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- PDB-3t97: Molecular Architecture of the Transport Channel of the Nuclear Po... -

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Basic information

Entry
Database: PDB / ID: 3t97
TitleMolecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup62/Nup54
Components
  • Nuclear pore complex protein Nup54Nuclear pore
  • Nuclear pore glycoprotein p62
KeywordsPROTEIN TRANSPORT / nucleoporin / coiled-coil / nuclear pore complex / central transport channel / alpha helical proteins / triple helix / buried polar residues / structural proteins / nucleoporins / FG repeat / nucleocytoplasmic transport / Nup58 / Nup88 / Nup93 / karyopherin / nuclear envelope / nuclear pore membrane domain / central channel
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 / positive regulation of mitotic cytokinetic process / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / protein localization to nuclear inner membrane / annulate lamellae / Regulation of HSF1-mediated heat shock response / nuclear pore central transport channel / nuclear pore organization / positive regulation of protein localization to centrosome / negative regulation of Ras protein signal transduction / structural constituent of nuclear pore / Flemming body / negative regulation of programmed cell death / RNA export from nucleus / mitotic centrosome separation / centrosome cycle / nucleocytoplasmic transport / nuclear thyroid hormone receptor binding / PTB domain binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / negative regulation of epidermal growth factor receptor signaling pathway / kinesin binding / mRNA transport / protein targeting / nuclear pore / regulation of mitotic spindle organization / Hsp70 protein binding / SH2 domain binding / positive regulation of mitotic nuclear division / ubiquitin binding / Hsp90 protein binding / phospholipid binding / mitotic spindle / spindle pole / protein import into nucleus / cellular senescence / signaling receptor complex adaptor activity / nuclear envelope / spermatogenesis / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / ribonucleoprotein complex / negative regulation of cell population proliferation / centrosome / protein-containing complex binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Single helix bin / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 ...Single helix bin / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / 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
Nuclear pore glycoprotein p62 / Nuclear pore complex protein Nup54
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsChauhan, 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
B: Nuclear pore complex protein Nup54
C: Nuclear pore glycoprotein p62
A: Nuclear pore glycoprotein p62


Theoretical massNumber of molelcules
Total (without water)22,7003
Polymers22,7003
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-50 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.010, 62.350, 121.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 7624.819 Da / Num. of mol.: 1 / Fragment: UNP residues 346-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup54 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P70582
#2: Protein Nuclear pore glycoprotein p62 / / 62 kDa nucleoporin / Nucleoporin Nup62


Mass: 7537.403 Da / Num. of mol.: 2 / Fragment: UNP residues 362-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup62 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)RIL / References: UniProt: P17955
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 18-22% PEG 4000,0.1M Tris-acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2008
RadiationMonochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 4819 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 70.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 41.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 329 / Rsym value: 0.244 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 888 -random
Rwork0.2353 ---
obs0.2305 4802 100 %-
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 0 29 1434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.102
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection
Rfree0.449 85
Rwork0.3291 -
obs-782

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