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- PDB-6x2v: Crystal Structure of PKI(DE)NES peptide bound to CRM1 -

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Basic information

Entry
Database: PDB / ID: 6x2v
TitleCrystal Structure of PKI(DE)NES peptide bound to CRM1
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsPROTEIN TRANSPORT / Nuclear export / CRM1 / XPO1 / Exportin-1
Function / homology
Function and homology information


positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / negative regulation of cAMP-dependent protein kinase activity / Regulation of HSF1-mediated heat shock response / manchette ...positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / negative regulation of cAMP-dependent protein kinase activity / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / spindle pole body / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / cAMP-dependent protein kinase inhibitor activity / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / negative regulation of protein import into nucleus / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / protein kinase A catalytic subunit binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / ribosomal subunit export from nucleus / nuclear pore / U1 snRNA binding / regulation of G2/M transition of mitotic cell cycle / centriole / protein export from nucleus / viral process / GTPase activator activity / 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 / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / G1/S transition of mitotic cell cycle / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / cAMP-dependent protein kinase inhibitor alpha / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.822 Å
AuthorsBaumhardt, J.M.
Funding support2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)
Welch Foundation
CitationJournal: Mol.Biol.Cell / Year: 2020
Title: Recognition of nuclear export signals by CRM1 carrying the oncogenic E571K mutation.
Authors: Baumhardt, J.M. / Walker, J.S. / Lee, Y. / Shakya, B. / Brautigam, C.A. / Lapalombella, R. / Grishin, N. / Chook, Y.M.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,6928
Polymers159,9624
Non-polymers7314
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.243, 107.243, 305.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 24456.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16320.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117442.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 1741.958 Da / Num. of mol.: 1 / Fragment: residues 34-49 / Mutation: N48D, K49E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKIA, PRKACN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61925

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Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Details

Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 17% (weight/vol) PEG3350, 100 mM Bis-Tris (pH 6.4), 200 mM ammonium nitrate, and 10 mM Spermine HCl

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.822→50 Å / Num. obs: 43919 / % possible obs: 100 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.388 / Rpim(I) all: 0.106 / Rrim(I) all: 0.4 / Χ2: 1.018 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.86-2.9116.421280.4552.5580.934100
2.91-2.9616.321490.5141.6160.9351006.3756.58
2.96-3.0216.121700.5411.5380.9471006.0516.247
3.02-3.0815.821480.6750.9960.9531003.8864.013
3.08-3.1514.521360.7671.0110.9621003.823.954
3.15-3.2215.921680.8760.7690.9681003.0223.12
3.22-3.317.521640.8790.5910.9491002.412.482
3.3-3.3917.521470.9280.4480.9531001.8271.882
3.39-3.4917.521760.950.3430.9761001.4041.446
3.49-3.617.421620.970.2650.9891001.0811.114
3.6-3.7317.521850.980.18411000.7530.775
3.73-3.8817.221860.9890.1351.0141000.5490.566
3.88-4.0616.321860.9910.0961.0311000.380.393
4.06-4.2715.921820.9940.0651.0361000.2540.262
4.27-4.5418.122080.9960.0441.0951000.1830.189
4.54-4.8917.921950.9970.0321.1411000.1350.139
4.89-5.3817.422350.9970.0281.1171000.1170.12
5.38-6.1615.422450.9960.0291.0611000.1120.116
6.16-7.7517.222940.9970.021.051000.0830.086
7.75-5015.224550.9970.0161.21199.90.0610.063

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HB2

4hb2


Resolution: 2.822→47.961 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1998 4.9 %
Rwork0.2028 38751 -
obs0.2057 40749 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.57 Å2 / Biso mean: 43.2667 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: final / Resolution: 2.822→47.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10615 0 0 0 10615
Num. residues----1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311132
X-RAY DIFFRACTIONf_angle_d0.54415079
X-RAY DIFFRACTIONf_chiral_restr0.0391719
X-RAY DIFFRACTIONf_plane_restr0.0041915
X-RAY DIFFRACTIONf_dihedral_angle_d5.1129370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8222-2.89280.4317620.299121742
2.8928-2.9710.3681070.2826205971
2.971-3.05840.38291360.2689264090
3.0584-3.15710.35581480.2566285097
3.1571-3.26990.30591480.25182896100
3.2699-3.40080.30871530.24342934100
3.4008-3.55550.28181520.22212954100
3.5555-3.74290.27841510.19442939100
3.7429-3.97730.26631540.18612976100
3.9773-4.28420.25381540.17162977100
4.2842-4.7150.19641530.15642986100
4.715-5.39650.21721570.16883020100
5.3965-6.79590.26471570.21343060100
6.7959-47.9610.20341660.18693243100

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