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- PDB-6x03: Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 an... -

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Basic information

Entry
Database: PDB / ID: 6x03
TitleNup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9
Components
  • Nucleoporin NUP133
  • Nucleoporin NUP84
  • VHH-SAN8
  • VHH-SAN9
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / Nanobody
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus ...mRNA export from nucleus in response to heat stress / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / subtelomeric heterochromatin formation / mRNA export from nucleus / nuclear pore / protein import into nucleus / double-strand break repair / nuclear envelope / 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 / MOLECULAR REPLACEMENT / Resolution: 7.3 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
D: VHH-SAN9


Theoretical massNumber of molelcules
Total (without water)186,7064
Polymers186,7064
Non-polymers00
Water0
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)72.252, 295.205, 295.609
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) / Strain (production host): LOBSTR / References: UniProt: P52891
#2: Protein Nucleoporin NUP133 / Nuclear pore protein NUP133


Mass: 75009.930 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) / Strain (production host): LOBSTR / 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) / Strain (production host): LOBSTR
#4: Antibody VHH-SAN9


Mass: 13826.207 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) / Strain (production host): LOBSTR

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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: 7.92 Å3/Da / Density % sol: 84.5 %
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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 7.3→147.8 Å / Num. obs: 9375 / % possible obs: 99.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 763.9 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.03 / Net I/σ(I): 41.9
Reflection shellResolution: 7.32→7.71 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 1263 / CC1/2: 0.569 / Rpim(I) all: 0.597

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 7.3→147.8 Å / SU ML: 1.051 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3534 936 9.98 %
Rwork0.3352 8439 -
obs0.3365 9375 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 668.33 Å2
Refinement stepCycle: LAST / Resolution: 7.3→147.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 0 0 0 7091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00297072
X-RAY DIFFRACTIONf_angle_d0.80929838
X-RAY DIFFRACTIONf_chiral_restr0.04631375
X-RAY DIFFRACTIONf_plane_restr0.00351410
X-RAY DIFFRACTIONf_dihedral_angle_d4.37081410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.3-7.680.42531250.37121144X-RAY DIFFRACTION99.92
7.69-8.170.36241340.35081191X-RAY DIFFRACTION99.85
8.17-8.80.32861280.27321177X-RAY DIFFRACTION100
8.8-9.680.29911310.26451191X-RAY DIFFRACTION99.92
9.69-11.080.27531350.25931199X-RAY DIFFRACTION99.78
11.08-13.960.36151380.30121225X-RAY DIFFRACTION99.34
13.96-147.80.38741450.39761312X-RAY DIFFRACTION99.52
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)
10.3550230524640.1319846939980.1354833050710.06366982600940.1826226098071.099406958740.3022179364310.048627514972-0.3066788829570.0629569096706-0.372482714928-0.0198241113117-0.885638873664-0.134139603074-0.2291389088828.60052685944-1.09723859396-0.8624150632084.93564169285-3.897845570586.8979581714621.87008857028.9020733974641.2465722082
20.2838482192240.03951256300770.05694356712340.104881321043-0.01628042286330.0156057635891-0.07055691475060.298776247286-0.078351211962-0.240197267046-0.378794996303-0.0403371581658-0.04701657113710.1157343930620.1860381433955.121468862572.36565667659-2.663440354819.55002764214-0.14213690794911.617965432918.27086333191.0631726376354.0942074147
30.6943048701681.49544957915-0.07313544183242.48018304760.0725058252048-0.02084204050972.34206979301-1.85085908038-1.61713730372-0.239213537908-1.66320464118-1.9116065859-2.154187025992.79854042653.356041348574.97359547145-1.802787453010.7978016326594.78608577853-2.507996750479.8655452461620.636226216433.640719263253.8757534155
41.73739451642-1.12045994842-2.253681882880.7133046429471.443958184252.929574363851.3326955622-3.039155694591.684012453670.953176640102-0.6483285648521.49335137433-0.603151808597-3.66768024462.176285369959.904221905850.812784937793-3.017874462179.06832006845-1.515341403482.843669181888.538892237145.171036069962.4823715145
50.74891793765-0.5701535186351.164980268571.31536878836-1.492888456192.22918960224-0.6767167512170.1387998663480.21409342097-0.10893255939-0.389787013013-0.108085854807-1.069526669520.9462865017140.97711340031411.42808191041.291283280311.8938678728311.4723904079-1.8516530344710.322820796-1.8080007563548.913533114776.4900555679
60.1399254190750.3402407358730.1714511112630.8298579336080.4196396414320.211445993749-0.7822342598581.431742261380.3578477843630.81744664847-0.336492262119-0.312106646428-0.5694978194031.150932473990.1094066549727.355539823882.194157858441.3912160914210.9501729455-0.34412651187212.4198434148-5.0607655288140.18887338862.5015970218
70.048396196373-0.2327213960740.5641737692592.93922729981-3.108495028836.699010584350.5585860090440.486730000849-0.927203235473-1.07714840503-0.08645863976880.3956565145050.3125759108490.414287496960.4778744348086.24031279594-0.163677141436-2.748157429745.491589396440.344540316983.143012274511.0523392529634.580048478545.5297907576
80.744197759695-0.314538655845-0.2772881559320.5999835534110.2090262918610.1215417057360.0435451242610.05660908679890.1673512259460.04925763346620.1274236096990.0623361928380.00694715296352-0.1146063042080.0076008883033910.57781650961.70191170633-2.663321397434.917396232221.995397547967.256276038587.2702465781726.326768658641.9711456143
90.009217802554710.06761065105420.05571062288760.8602346656730.4032246017690.294346723647-0.09828104240060.0793860327451-0.115658879104-0.5890737201260.004485308235960.1472263743410.6840897129670.105336666579-0.1643091877929.121461913380.9016584388260.8883085448194.59184009357-4.363696697666.541438551432.1276743595221.985347212650.4578359664
103.47850820908-1.605596894082.169329045563.20987701578-1.796296617813.40637488250.0917495087539-0.4548477259881.9144603806-1.10220269506-0.2312984485170.4301881492290.00768811865563-0.04928229784770.288379281523.637024636512.33540083219-1.950949796038.086179744161.29771245628.98280301194-1.6430559750716.443674500436.237330273
119.137470686572.746836610930.1414038294192.003467835077.055043145384.975120968930.938460177771-0.115171068364-0.955801617505-3.9671029643-0.1421336609370.9652280441280.788164648819-3.414600708320.2362429645577.939201578750.7155966443651.332731018253.90721026241.8656268961810.54729878634.45415928138.0945600214145.36766543
123.9073907294-1.724780668540.07497579756585.700901679420.4296156778742.292640854490.2187410287840.110825814949-0.6367019860230.561826469028-0.282404602632.142525655880.182113959616-3.554076373280.05593400238559.690786582321.26824910551-0.9617311008917.58716611824-2.945202756625.060104831378.30621846201-3.5920430509240.8657986662
136.002930457725.659076050245.163213906085.924216753533.509922569417.507682794061.70098606057-4.677693588853.484502749582.11742220482-0.06341990469390.123451219809-0.5784703259830.74880208408-0.2654984593334.795621581510.970408098956-1.023151458946.81193153528-0.6262847022224.278295254119.5201694371-14.084933927134.7602806846
142.04500655728-0.5753018466961.014373748531.49656048345-0.4026168158980.7731142165630.3137277551790.8774559231470.695509165582-0.1178446675710.0472136904760.649077064326-0.5675188104850.06870326674130.6345052874578.595188674331.40743712924-1.428053496974.736727247552.904395706256.502812742517.75907047139-18.947139825515.8917563898
154.613450073622.281853242631.893079227975.678858908272.894981131469.93802108563-0.692790665356-4.69808656362-1.993757335571.606436496613.20673142245-2.233427669922.70082360107-1.508985476021.862242623723.411295873221.29507569942-2.361120899623.985103543381.21592321968.930917698312.5818353605-31.311607854428.3931228829
160.901369451323-1.814107370810.0510309277264.35883813621.218028643532.26428601981-0.447845074990.6161449777141.022967649620.09816948191290.804966209053-3.528503697070.03948562385021.56875655614-0.2836142793642.9071292033-1.06735311391-3.032991110522.68555602757-1.082290158136.6057262024814.6470743191-42.592198205114.7029372199
171.33778358166-1.243692958232.231293669421.59926974412-0.006408583136551.96160516483-1.428896648690.445358862218-0.1676574053990.585960887131-0.1866701727590.325590813467-0.3352369708222.38182146208-5.43433612440.951680071575-0.116215632908-1.595201041190.984992642991-1.854882665043.2861322557711.566086314-45.78388134571.97374103936
180.115040015788-0.2185605092930.5609708429611.25892569113-0.305929418233.182581579440.514457482241-0.726839149379-0.259033784806-0.435183532020.1547129217920.7339501163460.03561652393980.7100069454671.366242121734.735240482962.71957231682.051409522076.351401668093.131163911662.6352619083415.2638199595-55.9486045677-69.5590987497
190.878499394112-0.3828493770311.161562213781.439873343511.608109049915.02217054503-0.907380196134-1.14098743972-0.8333069082831.22267707561.126038280310.1709590950851.70142463601-1.603880596470.1999077451164.894826337732.544173651390.7250592139987.90110340883.234642959813.8055480019632.8159603236-70.3058938451-60.1926387773
205.897466399810.68027062786-0.698982042773.14967477274-0.9110767601545.01546320530.118067643736-1.817817824130.8712901954160.926214390357-0.6156907673871.033573156440.4040011658320.0314195623541-2.806627967137.71296072187-1.06576281482.803100741642.37851272376-2.296908788684.0648808327328.2111148419-73.122710721-56.049494342
216.613027670591.776492297131.225991334563.4087002736-0.1013730690260.6992786128970.9046273329530.0305938756638-2.08892008626-0.4032601702340.103721010363-2.14616069885-0.1604243463181.57933089539-1.159035840725.77053952253-4.23240077241.682482444623.71679045685-2.055464652622.7419388825421.4604119403-58.4074786319-53.9098923128
226.02662809718-4.84821527205-1.29451767167.88043788185-2.59051276718.299753563020.193689744509-0.9265734888151.939760021.535299913592.872978212941.01729723608-0.6267969930570.2322526008050.4910344964045.92590465333-1.292454321870.01854428827811.616263069110.08517979030993.5745685173724.682254336-58.6983082299-42.614804158
231.664833606913.17036546729-2.175385157454.61414770308-1.906979704851.585089081742.83926200139-1.48132175404-1.813612030290.173320676325-2.521280699440.270292399304-0.278884948229-1.03464594837-1.358809127471.05538025499-2.4739700898-0.1988289169183.103784097160.4582305661714.765958299075.71478890804-68.3506808936-6.70607751576
243.975359197551.890852426375.269568656524.458878744782.770216527387.04948763424-0.880111389953-2.327371217220.2731904420720.714106505734-2.342738796041.93296634898-0.877810447448-6.42643040576-7.595189150472.96441321351.305047378641.625071963475.499710828950.3348015573091.25476443826-9.34602780995-86.464382056323.4833875601
251.09952575854-0.5768750700010.1846405215990.292231573685-0.05843974783790.05692528854190.7440831104140.216731253747-1.11157434737-1.480661264080.72875754566-2.42997879835-0.790659522771-0.8157947944361.471041151668.816262283181.83903773258-1.294330580386.31258239345-4.188803416416.3694473037132.758731917220.011564842864.8832020046
260.222438562292-0.2166985522590.04047896180060.293649069007-0.05226736311570.0212288309809-0.648680079191-0.681884775575-0.4464608433790.5605883933090.1412441643550.6450031908260.6398506062690.3749786660390.62022850161510.3242592256-0.77589158982-3.2087052443312.4520604859-0.1816059523039.70716132401-16.758544508831.74928646532.2867175076
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
2626chain 'D'DD1 - 1281 - 87

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