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- PDB-4jo7: Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex wi... -

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Basic information

Entry
Database: PDB / ID: 4jo7
TitleCrystal structure of the human Nup49CCS2+3* Nup57CCS3* complex with 2:2 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 / 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 ...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 / 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 / nuclear localization sequence binding / 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 / 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 / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin p58/p45 / 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 / Helix Hairpins ...Helix Hairpins - #1350 / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin p58/p45 / 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 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin p54 / Nucleoporin p58/p45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.752 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 17, 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 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleoporin p54
E: Nucleoporin p58/p45
H: Nucleoporin p54
D: Nucleoporin p54
G: Nucleoporin p58/p45
A: Nucleoporin p58/p45
C: Nucleoporin p58/p45
F: Nucleoporin p54


Theoretical massNumber of molelcules
Total (without water)61,0078
Polymers61,0078
Non-polymers00
Water8,179454
1
B: Nucleoporin p54
D: Nucleoporin p54
A: Nucleoporin p58/p45
C: Nucleoporin p58/p45


Theoretical massNumber of molelcules
Total (without water)30,5044
Polymers30,5044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-98 kcal/mol
Surface area13470 Å2
MethodPISA
2
E: Nucleoporin p58/p45
H: Nucleoporin p54
G: Nucleoporin p58/p45
F: Nucleoporin p54


Theoretical massNumber of molelcules
Total (without water)30,5044
Polymers30,5044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-98 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.689, 47.658, 71.324
Angle α, β, γ (deg.)88.870, 83.370, 81.420
Int Tables number1
Space group name H-MP1

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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: Protein
Nucleoporin p58/p45 / Nup58 / Nucleoporin-like protein 1


Mass: 10522.431 Da / Num. of mol.: 4 / Fragment: UNP residues 341-428
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.: 454 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 6.7% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9805 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 117121 / Biso Wilson estimate: 16.74 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: SAD / Resolution: 1.752→47.125 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.85 / SU ML: 0.18 / σ(F): 1.96 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2144 1911 3.36 %
Rwork0.1863 --
obs0.1873 116939 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.59 Å2 / Biso mean: 24.4628 Å2 / Biso min: 4.37 Å2
Refinement stepCycle: LAST / Resolution: 1.752→47.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 0 454 4556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084206
X-RAY DIFFRACTIONf_angle_d0.8045666
X-RAY DIFFRACTIONf_chiral_restr0.05633
X-RAY DIFFRACTIONf_plane_restr0.004729
X-RAY DIFFRACTIONf_dihedral_angle_d15.9471617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.752-1.77370.33121250.29553350347577
1.7737-1.79620.31651240.27223806393090
1.7962-1.81980.2871260.25864025415192
1.8198-1.84480.26661470.25283918406592
1.8448-1.87110.26671390.24373928406794
1.8711-1.8990.25571470.24194074422193
1.899-1.92870.28691580.24163925408393
1.9287-1.96030.2443980.23954063416194
1.9603-1.99410.28211410.23314107424894
1.9941-2.03040.28391380.22173873401194
2.0304-2.06950.25271340.20274220435495
2.0695-2.11170.21411460.18683943408995
2.1117-2.15760.20011590.18014151431095
2.1576-2.20780.22161130.17344028414195
2.2078-2.2630.17811620.16764090425295
2.263-2.32420.21541190.16274045416496
2.3242-2.39260.20911560.16914133428995
2.3926-2.46980.20391460.16464004415095
2.4698-2.55810.20841400.16584085422596
2.5581-2.66050.20751410.17234169431096
2.6605-2.78160.22381570.16854099425697
2.7816-2.92820.20141440.1754110425496
2.9282-3.11160.16451330.16614171430497
3.1116-3.35180.18471590.17144080423996
3.3518-3.6890.17931420.16344158430096
3.689-4.22250.17471400.15984144428498
4.2225-5.31880.18531490.16924198434797
5.3188-47.1420.28091420.22654117425997

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