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- PDB-4q9t: Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propel... -

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Basic information

Entry
Database: PDB / ID: 4q9t
TitleCrystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain
ComponentsNucleoporin NUP133
KeywordsPROTEIN TRANSPORT / Nuclear Pore Complex / Nucleoporin / Nup84 complex / ALPS motif / Structural genomics / PSI-Biology / Nucleocytoplasmic Transport: a Target for Cellular Control / NPCXstals / New York SGX Research Center for Structural Genomics / NYSGXRC / Nup133 / Beta-propeller domain / and New York Structural Genomics Research Center / NYSGRC / Protein Structure Initiative / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


nuclear pore localization => GO:0051664 / mRNA export from nucleus in response to heat stress / 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 / subtelomeric heterochromatin formation ...nuclear pore localization => GO:0051664 / mRNA export from nucleus in response to heat stress / 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 / subtelomeric heterochromatin formation / protein import into nucleus / double-strand break repair / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesVanderwaltozyma polyspora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsSampathkumar, P. / Bonanno, J.B. / Almo, S.C. / Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals) / New York SGX Research Center for Structural Genomics (NYSGXRC) / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain
Authors: Sampathkumar, P. / Bonanno, J.B. / Rout, M.P. / Almo, S.C.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NUP133
B: Nucleoporin NUP133


Theoretical massNumber of molelcules
Total (without water)103,7222
Polymers103,7222
Non-polymers00
Water00
1
A: Nucleoporin NUP133


Theoretical massNumber of molelcules
Total (without water)51,8611
Polymers51,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NUP133


Theoretical massNumber of molelcules
Total (without water)51,8611
Polymers51,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.172, 133.843, 136.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A63 - 497
2010B63 - 497

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Components

#1: Protein Nucleoporin NUP133 / Uncharacterized protein


Mass: 51860.855 Da / Num. of mol.: 2 / Fragment: Beta-propeller domain residues 55-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora (fungus) / Strain: DSM 70294 / Gene: Kpol_1018p77, Nup133 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus-RIL / References: UniProt: A7TDS5

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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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: Protein (10 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT), Reservoir (100mM Hepes pH 8.2, 10% PEG 3350, 100mM Ammonium Sulfate), Cryoprotection (30% Glycerol), VAPOR DIFFUSION, ...Details: Protein (10 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT), Reservoir (100mM Hepes pH 8.2, 10% PEG 3350, 100mM Ammonium Sulfate), Cryoprotection (30% Glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 21, 2008 / Details: MIRRORS
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 20381 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 88.3 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.18 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.02542 / Mean I/σ(I) obs: 1.2 / Num. unique all: 3224 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 59.442 / SU ML: 0.439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1042 5.1 %RANDOM
Rwork0.2149 ---
obs0.2175 20310 99.42 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 191.8 Å2 / Biso mean: 101.079 Å2 / Biso min: 62.93 Å2
Baniso -1Baniso -2Baniso -3
1--5.48 Å2-0 Å20 Å2
2--2.52 Å2-0 Å2
3---2.96 Å2
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6097 0 0 0 6097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196213
X-RAY DIFFRACTIONr_bond_other_d0.0030.026062
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9728412
X-RAY DIFFRACTIONr_angle_other_deg0.898314001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6115756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79325.118254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.698151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121516
X-RAY DIFFRACTIONr_chiral_restr0.0740.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026800
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021352
X-RAY DIFFRACTIONr_mcbond_it1.756.923054
X-RAY DIFFRACTIONr_mcbond_other1.756.923053
X-RAY DIFFRACTIONr_mcangle_it3.01710.3823800
Refine LS restraints NCS

Ens-ID: 1 / Number: 22068 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 77 -
Rwork0.417 1344 -
all-1421 -
obs-1344 95.31 %
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)
12.25851.556-0.98853.5068-1.45682.6179-0.10260.17860.2903-0.1623-0.1999-0.3124-0.29060.19080.30250.1854-0.0512-0.09410.09080.09940.249430.541166.495433.6594
24.77180.9516-0.52632.4159-0.2782.9620.0503-0.7853-0.48110.30640.03020.1676-0.1304-0.1697-0.08050.06490.0203-0.00640.16630.11980.16021.612539.351767.41
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 497
2X-RAY DIFFRACTION2B61 - 497

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