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- PDB-3jrp: SEC13 with NUP145C (AA109-179) insertion blade -

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Basic information

Entry
Database: PDB / ID: 3jrp
TitleSEC13 with NUP145C (AA109-179) insertion blade
ComponentsFUSION PROTEIN OF PROTEIN TRANSPORT PROTEIN SEC13 AND NUCLEOPORIN NUP145
KeywordsTRANSPORT PROTEIN / STRUCTURAL PROTEIN / PROTEIN COMPLEX / CYTOPLASMIC VESICLE / ENDOPLASMIC RETICULUM / ER-GOLGI TRANSPORT / MEMBRANE / MRNA TRANSPORT / NUCLEAR PORE COMPLEX / NUCLEUS / PROTEIN TRANSPORT / TRANSLOCATION / TRANSPORT / WD REPEAT / AUTOCATALYTIC CLEAVAGE / HYDROLASE / PHOSPHOPROTEIN / RNA-BINDING
Function / homology
Function and homology information


Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / nuclear pore central transport channel ...Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / nuclear pore central transport channel / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / COPII vesicle coat / nuclear pore cytoplasmic filaments / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / vacuolar membrane / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / subtelomeric heterochromatin formation / positive regulation of TOR signaling / mRNA transport / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum / RNA binding
Similarity search - Function
Nucleoporin FG repeat / Nucleoporin FG repeat region / Sec13/Seh1 family / 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 autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like ...Nucleoporin FG repeat / Nucleoporin FG repeat region / Sec13/Seh1 family / 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 autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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
Similarity search - Domain/homology
Nucleoporin NUP145 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrohawn, S.G. / Gogola, M. / Schwartz, T.U.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice.
Authors: Brohawn, S.G. / Schwartz, T.U.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 13, 2012Group: Other
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Sep 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 / 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: FUSION PROTEIN OF PROTEIN TRANSPORT PROTEIN SEC13 AND NUCLEOPORIN NUP145


Theoretical massNumber of molelcules
Total (without water)41,7011
Polymers41,7011
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.280, 93.878, 55.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein FUSION PROTEIN OF PROTEIN TRANSPORT PROTEIN SEC13 AND NUCLEOPORIN NUP145


Mass: 41700.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q04491, UniProt: P49687
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris, 22% PEG 4000, 0.25 M LiCl, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 11394 / Num. obs: 11148 / % possible obs: 97.84 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 63.6 Å2
Reflection shellResolution: 2.6→2.66 Å / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PM6

2pm6


Resolution: 2.6→35.717 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.779 / SU ML: 0.99 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1101 9.88 %Random
Rwork0.217 ---
obs0.221 11148 97.84 %-
all-11394 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.406 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 198.98 Å2 / Biso mean: 70.814 Å2 / Biso min: 22.86 Å2
Baniso -1Baniso -2Baniso -3
1--11.514 Å20 Å20 Å2
2--10.902 Å2-0 Å2
3---0.612 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 0 67 2687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032685
X-RAY DIFFRACTIONf_angle_d0.6793649
X-RAY DIFFRACTIONf_chiral_restr0.047408
X-RAY DIFFRACTIONf_plane_restr0.002454
X-RAY DIFFRACTIONf_dihedral_angle_d14.282935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.7180.361410.291218135997
2.718-2.8620.3721250.2921234135998
2.862-3.0410.2571270.2641249137699
3.041-3.2750.311410.2341249139098
3.275-3.6050.2381510.2121238138999
3.605-4.1260.2391240.2051271139599
4.126-5.1950.1921430.1691269141297
5.195-35.720.2491490.2131319146896
Refinement TLS params.Method: refined / Origin x: -24.6989 Å / Origin y: -18.3084 Å / Origin z: 13.9571 Å
111213212223313233
T0.0938 Å20.0291 Å20.0121 Å2-0.0279 Å2-0.0375 Å2--0.1207 Å2
L2.6994 °20.079 °20.1872 °2-1.5426 °2-0.5001 °2--3.0147 °2
S0.0976 Å °-0.0849 Å °0.2225 Å °-0.0243 Å °-0.0282 Å °0.0748 Å °-0.1508 Å °-0.043 Å °-0.0089 Å °
Refinement TLS groupSelection details: NOT WATER

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