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- PDB-3pbp: Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleop... -

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Basic information

Entry
Database: PDB / ID: 3pbp
TitleStructure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex
Components
  • Nucleoporin NUP116/NSP116
  • Nucleoporin NUP159
  • Nucleoporin NUP82
KeywordsTRANSPORT PROTEIN / STRUCTURAL PROTEIN / beta-propeller / nucleoporin / mRNA export / mRNP remodelling / NUCLEOCYTOPLASMIC Transport / PROTEIN TRANSPORT / TRANSLOCATION / TRANSPORT / autoproteolysis / Fusion protein / PROTOONCOGENE / ONCOPROTEIN / Protein COMPLEX / Nucleus / Nuclear Envelope / Nuclear Pore Complex
Function / homology
Function and homology information


nuclear pore linkers / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery ...nuclear pore linkers / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / ribosomal large subunit export from nucleus / nuclear pore / mRNA export from nucleus / ribosomal small subunit export from nucleus / protein export from nucleus / protein import into nucleus / transcription corepressor activity / nuclear envelope / ATPase binding / nuclear membrane / RNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin NUP88/NUP82 / Nucleoporin Nup159/Nup146, N-terminal / NUP159/214 beta propeller / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like ...Peptidase S59, nucleoporin / c-terminal autoproteolytic domain of nucleoporin nup98 / Nucleoporin NUP88/NUP82 / Nucleoporin Nup159/Nup146, N-terminal / NUP159/214 beta propeller / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Nucleoporin NUP82 / Nucleoporin NUP159 / Nucleoporin NUP116/NSP116
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsDebler, E.W. / Hoelz, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex.
Authors: Yoshida, K. / Seo, H.S. / Debler, E.W. / Blobel, G. / Hoelz, A.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NUP82
B: Nucleoporin NUP116/NSP116
C: Nucleoporin NUP159
D: Nucleoporin NUP82
E: Nucleoporin NUP116/NSP116
F: Nucleoporin NUP159
G: Nucleoporin NUP82
H: Nucleoporin NUP116/NSP116
I: Nucleoporin NUP159
J: Nucleoporin NUP82
K: Nucleoporin NUP116/NSP116
L: Nucleoporin NUP159
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,07913
Polymers291,92912
Non-polymers1501
Water00
1
A: Nucleoporin NUP82
B: Nucleoporin NUP116/NSP116
C: Nucleoporin NUP159


Theoretical massNumber of molelcules
Total (without water)72,9823
Polymers72,9823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-24 kcal/mol
Surface area28630 Å2
MethodPISA
2
D: Nucleoporin NUP82
E: Nucleoporin NUP116/NSP116
F: Nucleoporin NUP159
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1324
Polymers72,9823
Non-polymers1501
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-17 kcal/mol
Surface area28300 Å2
MethodPISA
3
G: Nucleoporin NUP82
H: Nucleoporin NUP116/NSP116
I: Nucleoporin NUP159


Theoretical massNumber of molelcules
Total (without water)72,9823
Polymers72,9823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-24 kcal/mol
Surface area28930 Å2
MethodPISA
4
J: Nucleoporin NUP82
K: Nucleoporin NUP116/NSP116
L: Nucleoporin NUP159


Theoretical massNumber of molelcules
Total (without water)72,9823
Polymers72,9823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-25 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.503, 96.770, 144.282
Angle α, β, γ (deg.)105.98, 93.97, 108.24
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoporin NUP82 / Nuclear pore protein NUP82


Mass: 51982.461 Da / Num. of mol.: 4 / Fragment: N-terminal domain (NTD), UNP residues 1-452 / Mutation: C396S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP82, YJL061W, J1135, HRB187 / Production host: Escherichia coli (E. coli) / References: UniProt: P40368
#2: Protein
Nucleoporin NUP116/NSP116 / Nuclear pore protein NUP116/NSP116


Mass: 16832.180 Da / Num. of mol.: 4 / Fragment: C-terminal domain (CTD), UNP residues 967-1113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP116, NSP116, YMR047C, YM9532.12C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02630
#3: Protein/peptide
Nucleoporin NUP159 / Nuclear pore protein NUP159


Mass: 4167.491 Da / Num. of mol.: 4 / Fragment: Tail, UNP residues 1425-1460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP159, NUP158, RAT7, YIL115C / Production host: Escherichia coli (E. coli) / References: UniProt: P40477
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PEG 400, sodium cacodylate, lithium sulfate, 2,5-hexanediol, pH 6.6, 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: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2009
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 184127 / Num. obs: 181917 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rsym value: 0.097 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3 / Num. unique all: 17910 / Rsym value: 0.473 / % possible all: 98.3

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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→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 14690 RANDOM
Rwork0.257 --
all-184127 -
obs-168608 -
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19643 0 10 0 19653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.4

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