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- PDB-3jro: NUP84-NUP145C-SEC13 edge element of the NPC lattice -

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Basic information

Entry
Database: PDB / ID: 3jro
TitleNUP84-NUP145C-SEC13 edge element of the NPC lattice
Components
  • Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145
  • Nucleoporin NUP84
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
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / COPII-mediated vesicle transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling ...mRNA export from nucleus in response to heat stress / positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / COPII-mediated vesicle transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore localization / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / nuclear pore central transport channel / nuclear pore outer ring / telomere tethering at nuclear periphery / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coat / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / tRNA export from nucleus / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / nuclear localization sequence binding / RNA export from nucleus / SUMOylation of chromatin organization proteins / vacuolar membrane / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / mRNA transport / nuclear pore / subtelomeric heterochromatin formation / mRNA export from nucleus / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / nuclear envelope / double-strand break repair / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding
Similarity search - Function
Hyaluronidase domain-like - #20 / Hyaluronidase domain-like / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / 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 ...Hyaluronidase domain-like - #20 / Hyaluronidase domain-like / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / 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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP145 / Nucleoporin NUP84 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4.004 Å
AuthorsBrohawn, S.G. / 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: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145
C: Nucleoporin NUP84


Theoretical massNumber of molelcules
Total (without water)134,6132
Polymers134,6132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-29 kcal/mol
Surface area50410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.472, 170.472, 270.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145


Mass: 85364.219 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: Protein Nucleoporin NUP84 / Nuclear pore protein NUP84


Mass: 49248.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUP84, YDL116W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: P52891
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: 4.22 Å3/Da / Density % sol: 70.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 1.15M sodium malonate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 37090 / Num. obs: 37016 / % possible obs: 99.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shellResolution: 4→4.14 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 4.004→49.887 Å / SU ML: -0 / σ(F): 1.89 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3289 2909 7.86 %Random
Rwork0.2821 ---
obs0.2858 37016 99.8 %-
all-37090 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 134.876 Å2 / ksol: 0.311 e/Å3
Refinement stepCycle: LAST / Resolution: 4.004→49.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8671 0 0 0 8671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048857
X-RAY DIFFRACTIONf_angle_d0.76212014
X-RAY DIFFRACTIONf_dihedral_angle_d14.2343212
X-RAY DIFFRACTIONf_chiral_restr0.0521361
X-RAY DIFFRACTIONf_plane_restr0.0031517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.004-4.06910.52451360.38661632X-RAY DIFFRACTION100
4.0691-4.13930.37151210.35681639X-RAY DIFFRACTION99
4.1393-4.21450.39451540.34171590X-RAY DIFFRACTION100
4.2145-4.29550.38011450.33181625X-RAY DIFFRACTION99
4.2955-4.38310.41621300.32431643X-RAY DIFFRACTION100
4.3831-4.47840.35181440.29481595X-RAY DIFFRACTION100
4.4784-4.58250.3551490.29591609X-RAY DIFFRACTION99
4.5825-4.6970.31111210.28341661X-RAY DIFFRACTION100
4.697-4.82390.31891310.26551613X-RAY DIFFRACTION100
4.8239-4.96570.28861550.26071600X-RAY DIFFRACTION100
4.9657-5.12580.31981380.26651626X-RAY DIFFRACTION100
5.1258-5.30890.30261240.26241654X-RAY DIFFRACTION100
5.3089-5.52110.33881450.27091605X-RAY DIFFRACTION100
5.5211-5.77210.3611670.29131591X-RAY DIFFRACTION100
5.7721-6.07590.37041400.29671629X-RAY DIFFRACTION100
6.0759-6.45580.34871240.26371645X-RAY DIFFRACTION100
6.4558-6.95310.36771410.27621614X-RAY DIFFRACTION100
6.9531-7.65050.31271440.26341632X-RAY DIFFRACTION100
7.6505-8.75240.24461430.19811614X-RAY DIFFRACTION100
8.7524-11.00760.19211390.16441637X-RAY DIFFRACTION100
11.0076-49.89060.29431180.26361653X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.48860.2480.91981.1297-0.3811.3894-0.09980.12371.14-0.05040.16140.064-0.09860.2384-0.11911.8735-0.2019-0.01782.38950.1222.4632-122.114295.925629.9346
23.5324-0.3671-0.44180.12570.4468-0.05790.07260.18710.4152-0.0249-0.1205-0.1597-0.08210.05290.0211.77740.00780.11892.3124-0.03342.069
32.3761-1.4342-0.38710.98370.79951.47070.15680.0398-0.0852-0.1645-0.178-0.0839-0.07680.0475-0.05611.5241-0.14780.28961.8196-0.24731.5282
Refinement TLS groupSelection details: CHAIN C

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