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- PDB-3t98: Molecular Architecture of the Transport Channel of the Nuclear Po... -

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Basic information

Entry
Database: PDB / ID: 3t98
TitleMolecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup54/Nup58
Components
  • Nuclear pore complex protein Nup54
  • Nucleoporin Nup58/Nup45
KeywordsPROTEIN TRANSPORT / Nup58 / Nup54 / Nup62 complex / nuclear import / coiled-coil / helix / hairpin / FG-repeat / nucleoporin / NPC / nuclear tranport / transport channel / Nup62 / Nup45 / Nup93 / karyopherin / nuclear pore complex / nuclear pore domain / nuclear envelope
Function / homology
Function and homology information


Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins ...Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / regulation of protein import into nucleus / protein localization to nuclear inner membrane / Regulation of HSF1-mediated heat shock response / nuclear pore central transport channel / nuclear pore organization / NLS-bearing protein import into nucleus / structural constituent of nuclear pore / nuclear localization sequence binding / nucleocytoplasmic transport / mRNA transport / nuclear pore / protein targeting / nuclear envelope / protein transport / nuclear membrane / protein-containing complex binding / protein-containing complex / 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 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Nucleoporin p58/p45 / Nuclear pore complex protein Nup54
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSolmaz, S.R. / Blobel, G. / Melcak, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Molecular architecture of the transport channel of the nuclear pore complex.
Authors: Solmaz, S.R. / Chauhan, R. / Blobel, G. / Melcak, I.
History
DepositionAug 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Feb 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: Nuclear pore complex protein Nup54
B: Nucleoporin Nup58/Nup45
C: Nuclear pore complex protein Nup54


Theoretical massNumber of molelcules
Total (without water)22,7893
Polymers22,7893
Non-polymers00
Water1,00956
1
A: Nuclear pore complex protein Nup54
B: Nucleoporin Nup58/Nup45
C: Nuclear pore complex protein Nup54
x 32


Theoretical massNumber of molelcules
Total (without water)729,24696
Polymers729,24696
Non-polymers00
Water1,72996
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation1_558x,y,z+31
crystal symmetry operation2_534-x,-y-2,z-1/21
crystal symmetry operation2_535-x,-y-2,z+1/21
crystal symmetry operation2_536-x,-y-2,z+3/21
crystal symmetry operation2_537-x,-y-2,z+5/21
crystal symmetry operation3_445-y-1,x-1,z+1/41
crystal symmetry operation3_446-y-1,x-1,z+5/41
crystal symmetry operation3_447-y-1,x-1,z+9/41
crystal symmetry operation3_448-y-1,x-1,z+13/41
crystal symmetry operation4_644y+1,-x-1,z-1/41
crystal symmetry operation4_645y+1,-x-1,z+3/41
crystal symmetry operation4_646y+1,-x-1,z+7/41
crystal symmetry operation4_647y+1,-x-1,z+11/41
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation5_557-x,y,-z+21
crystal symmetry operation5_558-x,y,-z+31
crystal symmetry operation6_535x,-y-2,-z+1/21
crystal symmetry operation6_536x,-y-2,-z+3/21
crystal symmetry operation6_537x,-y-2,-z+5/21
crystal symmetry operation6_538x,-y-2,-z+7/21
crystal symmetry operation7_644y+1,x-1,-z-1/41
crystal symmetry operation7_645y+1,x-1,-z+3/41
crystal symmetry operation7_646y+1,x-1,-z+7/41
crystal symmetry operation7_647y+1,x-1,-z+11/41
crystal symmetry operation8_445-y-1,-x-1,-z+1/41
crystal symmetry operation8_446-y-1,-x-1,-z+5/41
crystal symmetry operation8_447-y-1,-x-1,-z+9/41
crystal symmetry operation8_448-y-1,-x-1,-z+13/41
Buried area11490 Å2
ΔGint-93 kcal/mol
Surface area18680 Å2
Unit cell
Length a, b, c (Å)54.960, 54.960, 190.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-44-

HOH

DetailsTHE BIOLOGICAL UNIT IS A 32MER OF THE ASYMMETRIC UNIT IN THE SHAPE OF A SPIRAL.

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Components

#1: Protein Nuclear pore complex protein Nup54 / 54 kDa nucleoporin / Nucleoporin Nup54


Mass: 6003.876 Da / Num. of mol.: 2 / Fragment: UNP residues 445-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup54 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)RIL / References: UniProt: P70582
#2: Protein Nucleoporin Nup58/Nup45 / NUCLEOPORIN P58/P45 / Nucleoporin-like protein 1


Mass: 10781.189 Da / Num. of mol.: 1 / Fragment: UNP residues 327-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nupl1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)RIL / References: UniProt: P70581
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Protein concentration 14-17 mg/ml Drop size 2.4 ul Reservoir: 0.1 M Sodium Acetate pH 3.8-4.1 and 0.08-0.1 M CaCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 11076 / Num. obs: 11076 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 54 Å2 / Rsym value: 0.098 / Net I/σ(I): 23
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.43 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 1053 RANDOM
Rwork0.25 --
all0.253 10263 -
obs0.253 10263 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 56 1394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.097

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