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- PDB-2q5y: Crystal Structure of the C-terminal domain of hNup98 -

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Basic information

Entry
Database: PDB / ID: 2q5y
TitleCrystal Structure of the C-terminal domain of hNup98
Components
  • Nuclear pore complex protein Nup96Nuclear pore
  • Nuclear pore complex protein Nup98Nuclear pore
KeywordsPROTEIN TRANSPORT / Nup98 / nucleoporin / autoproteolysis
Function / homology
Function and homology information


telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus ...telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / 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 / positive regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / 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 / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like ...Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSun, Y. / Guo, H.C.
CitationJournal: Protein Sci. / Year: 2008
Title: Structural constraints on autoprocessing of the human nucleoporin Nup98.
Authors: Sun, Y. / Guo, H.C.
History
DepositionJun 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup98
B: Nuclear pore complex protein Nup96
C: Nuclear pore complex protein Nup98
D: Nuclear pore complex protein Nup96


Theoretical massNumber of molelcules
Total (without water)36,0314
Polymers36,0314
Non-polymers00
Water1,60389
1
A: Nuclear pore complex protein Nup98
B: Nuclear pore complex protein Nup96


Theoretical massNumber of molelcules
Total (without water)18,0152
Polymers18,0152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-4 kcal/mol
Surface area8960 Å2
MethodPISA
2
C: Nuclear pore complex protein Nup98
D: Nuclear pore complex protein Nup96


Theoretical massNumber of molelcules
Total (without water)18,0152
Polymers18,0152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-3 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.301, 90.301, 97.648
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nuclear pore complex protein Nup98 / Nuclear pore / Nucleoporin Nup98 / 98 kDa nucleoporin


Mass: 17204.516 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 729-880
Source method: isolated from a genetically manipulated source
Details: Truncated 712-870 / Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52948
#2: Protein/peptide Nuclear pore complex protein Nup96 / Nuclear pore


Mass: 810.873 Da / Num. of mol.: 2 / Fragment: residues 881-887 / Source method: obtained synthetically / Details: This sequence is naturally present in humans / References: UniProt: P52948
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 0.1M Tris, 0.2M MgAc2, 22% PEG8000, microseeding, pH 8.1, vapor diffusion, hanging drop, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11.1
SYNCHROTRONNSLS X12C20.94793, 0.97788, 0.97834
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 18, 2003
ADSC QUANTUM 2102CCDOct 18, 2003
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2MADx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.947931
30.977881
40.978341
Reflection

D res high: 3.3 Å / D res low: 100 Å / Redundancy: 2.7 %

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
19.3620260.1061.01745398.4
29.5622400.1061.06744998.4
38606390.1231.06744798.3
48606390.1231.06744798.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.1110095.410.0551.0042.6
5.647.1197.510.0910.9882.7
4.935.649810.0851.032.6
4.484.9398.710.0780.9832.7
4.164.4899.310.091.0122.7
3.914.1698.710.1191.0052.7
3.723.9199.310.1250.9972.7
3.553.7298.910.1480.9792.7
3.423.5599.110.1851.0062.7
3.33.429910.2311.0732.7
7.1110095.320.0591.1482.6
5.647.1197.720.0961.1722.7
4.935.6498.120.0841.0842.6
4.484.9398.720.0781.0462.7
4.164.4899.320.0891.0292.7
3.914.1698.720.121.0712.7
3.723.9199.320.1220.9932.7
3.553.7298.920.1460.9982.7
3.423.5599.120.181.0382.7
3.33.4299.220.2251.0672.7
7.111009530.0611.0162.6
5.647.1197.530.1081.1042.7
4.935.649830.0971.0342.6
4.484.9398.730.0911.0232.7
4.164.4899.330.1071.062.7
3.914.1698.730.1441.072.7
3.723.9199.330.1481.0372.7
3.553.7298.930.1821.0872.7
3.423.5599.130.2151.0712.7
3.33.4298.530.2681.0772.7
7.111009540.0611.0162.6
5.647.1197.540.1081.1042.7
4.935.649840.0971.0342.6
4.484.9398.740.0911.0232.7
4.164.4899.340.1071.062.7
3.914.1698.740.1441.072.7
3.723.9199.340.1481.0372.7
3.553.7298.940.1821.0872.7
3.423.5599.140.2151.0712.7
3.33.4298.540.2681.0772.7
ReflectionResolution: 2.3→100 Å / Num. obs: 20739 / % possible obs: 98.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.058 / Χ2: 0.989 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.382.70.29920520.99597.6
2.38-2.482.70.25220191.00198.6
2.48-2.592.70.21820670.96698.8
2.59-2.732.70.18320460.9797.5
2.73-2.92.70.12320700.9599.5
2.9-3.122.70.08120820.98599.3
3.12-3.442.70.05120891.00299.1
3.44-3.932.60.03720500.99496.1
3.93-4.962.70.02821080.99598.9
4.96-1002.60.02921561.03795.6

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Phasing

Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 6975
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.93-10047.40.827509
6.3-7.9357.70.891508
5.51-6.363.30.895511
5-5.5160.90.905506
4.64-5660.867515
4.37-4.6466.70.889508
4.14-4.3771.10.876513
3.96-4.1474.60.883515
3.8-3.9675.30.898511
3.67-3.881.90.904506
3.56-3.6775.50.91503
3.45-3.5679.70.915512
3.3-3.4576.80.876858

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
DM4.1phasing
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→6 Å / FOM work R set: 0.816 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 1914 9.8 %
Rwork0.228 --
obs-19412 98.9 %
Solvent computationBsol: 85.148 Å2
Displacement parametersBiso mean: 33.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.546 Å2-3.576 Å20 Å2
2--0.546 Å20 Å2
3----1.091 Å2
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 0 89 2528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 38

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.320.292490.265450499
2.32-2.340.307410.255455496
2.34-2.360.305450.275470515
2.36-2.380.296490.264458507
2.38-2.40.263570.245423480
2.4-2.430.31540.248470524
2.43-2.450.313510.252452503
2.45-2.480.282590.271446505
2.48-2.50.352620.307462524
2.5-2.530.336500.276446496
2.53-2.560.233490.232463512
2.56-2.590.361540.265441495
2.59-2.620.299440.29466510
2.62-2.650.398590.283453512
2.65-2.690.237480.271436484
2.69-2.720.317400.272483523
2.72-2.760.306520.259450502
2.76-2.80.333430.269482525
2.8-2.850.293450.242462507
2.85-2.890.34450.268474519
2.89-2.940.243470.266458505
2.94-2.990.265640.249447511
2.99-3.050.34460.25463509
3.05-3.110.217570.204468525
3.11-3.180.264460.216464510
3.18-3.250.225400.215486526
3.25-3.330.269420.222474516
3.33-3.420.278470.233465512
3.42-3.520.24520.229437489
3.52-3.630.246610.236459520
3.63-3.750.201470.208461508
3.75-3.90.299470.207463510
3.9-4.070.259510.218451502
4.07-4.280.214590.189472531
4.28-4.530.231590.182457516
4.53-4.860.165480.159481529
4.86-5.310.205420.202484526
5.31-60.253630.217466529
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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