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- PDB-3f7f: Structure of Nup120 -

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Basic information

Entry
Database: PDB / ID: 3f7f
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 / mRNA transport / Nucleus / Protein transport / Translocation
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
: / Nucleoporin NUP120
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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
DepositionNov 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,93016
Polymers335,5234
Non-polymers2,40712
Water0
1
A: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4824
Polymers83,8811
Non-polymers6023
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Nucleoporin NUP120
B: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,9658
Polymers167,7612
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-32.6 kcal/mol
Surface area59970 Å2
MethodPISA
6
C: Nucleoporin NUP120
hetero molecules

D: Nucleoporin NUP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,9658
Polymers167,7612
Non-polymers1,2046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3050 Å2
ΔGint-32.9 kcal/mol
Surface area59900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.680, 117.478, 146.287
Angle α, β, γ (deg.)89.94, 89.77, 89.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 83880.680 Da / Num. of mol.: 4 / Fragment: UNP residues 1-729 / Mutation: S207C
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
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg

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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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Succinic acid, PEG 3350, Sodium bromide, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0049
SYNCHROTRONAPS 23-ID-D21.0049
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 26, 2008
ADSC QUANTUM 3152CCDJul 26, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.0049 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 217205 / Num. obs: 208082 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.041
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 21664 / Rsym value: 0.417 / % possible all: 81

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.254 18489
Rwork0.232 -
all0.232 190898
obs0.232 190898
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22864 0 12 0 22876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3

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