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- PDB-1xks: The crystal structure of the N-terminal domain of Nup133 reveals ... -

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Basic information

Entry
Database: PDB / ID: 1xks
TitleThe crystal structure of the N-terminal domain of Nup133 reveals a beta-propeller fold common to several nucleoporins
ComponentsNuclear pore complex protein Nup133
KeywordsPROTEIN TRANSPORT / beta-propeller / helical insertions
Function / homology
Function and homology information


nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / somite development / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) ...nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / somite development / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / neural tube development / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / neurogenesis / SUMOylation of chromatin organization proteins / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / kinetochore / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / membrane / cytosol
Similarity search - Function
Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Nuclear pore complex protein Nup133
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsBerke, I.C. / Boehmer, T. / Blobel, G. / Schwartz, T.U.
CitationJournal: J.Cell Biol. / Year: 2004
Title: Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex.
Authors: Berke, I.C. / Boehmer, T. / Blobel, G. / Schwartz, T.U.
History
DepositionSep 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup133


Theoretical massNumber of molelcules
Total (without water)48,7981
Polymers48,7981
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.588, 84.588, 139.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Nuclear pore complex protein Nup133 / / Nucleoporin Nup133 / 133 kDa nucleoporin


Mass: 48798.430 Da / Num. of mol.: 1 / Mutation: F345L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP133 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: Q8WUM0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / pH: 5.7
Details: PEG 3350, lithium sulfate, bis-tris, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K, pH 5.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 28, 2004
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.35→40.5 Å / Num. obs: 20899 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 71.03 Å2
Reflection shellResolution: 2.35→2.39 Å / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD
Starting model: Model built by SAD data from SeMet derivative

Resolution: 2.35→40.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2036 9.8 %RANDOM
Rwork0.196 ---
obs0.2 20899 96.5 %-
all-20899 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.79 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 0 95 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222895
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9523934
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66925.086116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46515468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.311159
X-RAY DIFFRACTIONr_chiral_restr0.1580.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022147
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.31164
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.51958
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.5266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.329
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.71621847
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.68632966
X-RAY DIFFRACTIONr_scbond_it2.98321048
X-RAY DIFFRACTIONr_scangle_it4.5393968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 135 -
Rwork0.342 1283 -
obs--100 %
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)
13.12792.9346-1.53332.7533-1.43850.7516-0.4510.1030.3670.0620.30650.54680.50510.12420.14450.017-0.0393-0.087-0.0882-0.01720.0111-25.98623.09855.174
23.44642.40022.25182.28631.10071.8267-0.0762-0.23840.42520.0763-0.1860.41040.2269-0.1060.26220.08730.01650.0478-0.0311-0.106-0.1134-22.71116.76470.729
31.108-0.38950.28661.8001-0.3931.1978-0.0183-0.1821-0.21150.0230.13720.1463-0.0870.0005-0.11890.11950.10330.00990.01480.0033-0.2198-9.88214.3774.858
40.5347-0.8219-0.25682.0996-0.66231.4592-0.2474-0.07990.09450.24170.25350.0763-0.00630.2324-0.00610.12970.1981-0.03160.0386-0.0051-0.21232.34619.12171.134
50.26480.04560.47442.2138-1.4051.85180.04710.05060.2496-0.1584-0.18920.07930.21490.32450.14210.050.1610.02690.07170.0485-0.19833.97122.89659.136
61.1922-1.86520.47053.149-1.08550.71430.16730.09290.2138-0.1303-0.3976-0.09140.10960.11750.23030.06730.06880.0127-0.04060.0472-0.0847-3.86139.5749.402
72.11512.5287-0.7593.0233-0.90750.2724-0.31350.17790.0549-0.12630.2350.4150.03070.30970.07840.09710.0327-0.0524-0.0275-0.0634-0.1278-16.42929.149.717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA75 - 8711 - 23
2X-RAY DIFFRACTION1AA450 - 477386 - 413
3X-RAY DIFFRACTION2AA88 - 14624 - 82
4X-RAY DIFFRACTION3AA149 - 20185 - 137
5X-RAY DIFFRACTION4AA206 - 251142 - 187
6X-RAY DIFFRACTION5AA270 - 310206 - 246
7X-RAY DIFFRACTION6AA312 - 397248 - 333
8X-RAY DIFFRACTION7AA404 - 443340 - 379

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