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- PDB-5c3l: Structure of the metazoan Nup62.Nup58.Nup54 nucleoporin complex. -

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Basic information

Entry
Database: PDB / ID: 5c3l
TitleStructure of the metazoan Nup62.Nup58.Nup54 nucleoporin complex.
Components
  • Nanobody Nb15
  • Nucleoporin Nup58
  • Nucleoporin Nup62
  • Nup54
  • Part of Nup54 N-terminus with weak electron density, built as poly-alanine.
KeywordsTRANSPORT PROTEIN / nucleoporin / heterotrimeric coiled coils / kink containing coiled-coils / six helix-bundle
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / structural constituent of nuclear pore / RNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mRNA transport / nuclear pore / phospholipid binding ...protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / structural constituent of nuclear pore / RNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mRNA transport / nuclear pore / phospholipid binding / protein import into nucleus / protein transport / cytosol
Similarity search - Function
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 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region ...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 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nucleoporin 54kDa S homeolog isoform X2 / MGC84997 protein / IL4I1 protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsChug, H. / Trakhanov, S. / Hulsmann, B.B. / Pleiner, T. / Gorlich, D.
CitationJournal: Science / Year: 2015
Title: Crystal structure of the metazoan Nup62Nup58Nup54 nucleoporin complex.
Authors: Chug, H. / Trakhanov, S. / Hulsmann, B.B. / Pleiner, T. / Gorlich, D.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nup54
B: Nucleoporin Nup58
C: Nucleoporin Nup62
D: Nanobody Nb15
H: Part of Nup54 N-terminus with weak electron density, built as poly-alanine.


Theoretical massNumber of molelcules
Total (without water)84,6965
Polymers84,6965
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-125 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.570, 167.570, 142.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Nup54


Mass: 37570.781 Da / Num. of mol.: 1 / Fragment: Coiled coil
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: K9ZTJ6
#2: Protein Nucleoporin Nup58


Mass: 16233.337 Da / Num. of mol.: 1 / Fragment: Coiled coil
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: MGC84997 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: Q5EAX5
#3: Protein Nucleoporin Nup62 / Nuclear pore complex glycoprotein p62


Mass: 17249.256 Da / Num. of mol.: 1 / Fragment: Coiled coil
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: nup62, IL4I1 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: Q91349
#4: Antibody Nanobody Nb15


Mass: 12432.701 Da / Num. of mol.: 1 / Fragment: Nanobody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: Immunoglobulin G / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB SHuffle
#5: Protein/peptide Part of Nup54 N-terminus with weak electron density, built as poly-alanine.


Mass: 1209.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli)

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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: 3.42 Å3/Da / Density % sol: 67 % / Description: Hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: PEG MME 2000, Trimethylamine N-oxide, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97864 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 24, 2014 / Details: dynamically bendable mirror
RadiationMonochromator: Double crystal fixed-exit monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.8→51 Å / Num. obs: 49303 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 101 % / Biso Wilson estimate: 83 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.235 / Rrim(I) all: 0.236 / Χ2: 0.934 / Net I/σ(I): 39.44 / Num. measured all: 5534630
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.870.7956.1061.66354611213720586.12396.3
2.87-2.950.9273.9832.82413877209320133.99396.2
2.95-3.040.9423.1463.7409879205219853.15396.7
3.04-3.130.9632.534.68395994196419302.53698.3
3.13-3.230.9771.7167389745195219261.7298.7
3.23-3.350.9881.2339.82365224183918231.23699.1
3.35-3.470.9930.86914.21353217180317940.87199.5
3.47-3.610.9960.64719.26336708174117360.64899.7
3.61-3.780.9980.46725.84310961166616590.46999.6
3.78-3.960.9990.32934.66276787160416000.3399.8
3.96-4.170.9990.22648.61263870153115290.22699.9
4.17-4.4310.15170.41274771146014560.15199.7
4.43-4.7310.13576.91266454136113590.13599.9
4.73-5.1110.10690.84246402128512850.107100
5.11-5.610.12779.57224955119211910.12899.9
5.6-6.2610.13176.26196378107110690.13199.8
6.26-7.2310.193.371654349729720.1100
7.23-8.8510.059122.231250598348340.059100
8.85-12.5210.042169.941098836606600.042100
12.5210.04152.14544214144040.0497.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: SAD
Starting model: 4hep

4hep


Resolution: 2.9→50.878 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3007 1479 3.01 %
Rwork0.2647 --
obs0.2658 26500 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→50.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 0 0 4020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074068
X-RAY DIFFRACTIONf_angle_d0.9225475
X-RAY DIFFRACTIONf_dihedral_angle_d17.5011578
X-RAY DIFFRACTIONf_chiral_restr0.035621
X-RAY DIFFRACTIONf_plane_restr0.004722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.99360.39831290.35384185X-RAY DIFFRACTION95
2.9936-3.10060.37791260.35054263X-RAY DIFFRACTION97
3.1006-3.22470.3241360.30224255X-RAY DIFFRACTION98
3.2247-3.37140.33011320.26944325X-RAY DIFFRACTION98
3.3714-3.54910.36611380.2534360X-RAY DIFFRACTION99
3.5491-3.77140.29011370.24464344X-RAY DIFFRACTION99
3.7714-4.06250.26451380.23244357X-RAY DIFFRACTION100
4.0625-4.47110.26911370.21644380X-RAY DIFFRACTION100
4.4711-5.11760.26321340.22954385X-RAY DIFFRACTION100
5.1176-6.44560.32241370.31344374X-RAY DIFFRACTION100
6.4456-50.88590.30441350.2814389X-RAY DIFFRACTION100

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