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- PDB-6q84: Crystal structure of RanGTP-Pdr6-eIF5A export complex -

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Basic information

Entry
Database: PDB / ID: 6q84
TitleCrystal structure of RanGTP-Pdr6-eIF5A export complex
Components
  • Eukaryotic translation initiation factor 5A-1
  • GTP-binding nuclear protein Ran
  • Importin beta-like protein KAP122
KeywordsPROTEIN TRANSPORT / Importin-Beta family / biportin / nuclear export / translation factor
Function / homology
Function and homology information


positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / translational elongation / regulation of cell size / dynein intermediate chain binding / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / positive regulation of translational initiation / ribosomal large subunit export from nucleus / sperm flagellum / translation elongation factor activity / rescue of stalled ribosome / nuclear pore / translation initiation factor activity / protein export from nucleus / centriole / viral process / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / ribosome binding / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / chromatin binding / chromatin / GTP binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / small GTPase Ran family profile. / Ran GTPase ...: / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / small GTPase Ran family profile. / Ran GTPase / SH3 type barrels. - #30 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Nucleic acid-binding proteins / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / SH3 type barrels. / Armadillo-like helical / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Small GTP-binding protein domain / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 5A-1 / Importin beta-like protein KAP122 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsAksu, M. / Trakhanov, S. / Vera-Rodriguez, A. / Gorlich, D.
CitationJournal: J.Cell Biol. / Year: 2019
Title: Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122.
Authors: Aksu, M. / Trakhanov, S. / Vera Rodriguez, A. / Gorlich, D.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin beta-like protein KAP122
B: GTP-binding nuclear protein Ran
C: Eukaryotic translation initiation factor 5A-1
D: Importin beta-like protein KAP122
E: GTP-binding nuclear protein Ran
F: Eukaryotic translation initiation factor 5A-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,51910
Polymers318,4246
Non-polymers1,0954
Water0
1
A: Importin beta-like protein KAP122
B: GTP-binding nuclear protein Ran
C: Eukaryotic translation initiation factor 5A-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7595
Polymers159,2123
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Importin beta-like protein KAP122
E: GTP-binding nuclear protein Ran
F: Eukaryotic translation initiation factor 5A-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7595
Polymers159,2123
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.540, 139.540, 346.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 129 or resid 141 through 386 or resid 395 through 1076))
21(chain D and (resid 3 through 103 or (resid 104...
12chain B
22chain E
13(chain C and (resid 18 through 46 or resid 57...
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 129 or resid 141 through 386 or resid 395 through 1076))A3 - 129
121(chain A and (resid 3 through 129 or resid 141 through 386 or resid 395 through 1076))A141 - 386
131(chain A and (resid 3 through 129 or resid 141 through 386 or resid 395 through 1076))A395 - 1076
211(chain D and (resid 3 through 103 or (resid 104...D3 - 103
221(chain D and (resid 3 through 103 or (resid 104...D104
231(chain D and (resid 3 through 103 or (resid 104...D3 - 1076
112chain BB8 - 178
212chain EE8 - 178
113(chain C and (resid 18 through 46 or resid 57...C18 - 46
123(chain C and (resid 18 through 46 or resid 57...C57 - 85
133(chain C and (resid 18 through 46 or resid 57...C86
143(chain C and (resid 18 through 46 or resid 57...C17 - 153
153(chain C and (resid 18 through 46 or resid 57...C17 - 153
163(chain C and (resid 18 through 46 or resid 57...C17 - 153
173(chain C and (resid 18 through 46 or resid 57...C17 - 153
213chain FF18 - 153

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Importin beta-like protein KAP122 / Karyopherin-122 / Pleiotropic drug resistance regulatory protein 6


Mass: 123492.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: KAP122, PDR6, YGL016W / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 F' / References: UniProt: P32767
#2: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 20192.484 Da / Num. of mol.: 2 / Mutation: Q69L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 F' / References: UniProt: P62826
#3: Protein Eukaryotic translation initiation factor 5A-1 / eIF-5A-1 / Hypusine-containing protein HP2 / eIF-4D


Mass: 15526.687 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HYP2, TIF51A, YEL034W, SYGP-ORF21 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: P23301
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 100 mM Sodium acetate pH 5.3 and 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.28
ReflectionResolution: 3.7→49.173 Å / Num. obs: 40583 / % possible obs: 99.83 % / Redundancy: 10.8 % / CC1/2: 1 / Rpim(I) all: 0.03048 / Rrim(I) all: 0.1006 / Rsym value: 0.09578 / Net I/σ(I): 17.74
Reflection shellResolution: 3.7→3.832 Å / Redundancy: 10 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 4014 / CC1/2: 0.527 / Rpim(I) all: 0.9533 / Rrim(I) all: 3.081 / Rsym value: 2.926 / % possible all: 99.65

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→49.173 Å / Cross valid method: THROUGHOUT / σ(F): 2.24 / Phase error: 40.93
RfactorNum. reflection% reflection
Rfree0.2471 2422 3.01 %
Rwork0.2065 --
obs0.2273 40554 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 338.38 Å2 / Biso mean: 198.6075 Å2 / Biso min: 103.23 Å2
Refinement stepCycle: final / Resolution: 3.7→49.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21141 0 66 0 21207
Biso mean--180.09 --
Num. residues----2641
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9779X-RAY DIFFRACTION4.836TORSIONAL
12D9779X-RAY DIFFRACTION4.836TORSIONAL
21B1734X-RAY DIFFRACTION4.836TORSIONAL
22E1734X-RAY DIFFRACTION4.836TORSIONAL
31C1221X-RAY DIFFRACTION4.836TORSIONAL
32F1221X-RAY DIFFRACTION4.836TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7008-3.77630.33741460.33254628477496
3.7763-3.85840.33491400.3134469460997
3.8584-3.94810.38961400.33474582472297
3.9481-4.04680.33441420.32264614475697
4.0468-4.15610.35171410.32024608474997
4.1561-4.27830.38011420.31434539468197
4.2783-4.41630.32181410.29124587472897
4.4163-4.5740.281440.27964599474397
4.574-4.7570.27611440.26874598474297
4.757-4.97320.29291440.25494616476097
4.9732-5.23510.25371420.25044568471097
5.2351-5.56250.26811440.25164618476297
5.5625-5.99120.27871420.25374560470297
5.9912-6.59250.30391420.22664590473297
6.5925-7.54280.26921410.22694586472797
7.5428-9.48920.19341420.16424566470897
9.4892-45.81760.21491440.17184597474196

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