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- PDB-3bg0: Architecture of a Coat for the Nuclear Pore Membrane -

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Basic information

Entry
Database: PDB / ID: 3bg0
TitleArchitecture of a Coat for the Nuclear Pore Membrane
Components
  • Nucleoporin NUP145
  • Protein SEC13 homolog
KeywordsPROTEIN TRANSPORT / HYDROLASE / NPC / Transport / WD repeat / Autocatalytic cleavage / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / RNA-binding / Translocation
Function / homology
Function and homology information


GATOR2 complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / COPII-coated vesicle cargo loading / nuclear pore outer ring / telomere tethering at nuclear periphery ...GATOR2 complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / COPII-coated vesicle cargo loading / nuclear pore outer ring / telomere tethering at nuclear periphery / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / tRNA export from nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NLS-bearing protein import into nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / mRNA transport / Regulation of HSF1-mediated heat shock response / cellular response to nutrient levels / subtelomeric heterochromatin formation / nuclear pore / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of TORC1 signaling / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / SUMOylation of chromatin organization proteins / HCMV Late Events / RHO GTPases Activate Formins / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / Transcriptional regulation by small RNAs / ER to Golgi transport vesicle membrane / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / double-strand break repair / snRNP Assembly / nuclear membrane / chromosome, telomeric region / hydrolase activity / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #690 / N-terminal domain of TfIIb - #170 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Sec13/Seh1 family / N-terminal domain of TfIIb / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #690 / N-terminal domain of TfIIb - #170 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Sec13/Seh1 family / N-terminal domain of TfIIb / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / 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. / Other non-globular / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Special / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP145 / Protein SEC13 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsHoelz, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Architecture of a coat for the nuclear pore membrane.
Authors: Hsia, K.C. / Stavropoulos, P. / Blobel, G. / Hoelz, A.
History
DepositionNov 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Protein SEC13 homolog
B: Nucleoporin NUP145
C: Nucleoporin NUP145
D: Protein SEC13 homolog
E: Protein SEC13 homolog
F: Nucleoporin NUP145
G: Nucleoporin NUP145
H: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)343,3468
Polymers343,3468
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein SEC13 homolog
B: Nucleoporin NUP145
C: Nucleoporin NUP145
D: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)171,6734
Polymers171,6734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
MethodPISA
3
E: Protein SEC13 homolog
F: Nucleoporin NUP145
G: Nucleoporin NUP145
H: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)171,6734
Polymers171,6734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13780 Å2
MethodPISA
4
A: Protein SEC13 homolog
B: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
MethodPISA
5
C: Nucleoporin NUP145
D: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
MethodPISA
6
E: Protein SEC13 homolog
F: Nucleoporin NUP145


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
MethodPISA
7
G: Nucleoporin NUP145
H: Protein SEC13 homolog


Theoretical massNumber of molelcules
Total (without water)85,8372
Polymers85,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.818, 216.575, 100.959
Angle α, β, γ (deg.)90.00, 108.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein SEC13 homolog / SEC13-related protein / SEC13-like protein 1


Mass: 34893.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC13, D3S1231E, SEC13L1, SEC13R / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P55735
#2: Protein
Nucleoporin NUP145 / Nuclear pore protein NUP145


Mass: 50942.820 Da / Num. of mol.: 4 / Fragment: Nucleoporin NUP145C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP145, RAT10 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: P49687, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 294 K / pH: 7.7
Details: 16 % (w/v) PEG 3,350, 400 mM NaCl, 100 mM Na-K tartrate, and 100 mM BIS-TRIS, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. all: 63724 / Num. obs: 55955 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 %
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.746 / % possible all: 77.7

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 3.15→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.294 2837 4.5 %
Rwork0.252 --
obs0.252 55955 95.7 %
all-63724 -
Solvent computationBsol: 87.62 Å2
Displacement parametersBiso mean: 153.3 Å2
Baniso -1Baniso -2Baniso -3
1--36.438 Å20 Å2-1.652 Å2
2---43.02 Å20 Å2
3---79.458 Å2
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22566 0 0 0 22566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:PROTEIN_REP.PARAM

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