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- PDB-6x06: Nup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11 -

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Basic information

Entry
Database: PDB / ID: 6x06
TitleNup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11
Components
  • Nucleoporin NUP120
  • VHH-SAN11
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / nanobody
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / 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 / SUMOylation of RNA binding proteins / structural constituent of nuclear pore ...mRNA export from nucleus in response to heat stress / nuclear pore localization / 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 / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / mRNA export from nucleus / nuclear pore / protein export from nucleus / protein import into nucleus / nuclear envelope / double-strand break repair / 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
Similarity search - Function
: / Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup120/160
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.27 Å
AuthorsKnockenhauer, K.E. / Nordeen, 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: A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure.
Authors: Nordeen, S.A. / Andersen, K.R. / Knockenhauer, K.E. / Ingram, J.R. / Ploegh, H.L. / Schwartz, T.U.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoporin NUP120
K: VHH-SAN11


Theoretical massNumber of molelcules
Total (without water)101,1212
Polymers101,1212
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)193.170, 193.170, 78.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 87432.547 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: NUP120, RAT2, YKL057C, YKL313, YKL314 / Production host: Escherichia coli (E. coli) / References: UniProt: P35729
#2: Antibody VHH-SAN11


Mass: 13688.305 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)
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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 19% PEG 8,000, 0.1M magnesium chloride, 0.1M Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.25→83.65 Å / Num. obs: 11664 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 196.87 Å2 / CC1/2: 0.938 / Rpim(I) all: 0.052 / Net I/σ(I): 18.7
Reflection shellResolution: 4.25→4.4 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 1141 / CC1/2: 0.524 / Rpim(I) all: 0.512

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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: 3HXR

3hxr


Resolution: 4.27→83.65 Å / SU ML: 0.8303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 48.547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3593 1154 9.91 %
Rwork0.3339 10487 -
obs0.3364 11641 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 240.98 Å2
Refinement stepCycle: LAST / Resolution: 4.27→83.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5650 0 0 0 5650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245763
X-RAY DIFFRACTIONf_angle_d0.60537850
X-RAY DIFFRACTIONf_chiral_restr0.0406924
X-RAY DIFFRACTIONf_plane_restr0.0041001
X-RAY DIFFRACTIONf_dihedral_angle_d14.84041964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.27-4.460.41731340.40421206X-RAY DIFFRACTION90.91
4.46-4.70.39621470.36631311X-RAY DIFFRACTION99.73
4.7-4.990.42851380.37781321X-RAY DIFFRACTION99.45
4.99-5.370.45951440.35861312X-RAY DIFFRACTION100
5.38-5.910.38991440.39231332X-RAY DIFFRACTION100
5.92-6.770.44541490.42641303X-RAY DIFFRACTION98.98
6.77-8.520.36321480.36241339X-RAY DIFFRACTION99.87
8.53-83.650.29681500.27121363X-RAY DIFFRACTION98.31
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)
14.538416538623.13785471519-0.5377508952851.347747648041.470546436858.00331310991-0.655553086494-0.1832198023920.505029496914-0.3193333346360.1553641585530.4365119580850.30428311028-1.373316211150.2354260726060.442722478879-0.1019259969850.0002612536898841.86193269063-0.1852282995181.074021722961.4225833968475.39632153862.29285336047
23.321759373111.667315852242.748207471370.864963959294-0.5600843842491.1117663341-0.351649039608-0.6052763269481.356292031910.6460648597520.255528379907-0.1075714828670.1023885321280.8193295488930.4099072237521.220254340740.1798592563480.07165547268932.21121807198-0.02582364155511.855562352835.592628339579.076816934-7.88586547317
33.42893979312-0.4241400245120.6908325823023.045352479473.684554493575.10045009077-0.359004938016-0.5081979881150.910355281516-1.420154661740.7856974606550.5969166112874.210142079890.228235845049-0.2671899453382.87395742304-0.7639607474820.09679050827031.891826774240.566571333372.1952742592325.76061397355.6661549119-56.7473845804
46.702218128021.898962565243.031186332752.131164606252.992773198224.11539272169-2.10091606049-1.883830558592.198077802660.835534973412.107483585311.30656534467-2.712996174250.8841434137990.1386668528441.87639047031-0.25545991579-0.8620565762611.988511038070.812486119432.7455048446123.307712875665.5535703074-49.7394353303
55.555574040542.22626470066-0.7372021412163.603327740652.342862459294.8863750295-0.637935819962-1.346829269131.10821567956-2.361045248041.47277534053-0.322634315068-0.2293424666710.4128400063970.9838858251160.6041558673890.3705425006040.05200601036371.118380619080.5697880142922.6310005102619.9903553762.1254054152-43.45224015
62.16775182436-2.23418411431-2.33168443032.330747039192.41148279112.44732310928-0.0159273562567-1.83265138453-0.7765212409070.06378719210440.466091051064-0.4755407689150.8698142730831.32346328063-0.2294430494371.29375702692-0.503999650897-0.7122872264533.29181211751.311187624064.2878791504613.075688044455.2079899842-44.8617022097
70.929968677427-0.813056865247-0.5166623941373.64368313985-0.4246692416841.06098676861-1.7454284959-0.6635865031511.50347101065-2.716717770631.60403027018-1.42318284628-0.828265294580.05558551329290.2547921529361.07359237513-0.435529047736-0.233343195141.94762211946-0.08581160894191.7095527445220.987465096959.3665113438-49.1483099952
82.077222545283.9462216458-2.682988526869.60086080654-5.220732287815.65949817955-0.8726884445491.424520111111.08285802742-3.537944230590.5892965323571.188906425271.06594952056-1.62125878222-0.329795643974.280606443850.0221059124121-0.6317857434810.0872898523465-0.07987914354033.0350481509724.654432729666.4948804256-55.6785787219
95.06019529661.201980205771.007627373371.43140659717-0.1775828262911.201184801261.61587400894-0.929620943584-1.412326903610.672623509254-0.372118924854-1.002067607170.6268892215150.2643597274351.636171337282.5533782306-1.133661235510.2382621583011.69331127099-0.9614354968890.97870611675812.613672869551.2335165763-65.3148823685
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 392 )AA1 - 3921 - 311
22chain 'A' and (resid 393 through 714 )AA393 - 714312 - 615
33chain 'K' and (resid 1 through 24 )KB1 - 241 - 24
44chain 'K' and (resid 25 through 44 )KB25 - 4425 - 44
55chain 'K' and (resid 45 through 57 )KB45 - 5745 - 54
66chain 'K' and (resid 58 through 67 )KB58 - 6755 - 64
77chain 'K' and (resid 68 through 110 )KB68 - 11065 - 107
88chain 'K' and (resid 111 through 120 )KB111 - 120108 - 117
99chain 'K' and (resid 121 through 126 )KB121 - 124118 - 121

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