- PDB-6x02: Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6x02
Title
Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8
Components
Nucleoporin NUP133
Nucleoporin NUP84
VHH-SAN8
Keywords
STRUCTURAL 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
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
NucleoporinNUP133 / 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
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal grow
Temperature: 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
ID
Mean temperature (K)
Crystal-ID
Serial crystal experiment
1
100
1
N
2
100
1
N
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
APS
24-ID-C
1
0.9791
SYNCHROTRON
APS
24-ID-C
2
1.2141
Detector
Type
ID
Detector
Date
PSI PILATUS 6M
1
PIXEL
Aug 8, 2019
PSI PILATUS 6M
2
PIXEL
Oct 15, 2019
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.9791
1
2
1.2141
1
Reflection
Entry-ID: 6X02
Resolution (Å)
Num. obs
% possible obs (%)
Redundancy (%)
Biso Wilson estimate (Å2)
CC1/2
Rpim(I) all
Diffraction-ID
Net I/σ(I)
6.4-103.4
13539
99.8
24.1
614.5
1
0.022
1
55.3
7.8-147.8
7533
99.9
12.3
1
0.042
2
13.8
Reflection shell
Resolution (Å)
Mean I/σ(I) obs
Num. unique obs
CC1/2
Rpim(I) all
Diffraction-ID
6.38-6.63
1
1322
0.582
0.813
1
7.8-8.7
2.1
2067
0.891
0.305
2
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Processing
Software
Name
Version
Classification
PHENIX
1.18_3845
refinement
PHENIX
phasing
HKL-2000
datareduction
HKL-2000
datascaling
SHELXCD
phasing
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Rfree
0.3242
1350
10.03 %
Rwork
0.3138
12103
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obs
0.3149
13453
98.54 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL