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- PDB-4jq5: Crystal structure of the human Nup49CCS2+3* coiled-coil segment -

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Basic information

Entry
Database: PDB / ID: 4jq5
TitleCrystal structure of the human Nup49CCS2+3* coiled-coil segment
ComponentsNucleoporin p58/p45
KeywordsTRANSPORT PROTEIN / Nucleocytoplasmic transport
Function / homology
Function and homology information


regulation of protein import into nucleus / 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 ...regulation of protein import into nucleus / 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 / structural constituent of nuclear pore / nuclear localization sequence binding / 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 / mRNA transport / Regulation of HSF1-mediated heat shock response / 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 / protein transport / 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 / Nucleoporin p58/p45 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 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 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 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 p58/p45
B: Nucleoporin p58/p45
C: Nucleoporin p58/p45
D: Nucleoporin p58/p45
E: Nucleoporin p58/p45
F: Nucleoporin p58/p45
G: Nucleoporin p58/p45
H: Nucleoporin p58/p45
I: Nucleoporin p58/p45
J: Nucleoporin p58/p45
K: Nucleoporin p58/p45
L: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)121,66212
Polymers121,66212
Non-polymers00
Water00
1
A: Nucleoporin p58/p45
B: Nucleoporin p58/p45
C: Nucleoporin p58/p45
D: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)40,5544
Polymers40,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Nucleoporin p58/p45
F: Nucleoporin p58/p45
G: Nucleoporin p58/p45
H: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)40,5544
Polymers40,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Nucleoporin p58/p45
J: Nucleoporin p58/p45
K: Nucleoporin p58/p45
L: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)40,5544
Polymers40,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.820, 77.097, 77.197
Angle α, β, γ (deg.)120.040, 90.120, 89.960
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoporin p58/p45 / Nucleoporin-like protein 1


Mass: 10138.528 Da / Num. of mol.: 12 / Fragment: UNP residues 341-425
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

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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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% glycerol, 28% dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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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: 2.195→20 Å / Num. all: 64956 / Num. obs: 63140 / Biso Wilson estimate: 43.67 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: MOLECULAR REPLACEMENT / Resolution: 2.195→19.83 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6347 / SU ML: 0.42 / σ(F): 1.96 / Phase error: 41.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2929 1990 3.16 %
Rwork0.2849 --
obs0.2852 63070 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.8 Å2 / Biso mean: 58.073 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 2.195→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 0 0 8526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028682
X-RAY DIFFRACTIONf_angle_d0.52311720
X-RAY DIFFRACTIONf_chiral_restr0.0341291
X-RAY DIFFRACTIONf_plane_restr0.0021531
X-RAY DIFFRACTIONf_dihedral_angle_d15.8893278
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 (%)
2.195-2.24950.34411360.40083704384083
2.2495-2.31020.43221170.37514217433494
2.3102-2.37810.55361500.38524420457097
2.3781-2.45470.40081420.34694415455798
2.4547-2.54230.40391200.37184381450198
2.5423-2.64380.47191400.34974507464798
2.6438-2.76390.40981420.32964380452298
2.7639-2.90920.38331430.30594392453599
2.9092-3.09080.32661380.30864476461498
3.0908-3.32840.31651540.30244451460599
3.3284-3.66150.39291250.29014386451199
3.6615-4.18690.21971620.26574483464599
4.1869-5.25880.21461540.24134453460799
5.2588-19.83070.23051670.23444415458298

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