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- PDB-2rfo: Crystral Structure of the nucleoporin Nic96 -

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Basic information

Entry
Database: PDB / ID: 2rfo
TitleCrystral Structure of the nucleoporin Nic96
ComponentsNucleoporin NIC96
KeywordsSTRUCTURAL PROTEIN / Alpha-alpha-superhelix / mRNA transport / Nuclear pore complex / Nucleus / Protein transport / Translocation / Transport
Function / homology
Function and homology information


nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport ...nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / ribosomal large subunit export from nucleus / nuclear pore / protein import into nucleus / nuclear envelope / nuclear membrane
Similarity search - Function
Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsSchrader, N. / Stelter, P. / Flemming, D. / Kunze, K. / Hurt, E. / Vetter, I.R.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural basis of the nic96 subcomplex organization in the nuclear pore channel.
Authors: Schrader, N. / Stelter, P. / Flemming, D. / Kunze, R. / Hurt, E. / Vetter, I.R.
History
DepositionOct 1, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NIC96
B: Nucleoporin NIC96


Theoretical massNumber of molelcules
Total (without water)149,6392
Polymers149,6392
Non-polymers00
Water1,58588
1
A: Nucleoporin NIC96


Theoretical massNumber of molelcules
Total (without water)74,8191
Polymers74,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NIC96


Theoretical massNumber of molelcules
Total (without water)74,8191
Polymers74,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 100.000, 104.000
Angle α, β, γ (deg.)62.00, 82.00, 86.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nucleoporin NIC96 / Nuclear pore protein NIC96 / 96 kDa nucleoporin-interacting component


Mass: 74819.250 Da / Num. of mol.: 2 / Fragment: UNP residues 189-839
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NIC96 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL CodonPlus / References: UniProt: P34077
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3-10% PEG3350, 0.1M BisTris pH6.5, 0.05M lithium sulfate, 3% 1,6-hexandiole, 0.01mM DTE, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2006 / Details: mirrors
RadiationMonochromator: Sagitally - horizontally focused Si(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 64618 / % possible obs: 97.3 % / Observed criterion σ(F): -10 / Observed criterion σ(I): -10 / Redundancy: 4.4 % / Net I/σ(I): 25.64
Reflection shellResolution: 2.6→2.67 Å / Mean I/σ(I) obs: 3.89 / Num. unique all: 4694 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.78 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 26.07 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.405 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3313 5.1 %RANDOM
Rwork0.227 ---
obs0.23 62199 97.75 %-
all-62199 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å21.7 Å2-1.09 Å2
2--4.7 Å20.36 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9896 0 0 88 9984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9713615
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.87451215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.57324.722485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.894151879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.791560
X-RAY DIFFRACTIONr_chiral_restr0.1260.21555
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027472
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.25283
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26993
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5711.56233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00829854
X-RAY DIFFRACTIONr_scbond_it1.22734306
X-RAY DIFFRACTIONr_scangle_it1.9474.53761
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 245 -
Rwork0.363 4470 -
obs--96.96 %
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)
11.98710.75273.37581.29533.12349.1036-0.13570.3650.3477-0.4071-0.21210.0614-0.5597-0.09330.3478-0.04720.092-0.0139-0.0052-0.01240.03848.1653115.36523.9051
22.37010.76582.76821.22162.26216.37760.18030.0489-0.20640.115-0.06170.0550.3834-0.31-0.1186-0.0740.00030.0471-0.1018-0.016-0.019947.9614103.251722.6439
34.5332-0.39781.98575.61445.09637.570.00760.42680.4640.09870.5221-0.5427-0.06820.9391-0.5297-0.025-0.02350.06230.1626-0.33030.069471.5969130.567982.3346
49.64051.99643.55755.13511.91196.02910.13731.17140.52760.5784-0.2519-0.9657-0.39861.10060.11460.35990.0062-0.01410.42620.01190.348687.5735141.566495.9665
53.87991.03270.40531.3448-2.86418.29750.0723-0.38770.56670.3541-0.2222-0.2032-0.77060.42840.1499-0.1596-0.0863-0.0016-0.1645-0.0010.001726.6485115.381853.4949
62.8735-0.52432.7182.5581-1.64916.52030.0348-0.3575-0.1570.248-0.004-0.6260.33550.8915-0.0308-0.0310.01660.01520.11980.08690.131433.711596.495476.5711
75.2-0.06080.30513.754-2.452412.0429-0.07290.82950.0335-0.43010.1296-0.08550.6001-0.1179-0.0568-0.1989-0.08650.03-0.09170.0718-0.140321.7553111.395936.0361
83.1165-1.60073.5524.5005-4.06197.9274-0.1262-0.63870.0180.11950.33710.4581-0.0575-0.8305-0.21090.06670.0420.09860.17590.18230.03458.358131.43511.5963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA204 - 29516 - 107
2X-RAY DIFFRACTION2AA296 - 637108 - 449
3X-RAY DIFFRACTION3AA638 - 739450 - 551
4X-RAY DIFFRACTION4AA740 - 835552 - 647
5X-RAY DIFFRACTION5BB206 - 26118 - 73
6X-RAY DIFFRACTION6BB262 - 50274 - 314
7X-RAY DIFFRACTION7BB503 - 611315 - 423
8X-RAY DIFFRACTION8BB612 - 833424 - 645

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