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- PDB-5uwh: Crystal Structure of Paxillin NES Peptide in complex with CRM1-Ra... -

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Basic information

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


Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / MAPK6/MAPK4 signaling / RNA nuclear export complex / vinculin binding / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / MAPK6/MAPK4 signaling / RNA nuclear export complex / vinculin binding / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / neuropilin binding / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / U4 snRNA binding / spindle pole body / RNA export from nucleus / protein localization to kinetochore / nuclear export / signal complex assembly / 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 / microtubule associated complex / nuclear import signal receptor activity / growth hormone receptor signaling pathway / DNA metabolic process / NLS-bearing protein import into nucleus / dynein intermediate chain binding / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / Smooth Muscle Contraction / endothelial cell migration / U5 snRNA binding / sperm flagellum / GAB1 signalosome / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / nuclear pore / stress fiber / U1 snRNA binding / positive regulation of stress fiber assembly / protein export from nucleus / centriole / viral process / GTPase activator activity / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / kinetochore / recycling endosome / small GTPase binding / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / cell-cell junction / cell migration / mitotic cell cycle / lamellipodium / nuclear envelope / cell cortex / positive regulation of protein binding / midbody / ubiquitin-dependent protein catabolic process / actin cytoskeleton organization / protein phosphatase binding / cell adhesion / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / focal adhesion / GTPase activity / chromatin binding / chromatin / GTP binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / signal transduction / protein-containing complex
Similarity search - Function
Paxillin / : / : / Paxillin family / 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 ...Paxillin / : / : / Paxillin family / 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 / LIM zinc-binding domain signature. / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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 / Paxillin / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award 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 / Category: pdbx_audit_support / 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 1.5Oct 4, 2023Group: 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
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: Paxillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,0609
Polymers163,2374
Non-polymers8235
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-60 kcal/mol
Surface area57760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.984, 106.984, 304.880
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-1554-

HOH

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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: 117458.781 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 Paxillin /


Mass: 2497.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PXN / Plasmid: pMAL-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49023*PLUS

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Non-polymers , 4 types, 500 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 16% 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: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 77349 / % possible obs: 91.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.8919033835 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Net I/σ(I): 22.8
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 7 % / Num. unique all: 3826 / Num. unique obs: 3826 / CC1/2: 0.621 / Rpim(I) all: 0.461 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HB2

4hb2


Resolution: 2.26→47.266 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72
RfactorNum. reflection% reflection
Rfree0.2182 2000 2.67 %
Rwork0.1821 --
obs0.1831 74848 88.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→47.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10903 0 18 495 11416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311347
X-RAY DIFFRACTIONf_angle_d0.55415387
X-RAY DIFFRACTIONf_dihedral_angle_d14.786897
X-RAY DIFFRACTIONf_chiral_restr0.0391752
X-RAY DIFFRACTIONf_plane_restr0.0031960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2564-2.31280.29851140.24744149X-RAY DIFFRACTION72
2.3128-2.37530.26991320.22674798X-RAY DIFFRACTION83
2.3753-2.44520.29791390.22215066X-RAY DIFFRACTION88
2.4452-2.52420.24461430.2145203X-RAY DIFFRACTION90
2.5242-2.61440.29651450.19955288X-RAY DIFFRACTION92
2.6144-2.7190.26881460.19465329X-RAY DIFFRACTION92
2.719-2.84280.22711470.19335377X-RAY DIFFRACTION92
2.8428-2.99260.23731470.19915328X-RAY DIFFRACTION92
2.9926-3.18010.25471470.18965362X-RAY DIFFRACTION92
3.1801-3.42550.21751480.18475368X-RAY DIFFRACTION92
3.4255-3.77010.2031470.17535382X-RAY DIFFRACTION92
3.7701-4.31540.18781480.15455403X-RAY DIFFRACTION91
4.3154-5.43560.17871480.14665392X-RAY DIFFRACTION90
5.4356-47.27660.18371490.18025403X-RAY DIFFRACTION86
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)
11.0012-0.8415-0.21992.42860.21612.25480.0310.3186-0.1133-0.43960.1313-0.6772-0.25070.3882-0.15860.2557-0.07930.1340.4309-0.14790.43517.577545.817930.0291
21.0104-1.4228-0.36454.590.6062.34780.25480.06170.12530.06030.1291-1.0588-0.55510.5139-0.40090.2939-0.11450.10620.3867-0.17540.620911.919253.205638.3094
32.0974-0.53990.00220.8015-0.56730.48720.09690.1092-0.28640.01210.0562-0.62570.13610.2842-0.03130.1859-0.0022-0.02390.3817-0.16930.58248.282337.360537.3937
41.6905-1.10390.61313.3978-1.84644.39130.10110.0479-0.2717-0.10290.0139-0.17760.37720.098-0.1070.13230.0287-0.02080.2697-0.09940.3239-1.404234.238638.8875
53.0919-0.29170.79633.4107-0.56174.5606-0.1513-0.3355-0.06820.49690.1037-0.1988-0.13350.1003-0.03660.19670.0252-0.0230.3122-0.11450.33271.679143.58644.1318
61.75930.734-0.61622.4483-0.56364.45540.10120.19580.0442-0.28-0.03050.29830.0262-0.7598-0.20480.18790.0398-0.06830.3375-0.08210.2583-11.160641.642334.351
71.79790.07440.06932.4497-0.05922.36220.1173-0.01750.121-0.12590.036-0.2054-0.33110.0146-0.10290.19210.00040.01760.2865-0.08010.2457-1.715352.162138.4428
82.09871.4406-2.65381.0603-1.88363.40540.5278-0.05010.61070.00520.15890.1508-1.1231.2709-0.42810.5859-0.29580.14380.7466-0.13350.602610.268868.011934.0755
97.60032.4712-0.52453.0946-1.57882.22220.28930.20360.4973-0.19590.3288-0.2164-0.5890.8811-0.36570.5696-0.21170.25240.7594-0.24870.60539.175559.51147.8664
100.0825-0.0416-0.32370.00790.18082.13120.0947-0.16520.11560.03890.1484-0.2498-0.73240.7599-0.22750.7883-0.17890.29920.6077-0.05150.664.152673.254930.4305
110.84080.95680.68031.36910.51870.87880.02850.16240.1648-0.1450.1240.088-0.77590.7315-0.04260.7511-0.25020.32020.5527-0.04840.55628.127669.49416.8457
120.9726-0.00070.09731.62270.57170.5368-0.0586-0.1914-0.05910.9070.3338-0.97080.49770.3697-0.0920.25670.1734-0.36930.4525-0.16030.718210.130825.052153.298
132.224-0.5510.81381.8918-0.13931.93760.05760.0116-0.03410.15210.0155-0.02020.13630.0088-0.08110.2178-0.02040.00650.3017-0.08370.1317-21.595145.929754.6673
140.7534-0.1735-0.65860.73250.54091.99020.21380.05690.2286-0.2363-0.0058-0.125-0.5314-0.1679-0.11290.35270.07080.06420.32070.040.2536-28.228258.893513.7361
150.9401-0.78180.8171.1656-1.3632.15570.14110.1015-0.2786-0.12490.06870.13290.08550.0384-0.14150.22130.01570.02250.2654-0.08940.2994-8.641717.520714.745
169.09382.0588-3.12224.4197-1.0614.20760.18-0.02480.32190.14-0.04960.2854-0.3259-0.042-0.10441.07240.25880.30120.56690.0150.8026-39.333376.330728.696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 142 )
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 169 )
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 193 )
9X-RAY DIFFRACTION9chain 'A' and (resid 194 through 216 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 97 )
11X-RAY DIFFRACTION11chain 'B' and (resid 98 through 198 )
12X-RAY DIFFRACTION12chain 'C' and (resid -1 through 245 )
13X-RAY DIFFRACTION13chain 'C' and (resid 246 through 478 )
14X-RAY DIFFRACTION14chain 'C' and (resid 479 through 808 )
15X-RAY DIFFRACTION15chain 'C' and (resid 809 through 1053 )
16X-RAY DIFFRACTION16chain 'D' and (resid 265 through 278 )

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