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- PDB-4jnu: Crystal structure of the human Nup57CCS3* coiled-coil segment, sp... -

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Basic information

Entry
Database: PDB / ID: 4jnu
TitleCrystal structure of the human Nup57CCS3* coiled-coil segment, space group P21
ComponentsNucleoporin p54
KeywordsTRANSPORT PROTEIN / nucleocytoplasmic transport
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways ...protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / 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 / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / nuclear envelope / snRNP Assembly / nuclear membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.445 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 15, 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

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin p54
B: Nucleoporin p54
C: Nucleoporin p54
D: Nucleoporin p54


Theoretical massNumber of molelcules
Total (without water)18,9184
Polymers18,9184
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-77 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.909, 45.126, 46.384
Angle α, β, γ (deg.)90.000, 113.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 4729.410 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M sodium acetate, pH 5.3, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.445→20 Å / Num. obs: 26320 / Observed criterion σ(F): 0 / Biso Wilson estimate: 17.63 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.445→19.946 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.8461 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 1990 7.57 %
Rwork0.1831 --
obs0.1856 26274 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.18 Å2 / Biso mean: 27.8702 Å2 / Biso min: 8.65 Å2
Refinement stepCycle: LAST / Resolution: 1.445→19.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 0 131 1459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071486
X-RAY DIFFRACTIONf_angle_d1.0042010
X-RAY DIFFRACTIONf_chiral_restr0.054234
X-RAY DIFFRACTIONf_plane_restr0.004257
X-RAY DIFFRACTIONf_dihedral_angle_d15.831594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.445-1.48070.27841120.26461336144874
1.4807-1.52070.26611270.22031522164986
1.5207-1.56550.26121360.20711655179194
1.5655-1.6160.22371470.20311773192099
1.616-1.67370.23481400.192518141954100
1.6737-1.74070.22221500.196517711921100
1.7407-1.81990.21371480.194917841932100
1.8199-1.91570.23711450.190817801925100
1.9157-2.03570.20351450.174917831928100
2.0357-2.19260.18791480.160718081956100
2.1926-2.4130.19531440.156218071951100
2.413-2.76130.22581490.174317871936100
2.7613-3.4760.22181470.193118071954100
3.476-19.94740.21711520.182518572009100

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