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- PDB-6cit: Crystal Structure of MVM NS2 NES Peptide in complex with CRM1-Ran... -

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Basic information

Entry
Database: PDB / ID: 6cit
TitleCrystal Structure of MVM NS2 NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • NS2
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / Karyopherin / CRM1 / XPO1 / Exportin-1 / MVM / NES / Nuclear Export
Function / homology
Function and homology information


exit of virus from host cell nucleus through nuclear pore / MAPK6/MAPK4 signaling / RNA nuclear export complex / 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 ...exit of virus from host cell nucleus through nuclear pore / MAPK6/MAPK4 signaling / RNA nuclear export complex / 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 / U4 snRNA binding / RNA export from nucleus / spindle pole body / protein localization to kinetochore / nuclear export / 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 / 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 / U5 snRNA binding / sperm flagellum / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / nuclear pore / U1 snRNA binding / protein export from nucleus / centriole / 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 / 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 / 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 / host cell nucleus / chromatin binding / chromatin / GTP binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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 / 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 / Non-structural protein NS2 / 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)
Minute virus of mice
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.027 Å
AuthorsFung, H.Y.J. / Chook, Y.M.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)International Student Research Fellowship United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP150053, RP170170 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Welch FoundationI-1532 United States
University of Texas Southwestern Medical CenterEndowed Scholars Program United States
CitationJournal: Mol. Biol. Cell / Year: 2018
Title: Correlation of CRM1-NES affinity with nuclear export activity.
Authors: Fu, S.C. / Fung, H.Y.J. / Cagatay, T. / Baumhardt, J. / Chook, Y.M.
History
DepositionFeb 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 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

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: NS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,16413
Polymers163,0304
Non-polymers1,1359
Water15,619867
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Coelutes in size-exclusion
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-65 kcal/mol
Surface area58080 Å2
Unit cell
Length a, b, c (Å)106.570, 106.570, 304.079
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-1104-

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: 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 NS2


Mass: 2290.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Minute virus of mice / Gene: NS2 / Plasmid: pMAL-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DJZ2*PLUS

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Non-polymers , 5 types, 876 molecules

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


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 53.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 17% PEG3350, 100 MM Bis-Tris, pH 6.4, 200 mM ammonium nitrate

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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 13, 2016
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.027→50 Å / Num. obs: 114290 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Net I/σ(I): 31.4
Reflection shellResolution: 2.027→2.07 Å / Redundancy: 9 % / Rmerge(I) obs: 1.327 / Num. unique obs: 5641 / CC1/2: 0.591 / Rpim(I) all: 0.46 / % possible all: 100

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Processing

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

4hb2


Resolution: 2.027→40.226 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2000 1.83 %Random
Rwork0.1881 ---
obs0.1885 109505 95.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.027→40.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10891 0 70 867 11828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211394
X-RAY DIFFRACTIONf_angle_d0.50415447
X-RAY DIFFRACTIONf_dihedral_angle_d13.8926928
X-RAY DIFFRACTIONf_chiral_restr0.0381759
X-RAY DIFFRACTIONf_plane_restr0.0031968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0273-2.0780.2862800.26824337X-RAY DIFFRACTION55
2.078-2.13410.31251300.24766972X-RAY DIFFRACTION88
2.1341-2.19690.23821450.23217746X-RAY DIFFRACTION98
2.1969-2.26780.24421470.227914X-RAY DIFFRACTION100
2.2678-2.34890.24841460.20537877X-RAY DIFFRACTION100
2.3489-2.44290.24761480.20457942X-RAY DIFFRACTION100
2.4429-2.55410.22241480.20197950X-RAY DIFFRACTION100
2.5541-2.68870.22521480.19427953X-RAY DIFFRACTION100
2.6887-2.85710.19891480.19137974X-RAY DIFFRACTION100
2.8571-3.07760.22321490.18958003X-RAY DIFFRACTION100
3.0776-3.38720.22061490.188033X-RAY DIFFRACTION100
3.3872-3.8770.2011500.16898084X-RAY DIFFRACTION100
3.877-4.88330.14481530.15218197X-RAY DIFFRACTION100
4.8833-40.23430.23091590.18688523X-RAY DIFFRACTION100
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)
11.1178-0.6757-0.32960.981-0.50940.98720.06950.21140.0483-0.06680.0042-0.4694-0.25570.3441-0.0370.1519-0.07610.07190.3476-0.13890.45319.152648.514533.111
21.5755-0.6582-0.03570.4881-0.24410.31190.03180.0681-0.36460.03290.0313-0.29670.12280.244-0.06760.04430.0312-0.05370.3106-0.13950.50237.972237.116537.3455
32.233-0.6835-0.56483.2828-1.00341.96480.00760.1148-0.3006-0.20190.0717-0.12580.1244-0.1413-0.07470.07660.0161-0.00590.1902-0.09120.2495-3.526938.608436.5626
41.63740.3763-0.8372.8042-2.0183.76650.03910.09970.0853-0.18790.06720.1236-0.0329-0.1509-0.07860.10570.0332-0.02550.1947-0.0720.1612-7.003646.422537.6399
52.81491.1947-0.67887.63991.64351.86160.0191-0.22960.28390.239-0.0214-0.1233-0.45730.06640.00260.1546-0.025-0.00850.2391-0.08440.21751.914354.312443.8548
60.2028-0.09070.03620.3789-0.17610.08120.04550.19380.011-0.17070.1684-0.1996-0.56240.7227-0.13070.5236-0.22570.1670.7201-0.14650.506610.629263.368818.3322
70.6097-0.0328-1.46930.09590.75078.30050.1898-0.02760.2281-0.22320.2113-0.273-0.580.4566-0.39190.9882-0.08840.08860.70960.08890.71542.140982.157351.0931
83.5949-0.7042-0.01995.61630.57753.4533-0.07080.1583-0.24690.03090.0396-0.1212-0.21060.55030.02660.356-0.15080.16940.4669-0.02760.44037.333862.757417.4211
92.21410.47810.52043.4204-1.0520.5903-0.0904-0.02390.32970.1257-0.03220.067-0.58410.41450.15940.6569-0.27160.20150.4157-0.05460.4546.710473.08625.1432
103.05192.43240.18542.76410.41130.2911-0.08560.0250.231-0.2310.05110.0075-0.74450.64490.09290.6391-0.29590.15850.5391-0.03810.4178.355970.541113.2406
110.5133-0.06250.16280.89470.29590.2208-0.0146-0.2603-0.06770.87750.1701-0.82740.33280.29030.07380.16530.1977-0.34750.3066-0.08240.6417.903725.523453.6369
120.8956-0.37640.49751.0014-0.13262.09340.0468-0.00320.0640.03190.0192-0.0114-0.2481-0.2795-0.04980.16280.0410.01210.2821-0.07540.086-26.47954.405148.5088
130.7708-0.31120.20521.10350.15131.73030.1020.00840.2836-0.15620.1495-0.0897-0.703-0.31390.20130.52790.22510.08760.41390.12020.142-33.239762.83529.7357
141.9804-0.6435-0.49551.22540.00910.9714-0.00540.29160.0499-0.23380.1599-0.0699-0.2391-0.0586-0.14910.25750.02220.0670.3039-0.01770.1299-18.510147.8065-1.9797
150.5971-0.68140.64540.9946-1.05431.59490.16050.1062-0.3453-0.13720.06540.2720.1610.0409-0.17390.15730.01830.02290.2261-0.08510.301-8.953717.397414.627
167.0134.685-0.09646.2483-1.30832.72120.1648-0.19950.77750.09530.01380.3577-0.3793-0.1016-0.18250.77490.34910.06390.4835-0.00580.4038-38.157876.44428.9136
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 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 158 )
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 169 )
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 216 )
7X-RAY DIFFRACTION7chain 'B' and (resid 63 through 82 )
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 107 through 133 )
10X-RAY DIFFRACTION10chain 'B' and (resid 134 through 201 )
11X-RAY DIFFRACTION11chain 'C' and (resid -1 through 268 )
12X-RAY DIFFRACTION12chain 'C' and (resid 269 through 569 )
13X-RAY DIFFRACTION13chain 'C' and (resid 570 through 692 )
14X-RAY DIFFRACTION14chain 'C' and (resid 693 through 808 )
15X-RAY DIFFRACTION15chain 'C' and (resid 809 through 1053 )
16X-RAY DIFFRACTION16chain 'D' and (resid 77 through 93 )

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