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- PDB-5uwp: Crystal Structure of mDia2 NES Peptide in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 5uwp
TitleCrystal Structure of mDia2 NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Protein diaphanous homolog 3
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


MAPK6/MAPK4 signaling / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / RHOF GTPase cycle ...MAPK6/MAPK4 signaling / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / RHOF GTPase cycle / spindle pole body / protein localization to kinetochore / RHOD GTPase cycle / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / RNA export from nucleus / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / NLS-bearing protein import into nucleus / dynein intermediate chain binding / DNA metabolic process / RHOB GTPase cycle / ribosomal subunit export from nucleus / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / CDC42 GTPase cycle / RHOG GTPase cycle / ribosomal large subunit export from nucleus / RHOA GTPase cycle / sperm flagellum / RAC2 GTPase cycle / RAC3 GTPase cycle / U5 snRNA binding / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / nuclear pore / U1 snRNA binding / cytoskeleton organization / RAC1 GTPase cycle / actin filament polymerization / centriole / protein export from nucleus / viral process / GTPase activator activity / mitotic spindle organization / G protein activity / male germ cell nucleus / RHO GTPases Activate Formins / actin filament / 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 / positive regulation of protein binding / mitotic cell cycle / nuclear envelope / actin binding / midbody / ubiquitin-dependent protein catabolic process / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain ...Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / 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 / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran / Protein diaphanous homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.054 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 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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: Protein diaphanous homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,5659
Polymers162,7434
Non-polymers8235
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-52 kcal/mol
Surface area57920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.183, 106.183, 303.321
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-1277-

HOH

21C-1777-

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 Protein diaphanous homolog 3


Mass: 2003.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIAPH3 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NSV4*PLUS

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Non-polymers , 4 types, 894 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.: 889 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
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, 8 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: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 108570 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Net I/σ(I): 23.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5319 / CC1/2: 0.668 / Rpim(I) all: 0.409 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.054→36.442 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 2000 1.89 %
Rwork0.1782 --
obs0.1788 105802 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.054→36.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10884 0 18 889 11791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311280
X-RAY DIFFRACTIONf_angle_d0.54715301
X-RAY DIFFRACTIONf_dihedral_angle_d14.6426860
X-RAY DIFFRACTIONf_chiral_restr0.0391744
X-RAY DIFFRACTIONf_plane_restr0.0031952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0545-2.10590.3196980.24835065X-RAY DIFFRACTION67
2.1059-2.16280.27751380.23017163X-RAY DIFFRACTION95
2.1628-2.22640.25761430.21697446X-RAY DIFFRACTION99
2.2264-2.29830.24891460.20217529X-RAY DIFFRACTION100
2.2983-2.38040.21771440.18987525X-RAY DIFFRACTION100
2.3804-2.47570.23311460.18297557X-RAY DIFFRACTION100
2.4757-2.58840.19491460.18287579X-RAY DIFFRACTION100
2.5884-2.72480.25461460.18467567X-RAY DIFFRACTION100
2.7248-2.89540.21921450.18657580X-RAY DIFFRACTION100
2.8954-3.11890.22411480.18527608X-RAY DIFFRACTION100
3.1189-3.43250.23251470.17777649X-RAY DIFFRACTION100
3.4325-3.92870.18561480.16197693X-RAY DIFFRACTION100
3.9287-4.94780.1561500.13867777X-RAY DIFFRACTION100
4.9478-36.44720.20931550.17988064X-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)
10.0108-0.03060.02080.256-0.10010.08690.14780.02270.0009-0.1624-0.0149-0.2347-0.11550.06540.05960.1421-0.07520.02390.2168-0.07530.2688.72645.409338.2093
20.52190.01610.27140.46730.15410.27580.08860.18490.0744-0.24810.0867-0.4704-0.45280.46910.05620.2635-0.12310.09220.2204-0.03420.28639.439849.698631.4864
30.01750.0344-0.03110.3685-0.24310.16140.07970.1018-0.11370.0528-0.0637-0.42710.07130.284-0.00980.1066-0.005-0.01750.2143-0.06020.32747.919137.202336.7878
40.24660.1-0.23740.3392-0.05310.23270.00690.0956-0.1762-0.1269-0.0044-0.00340.0365-0.0891-0.01250.1251-0.0033-0.02460.1683-0.05110.194-5.178239.720638.157
50.3508-0.1823-0.24110.11650.13880.25290.17020.10190.3357-0.1856-0.01180.049-0.61210.10480.0340.3327-0.05470.02460.1645-0.02930.22790.453256.557738.5242
60.0465-0.0782-0.010.13790.01810.00380.03960.04540.05550.05150.0174-0.1496-0.01140.05840.01060.6029-0.43510.02280.8325-0.02870.30919.413573.99619.9958
70.00620.0103-0.00750.0114-0.01330.01580.1170.00030.1196-0.14770.107-0.19350.0360.109900.5627-0.21630.1260.8226-0.10970.652918.932762.8894.4732
80.0125-0.00630.0160.0096-0.00640.0157-0.06580.05820.00520.02010.07260.0748-0.05350.073200.4043-0.09320.08910.4189-0.03210.6095-0.972356.29911.067
90.02180.03030.01040.0404-0.00290.01760.03020.04870.08410.1285-0.0399-0.0509-0.07980.085400.9172-0.3270.15150.81570.01310.83742.637282.162648.3834
100.1160.02850.07570.038-0.02660.1086-0.0474-0.11010.01250.18790.09370.003-0.22110.215700.4094-0.10530.06630.31660.01260.43296.58763.155517.0926
110.04330.031-0.04290.070.01930.185-0.146-0.0358-0.02480.0386-0.01740.0191-0.4010.2803-0.24230.7841-0.36450.170.2180.02510.42566.279973.152924.7362
120.16290.02240.06880.6020.3260.176-0.00580.1497-0.206-0.1754-0.0407-0.1423-0.63390.59770.03320.4127-0.26460.06290.37080.02870.36389.587667.020813.9153
130.0077-0.0603-0.03490.43970.28230.18140.02120.03950.1555-0.2727-0.21770.2167-0.44010.1746-0.02850.8383-0.205-0.04270.26240.05270.43373.577477.893710.8318
140.6817-0.27920.47711.52850.3640.8344-0.1127-0.1474-0.06430.54780.1848-0.55830.39590.54110.16460.01440.0949-0.1260.2916-0.05630.37029.876424.895452.8106
150.7036-0.3149-0.26410.90880.04482.17150.03960.0616-0.0053-0.02590.054-0.0378-0.2997-0.3890.33910.13490.03070.02090.1851-0.02350.1172-25.468452.456549.2903
160.28540.092-0.51060.3916-0.00131.73870.33830.2530.5133-0.12450.41140.2498-1.5705-1.11362.69640.61140.50010.10350.47020.20230.2322-33.77162.33979.6196
170.6597-0.60650.14340.7665-0.07981.04630.02350.12060.0197-0.04240.0843-0.0055-0.0761-0.05550.1510.0980.01010.01690.2602-0.01720.1464-15.984939.38010.7019
180.376-0.31750.3330.4973-0.32840.75160.0784-0.0503-0.3058-0.13370.04390.22520.1958-0.08340.00870.17060.0169-0.02280.2214-0.03690.2913-7.144610.239620.3201
190.025-0.0033-0.03070.05640.05870.0932-0.0838-0.0380.07830.0105-0.00640.0802-0.0678-0.0766-0.01861.32080.70960.02770.92140.13210.6556-40.765875.571528.1021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 148 )
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 179 )
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 190 )
7X-RAY DIFFRACTION7chain 'A' and (resid 191 through 205 )
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 216 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 106 )
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 133 )
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 180 )
13X-RAY DIFFRACTION13chain 'B' and (resid 181 through 200 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 245 )
15X-RAY DIFFRACTION15chain 'C' and (resid 246 through 569 )
16X-RAY DIFFRACTION16chain 'C' and (resid 570 through 692 )
17X-RAY DIFFRACTION17chain 'C' and (resid 693 through 897 )
18X-RAY DIFFRACTION18chain 'C' and (resid 898 through 1053 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1183 through 1193 )

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