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- PDB-5uwt: Crystal Structure of Hxk2 Peptide in complex with CRM1 K579A muta... -

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Basic information

Entry
Database: PDB / ID: 5uwt
TitleCrystal Structure of Hxk2 Peptide in complex with CRM1 K579A mutant-Ran-RanBP1
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Hexokinase-2
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / regulation of transcription by glucose / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / MAPK6/MAPK4 signaling / fructokinase activity / carbohydrate phosphorylation ...fructose import across plasma membrane / Regulation of Glucokinase by Glucokinase Regulatory Protein / regulation of transcription by glucose / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / MAPK6/MAPK4 signaling / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / RNA nuclear export complex / glucose 6-phosphate metabolic process / nuclear export signal receptor activity / 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 / glucose binding / U4 snRNA binding / RNA export from nucleus / spindle pole body / protein localization to kinetochore / nuclear export / fructose metabolic process / 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 / NLS-bearing protein import into nucleus / regulation of cell size / dynein intermediate chain binding / ribosomal subunit export from nucleus / glucose import / spermatid development / intracellular glucose homeostasis / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / negative regulation of apoptotic signaling pathway / ribosomal large subunit export from nucleus / U5 snRNA binding / sperm flagellum / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / nuclear pore / U1 snRNA binding / Neutrophil degranulation / protein export from nucleus / centriole / viral process / GTPase activator activity / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / mitochondrial membrane / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / glycolytic process / G1/S transition of mitotic cell cycle / kinetochore / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / glucose metabolic process / melanosome / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / midbody / ubiquitin-dependent protein catabolic process / 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
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / Exportin-1, C-terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / 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 / 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 / ATPase, nucleotide binding domain / 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 / Hexokinase-2 / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.342 Å
AuthorsFung, H.Y.J. / Chook, Y.M.
Funding support United States, Hong Kong, 7items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)International Student Research Fellowship United States
Croucher FoundationPredoc Research Scholarship Hong Kong
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Leukemia & Lymphoma SocietyScholar Award United States
Welch FoundationI-1532 United States
University of Texas Southwestern Medical CenterEndowed Scholars Program United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352, RP150053 United States
CitationJournal: Elife / Year: 2017
Title: Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals.
Authors: Fung, H.Y. / Fu, S.C. / Chook, Y.M.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,27110
Polymers163,3564
Non-polymers9156
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-64 kcal/mol
Surface area58080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.712, 106.712, 304.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1102-

GOL

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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: 26758.564 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 / Plasmid: pET15 / 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: 16521.867 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 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920
#3: Protein Exportin-1 / Karyopherin / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117400.672 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 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Hexokinase-2 /


Mass: 2675.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HXK2 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04807*PLUS

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Non-polymers , 4 types, 477 molecules

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


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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: isolated from a genetically manipulated source
Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 20 mM HCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 74959 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.042 / Net I/σ(I): 18.9
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3673 / CC1/2: 0.511 / Rpim(I) all: 0.519 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.342→47.723 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 1999 2.93 %
Rwork0.1869 --
obs0.1881 68195 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.342→47.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10962 0 24 471 11457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311253
X-RAY DIFFRACTIONf_angle_d0.46815230
X-RAY DIFFRACTIONf_dihedral_angle_d14.4946834
X-RAY DIFFRACTIONf_chiral_restr0.0371735
X-RAY DIFFRACTIONf_plane_restr0.0031933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3423-2.40090.2479520.24811714X-RAY DIFFRACTION34
2.4009-2.46580.2672850.23512829X-RAY DIFFRACTION55
2.4658-2.53830.29871310.22764343X-RAY DIFFRACTION85
2.5383-2.62020.28011510.22684980X-RAY DIFFRACTION98
2.6202-2.71390.28081550.22745130X-RAY DIFFRACTION100
2.7139-2.82250.26571550.21345137X-RAY DIFFRACTION100
2.8225-2.9510.25221560.20575151X-RAY DIFFRACTION100
2.951-3.10650.24421550.21425153X-RAY DIFFRACTION100
3.1065-3.30110.27591570.20335185X-RAY DIFFRACTION100
3.3011-3.55590.22461570.19325211X-RAY DIFFRACTION100
3.5559-3.91360.20351580.17265214X-RAY DIFFRACTION100
3.9136-4.47960.20981590.15155258X-RAY DIFFRACTION100
4.4796-5.64230.18111600.15085326X-RAY DIFFRACTION100
5.6423-47.73290.19581680.17825565X-RAY DIFFRACTION99
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)
10.0770.0586-0.07510.0417-0.05720.07160.10860.11190.0674-0.05920.1049-0.2371-0.23550.24260.39760.1454-0.1240.09410.3574-0.1910.42539.203748.805633.0103
20.0426-0.04990.00890.0586-0.01460.0051-0.00020.0159-0.03940.03930.0027-0.21570.02910.0961-0.08490.04570.0179-0.0130.3041-0.15750.41638.220137.376637.187
30.08650.0699-0.07330.0674-0.05610.0669-0.00660.0933-0.1218-0.0780.0464-0.08110.08240.00150.00470.09450.0327-0.05040.2442-0.10510.2591-4.399138.736837.2436
40.0209-0.04240.01860.1506-0.02670.02480.0998-0.04790.0567-0.1549-0.04340.0766-0.0475-0.0490.00450.1672-0.01020.02280.27-0.07390.1886-2.826350.474539.5197
50.0002-0.0075-0.00140.0315-0.00870.0374-0.07740.0586-0.00670.09490.22280.0161-0.11310.1383-0.00010.6133-0.21410.12670.5927-0.08320.47811.572468.91431.4138
60.00440.0045-0.00140.0033-0.00070.00490.04010.00260.0112-0.03560.0087-0.04070.03640.008500.6583-0.23060.29410.9546-0.19350.589319.287663.12284.7403
70.00320.0020.00370.00150.00210.00350.00870.0417-0.0131-0.04350.081-0.002-0.01670.069600.3998-0.0920.13610.4931-0.09830.54-0.763856.513711.3628
80.09950.00520.081-0.00340.00940.0580.0895-0.0783-0.20490.034-0.0058-0.1428-0.12910.21030.00820.4947-0.14190.17080.334-0.02680.50485.189471.347527.8734
90.0035-0.00420.02740.00160.00580.1355-0.05790.04150.04440.0026-0.0687-0.0147-0.26930.303-0.36190.697-0.36660.31940.4378-0.02230.45637.648369.235818.9585
100.0020.01280.00330.31190.10260.0333-0.05090.0061-0-0.15680.13820.1449-0.42260.31740.04350.602-0.27960.18610.4813-0.07160.52327.810471.483113.8184
110.3609-0.05580.08060.97760.39550.2352-0.0116-0.3842-0.10470.91170.2578-0.70160.4380.47240.85030.0880.1927-0.27630.4032-0.11580.53658.370825.59753.5239
120.4682-0.2697-0.04630.65640.2180.63970.0876-0.0278-0.00210.02830.0163-0.0408-0.2213-0.25930.46790.18890.03520.02720.3179-0.04910.1502-26.902155.56245.954
130.4841-0.25230.15480.46790.04340.73990.01610.09940.0422-0.14980.12280.0003-0.2842-0.15740.3970.29050.05390.07960.32530.03090.1725-21.700746.82433.0777
140.2008-0.1450.11360.1615-0.07030.37890.1111-0.0319-0.3501-0.09480.05440.13280.11760.04430.02360.18590.0253-0.0120.2325-0.05060.3524-6.827610.547720.6044
150.00130.0006-0.0010.0014-0.00150.00130.007-0.03980.0195-0.00440.03780.0034-0.0159-0.035200.80420.39670.09050.81770.11750.7101-38.855976.59327.3663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 138 )
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 169 )
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 190 )
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 205 )
7X-RAY DIFFRACTION7chain 'A' and (resid 206 through 216 )
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 100 )
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 200 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 268 )
12X-RAY DIFFRACTION12chain 'C' and (resid 269 through 590 )
13X-RAY DIFFRACTION13chain 'C' and (resid 591 through 897 )
14X-RAY DIFFRACTION14chain 'C' and (resid 898 through 1053 )
15X-RAY DIFFRACTION15chain 'D' and (resid 5 through 21 )

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