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- PDB-3h7n: Structure of Nup120 -

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Basic information

Entry
Database: PDB / ID: 3h7n
TitleStructure of Nup120
ComponentsNucleoporin NUP120
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / Nuclear Pore Complex / Macromolecular Assembly / Membrane Coat / Nucleocytoplasmic Transport / beta-propeller / alpha-helical solenoid domain / Coiled coil / Membrane / mRNA transport / Nucleus / Phosphoprotein / Protein transport / Translocation / Transport
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / nucleocytoplasmic transport / subtelomeric heterochromatin formation / ribosomal large subunit export from nucleus / mRNA export from nucleus ...mRNA export from nucleus in response to heat stress / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / nucleocytoplasmic transport / subtelomeric heterochromatin formation / ribosomal large subunit export from nucleus / mRNA export from nucleus / nuclear pore / protein export from nucleus / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
Nucleoporin Nup120/160 / Nucleoporin Nup120/160
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSeo, H.S. / Ma, Y. / Debler, E.W. / Blobel, G. / Hoelz, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex.
Authors: Seo, H.S. / Ma, Y. / Debler, E.W. / Wacker, D. / Kutik, S. / Blobel, G. / Hoelz, A.
History
DepositionApr 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Nucleoporin NUP120
B: Nucleoporin NUP120
C: Nucleoporin NUP120
D: Nucleoporin NUP120


Theoretical massNumber of molelcules
Total (without water)335,4584
Polymers335,4584
Non-polymers00
Water0
1
A: Nucleoporin NUP120


Theoretical massNumber of molelcules
Total (without water)83,8651
Polymers83,8651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoporin NUP120


Theoretical massNumber of molelcules
Total (without water)83,8651
Polymers83,8651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nucleoporin NUP120


Theoretical massNumber of molelcules
Total (without water)83,8651
Polymers83,8651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nucleoporin NUP120


Theoretical massNumber of molelcules
Total (without water)83,8651
Polymers83,8651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.995, 115.721, 156.083
Angle α, β, γ (deg.)90.06, 89.96, 90.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 83864.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP120, RAT2, YKL057C, YKL314, YKL313 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL / References: UniProt: P35729

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium citrate (tribasic dihydrate), Potassium thiocynate, PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2009
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 73282 / Num. obs: 66320 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rsym value: 0.047 / Net I/σ(I): 40.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7392 / Rsym value: 0.478 / % possible all: 47.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F7F

3f7f


Resolution: 3→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.274 3174
Rwork0.255 -
obs0.255 62846
all-66320
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22992 0 0 0 22992
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.51

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