424chain 'B' and (resid 1124 through 1157 )BB1124 - 1157569 - 602
2525chain 'C'CC1 - 1311 - 90

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