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- PDB-6q82: Crystal structure of the biportin Pdr6 in complex with RanGTP -

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Basic information

Entry
Database: PDB / ID: 6q82
TitleCrystal structure of the biportin Pdr6 in complex with RanGTP
Components
  • GTP-binding nuclear protein Ran
  • Importin beta-like protein KAP122
KeywordsPROTEIN TRANSPORT / Importin-Beta family / biportin / nuclear transport / GTPase
Function / homology
Function and homology information


pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / protein localization to nucleolus ...pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / protein localization to nucleolus / Nuclear import of Rev protein / nuclear export / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / regulation of cell size / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / spermatid development / viral process / positive regulation of protein binding / sperm flagellum / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / actin cytoskeleton organization / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / Ran GTPase / Small GTPase Ran-type domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical ...: / Ran GTPase / Small GTPase Ran-type domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / 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 / SAD / Resolution: 2.994 Å
AuthorsAksu, M. / Vera-Rodriguez, A. / Trakhanov, S. / 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 ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jun 12, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4524
Polymers144,9042
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-21 kcal/mol
Surface area52890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.990, 192.990, 229.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

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


Mass: 124711.898 Da / Num. of mol.: 1
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.: 1 / 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: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
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: 4.44 Å3/Da / Density % sol: 72.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.26
Details: Pentaerythritol propoxylate (17/8 PO/OH), MPD, Sodium acetate, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97796 Å / Relative weight: 1
ReflectionResolution: 2.994→59.894 Å / Num. obs: 51160 / % possible obs: 99.7 % / Redundancy: 399.8 % / Biso Wilson estimate: 106.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.2728 / Rpim(I) all: 0.01361 / Net I/σ(I): 44.7
Reflection shellResolution: 2.994→3.101 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4876 / CC1/2: 0.893 / % possible all: 97.42

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
RESOLVEmodel building
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.994→59.894 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.42
RfactorNum. reflection% reflection
Rfree0.2529 1532 3 %
Rwork0.2179 --
obs0.219 51055 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 332.1 Å2 / Biso mean: 111.0655 Å2 / Biso min: 46.45 Å2
Refinement stepCycle: final / Resolution: 2.994→59.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9649 0 33 0 9682
Biso mean--91.32 --
Num. residues----1198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9936-3.09020.35421320.31464300443297
3.0902-3.20070.32341370.30744074544100
3.2007-3.32880.3571380.297444674605100
3.3288-3.48030.35041380.277644384576100
3.4803-3.66380.26531370.24644504587100
3.6638-3.89330.25361390.222544834622100
3.8933-4.19380.26471390.204144734612100
4.1938-4.61570.21261390.178945164655100
4.6157-5.28330.22711410.190345444685100
5.2833-6.6550.26551420.252646054747100
6.655-59.90580.23431500.198948404990100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.76490.34760.28251.48850.25811.59090.1841-0.1103-0.14480.11090.1536-0.1468-0.198-0.22840.5680.63680.1995-0.08190.77620.08470.550934.6964133.4775130.9354
20.4737-0.311-0.1360.8864-0.12941.31250.10540.02740.0134-0.13710.0052-0.1291-0.19920.040600.4145-0.0558-0.06660.65470.01580.641140.023129.125679.691
31.56560.2617-0.62050.7116-0.10991.41750.1182-0.2553-0.00570.155-0.16990.11080.23460.0367-0.00030.5059-0.0547-0.04660.5978-0.03690.684946.565592.700895.4166
40.05370.05230.02490.05820.02760.07330.45570.5889-0.70950.20940.2159-0.6190.2987-0.0689-0.00090.80080.1120.01671.1576-0.06521.233955.6262122.4036111.373
50.02840.0381-0.02570.0503-0.03420.0231-0.02420.02420.21360.07690.2071-0.48550.24840.221501.11790.1284-0.0931.2733-0.01051.41456.4483115.4943113.4267
60.02170.01630.02850.01270.01680.0616-0.1391-0.17020.57470.3795-0.068-0.7099-0.0698-0.4556-0.00380.7901-0.02070.07120.67030.12411.385562.1002130.0362111.1436
70.1086-0.0357-0.11610.0807-0.02690.1855-0.08440.3434-0.14080.0681-0.010.4659-0.2642-0.1763-0.00270.80480.0698-0.07771.1899-0.01721.020843.0083124.022113.5845
80.2292-0.14680.11830.1206-0.02850.14240.59790.16870.4757-0.0857-0.1105-0.3528-0.2080.3437-0.00050.78850.0780.05471.0284-0.06180.744745.2012124.219104.4516
90.0240.02390.00690.02520.00620.00230.55490.09490.26710.04660.3871-0.0134-0.3955-0.4970.00181.14920.07540.16791.43720.06891.148542.9157130.625498.9354
100.7075-0.69660.69740.864-0.69930.68810.10510.42050.3757-0.6127-0.1167-0.426-0.14340.29020.51831.1079-0.14790.4370.6210.14021.280658.3074129.2984101.0666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 210 )A3 - 210
2X-RAY DIFFRACTION2chain 'A' and (resid 211 through 745 )A211 - 745
3X-RAY DIFFRACTION3chain 'A' and (resid 746 through 1076 )A746 - 1076
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 32 )B8 - 32
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 52 )B33 - 52
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 66 )B53 - 66
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 109 )B67 - 109
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 131 )B110 - 131
9X-RAY DIFFRACTION9chain 'B' and (resid 132 through 148 )B132 - 148
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 178 )B149 - 178

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