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- PDB-4mhc: Crystal Structure of a Nucleoporin -

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Basic information

Entry
Database: PDB / ID: 4mhc
TitleCrystal Structure of a Nucleoporin
ComponentsNucleoporin NUP157
KeywordsSTRUCTURAL PROTEIN / Nuclear pore complex / ADAPTOR NUCLEOPORIN / DNA BINDING PROTEIN / RNA BINDING PROTEIN / NUCLEOCYTOPLASMIC TRANSPORT / BETA-PROPELLER / ALPHA-HELICAL SOLENOID DOMAIN / MRNA TRANSPORT / NUCLEUS / GENE GATING / CHROMATIN ORGANIZATION
Function / homology
Function and homology information


nuclear pore inner ring / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / mRNA transport / nuclear pore ...nuclear pore inner ring / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / mRNA transport / nuclear pore / protein import into nucleus / nuclear envelope / nuclear membrane / DNA binding / RNA binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1780 / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSeo, H.S. / Blus, B.J. / Blobel, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure and nucleic acid binding activity of the nucleoporin Nup157.
Authors: Seo, H.S. / Blus, B.J. / Jankovic, N.Z. / Blobel, G.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: 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

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Assembly

Deposited unit
A: Nucleoporin NUP157


Theoretical massNumber of molelcules
Total (without water)91,5681
Polymers91,5681
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.110, 76.940, 82.630
Angle α, β, γ (deg.)90.00, 106.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoporin NUP157 / Nuclear pore protein NUP157


Mass: 91567.836 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 70-893)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NUP157, YER105C / Production host: Escherichia coli (E. coli) / References: UniProt: P40064
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5% PEG 4,000, 0.1 M MES, pH 6.0, 0.05 M Magnesium chloride, 3% (v/v) 1,4-dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2012
RadiationMonochromator: Double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→45.105 Å / Num. all: 29410 / Num. obs: 28352 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1596 / % possible all: 74.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.solve: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→45.1 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1432 5.05 %Random
Rwork0.1887 ---
obs0.1908 28337 96.39 %-
all-29398 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5299 0 0 148 5447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045402
X-RAY DIFFRACTIONf_angle_d0.8497330
X-RAY DIFFRACTIONf_dihedral_angle_d12.711956
X-RAY DIFFRACTIONf_chiral_restr0.058865
X-RAY DIFFRACTIONf_plane_restr0.004922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4-2.48580.31541190.2262056217575
2.4858-2.58530.2881400.21382501264190
2.5853-2.7030.33131410.21142751289299
2.703-2.84550.25931470.214927872934100
2.8455-3.02370.26511430.206427642907100
3.0237-3.25710.2451310.203928172948100
3.2571-3.58480.23231390.18127752914100
3.5848-4.10320.20331650.173428012966100
4.1032-5.16840.20641580.160328132971100
5.1684-45.1130.21211490.199628402989100

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