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- PDB-4jo9: Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex 1:... -

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Basic information

Entry
Database: PDB / ID: 4jo9
TitleCrystal structure of the human Nup49CCS2+3* Nup57CCS3* complex 1:2 stoichiometry
Components
  • Nucleoporin p54
  • Nucleoporin p58/p45
KeywordsTRANSPORT PROTEIN / nucleocytoplasmic transport
Function / homology
Function and homology information


regulation of protein import into nucleus / protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / 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 ...regulation of protein import into nucleus / protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / 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 / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / protein targeting / SUMOylation of DNA damage response and repair proteins / nuclear pore / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein transport / nuclear envelope / snRNP Assembly / nuclear membrane / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / identical protein binding
Similarity search - Function
Helix Hairpins - #1350 / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Nucleoporin p54 / Nucleoporin p58/p45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsStuwe, T. / Bley, C.J. / Mayo, D.J. / Hoelz, A.
CitationJournal: Science / Year: 2015
Title: Architecture of the fungal nuclear pore inner ring complex.
Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / ...Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / Kossiakoff, A.A. / Hoelz, A.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Structure summary
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoporin p54
B: Nucleoporin p58/p45
C: Nucleoporin p54


Theoretical massNumber of molelcules
Total (without water)19,6543
Polymers19,6543
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-37 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.483, 55.483, 191.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein/peptide Nucleoporin p54 / Nup54 / 54 kDa nucleoporin


Mass: 4729.410 Da / Num. of mol.: 2 / Fragment: UNP residues 453-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP54 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3B4
#2: Protein Nucleoporin p58/p45 / Nup58 / Nucleoporin-like protein 1


Mass: 10195.580 Da / Num. of mol.: 1 / Fragment: UNP residues 341-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUPL1, KIAA0410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BVL2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 3.8
Details: 0.1 M sodium citrate, pH 3.8, 0.07 M calcium chloride, VAPOR DIFFUSION, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 7, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. all: 11003 / Num. obs: 11003 / % possible obs: 98.8 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Biso Wilson estimate: 46.29 Å2
Reflection shellHighest resolution: 2.499 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.499→47.79 Å / Occupancy max: 1 / Occupancy min: 0.51 / FOM work R set: 0.678 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 35.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 1092 10.03 %
Rwork0.2465 --
obs0.2513 10891 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.2 Å2 / Biso mean: 86.2208 Å2 / Biso min: 39.04 Å2
Refinement stepCycle: LAST / Resolution: 2.499→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 17 1355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021356
X-RAY DIFFRACTIONf_angle_d0.4371822
X-RAY DIFFRACTIONf_chiral_restr0.028206
X-RAY DIFFRACTIONf_plane_restr0.001234
X-RAY DIFFRACTIONf_dihedral_angle_d14.845524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.499-2.61280.46631210.34811088120990
2.6128-2.75050.39121330.30921186131999
2.7505-2.92280.35321360.28751205134199
2.9228-3.14840.33981340.27151203133799
3.1484-3.46520.30061360.267212301366100
3.4652-3.96640.26531390.222812501389100
3.9664-4.99640.21051400.195912621402100
4.9964-47.79870.30831530.25313751528100

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