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- PDB-5uww: Crystal Structure of DEAF1 Peptide in complex with CRM1 K579A mut... -

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Basic information

Entry
Database: PDB / ID: 5uww
TitleCrystal Structure of DEAF1 Peptide in complex with CRM1 K579A mutant-Ran-RanBP1
Components
  • Deformed epidermal autoregulatory factor 1 homolog
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


regulation of mammary gland epithelial cell proliferation / embryonic skeletal system development / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity ...regulation of mammary gland epithelial cell proliferation / embryonic skeletal system development / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / importin-alpha family protein binding / SUMOylation of SUMOylation proteins / protein localization to kinetochore / spindle pole body / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / U4 snRNA binding / nuclear export / SUMOylation of RNA binding proteins / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / MAPK6/MAPK4 signaling / dynein intermediate chain binding / germ cell development / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / U5 snRNA binding / anatomical structure morphogenesis / spermatid development / viral process / U2 snRNA binding / U6 snRNA binding / positive regulation of protein binding / sperm flagellum / nuclear pore / behavioral fear response / mRNA export from nucleus / U1 snRNA binding / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / centriole / GTPase activator activity / protein export from nucleus / mitotic spindle organization / male germ cell nucleus / neural tube closure / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / recycling endosome / visual learning / kinetochore / positive regulation of protein import into nucleus / small GTPase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / fibrillar center / protein import into nucleus / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / negative regulation of DNA-templated transcription / GTPase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / GTP binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding
Similarity search - Function
Transcription factor DEAF-1 / Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal ...Transcription factor DEAF-1 / Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / SAND domain / SAND domain / SAND domain profile. / SAND domain / Ran binding protein RanBP1-like / SAND-like domain superfamily / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / 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 / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Deformed epidermal autoregulatory factor 1 homolog / 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: 2.152 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 / 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 / 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

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: Deformed epidermal autoregulatory factor 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,8449
Polymers163,0224
Non-polymers8235
Water12,971720
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-53 kcal/mol
Surface area57520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.043, 106.043, 304.207
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-1704-

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 / 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 Deformed epidermal autoregulatory factor 1 homolog


Mass: 2340.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEAF1 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75398*PLUS

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Non-polymers , 4 types, 725 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 720 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
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, 16 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: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 95096 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.025 / Net I/σ(I): 32.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4653 / CC1/2: 0.526 / Rpim(I) all: 0.543 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.152→40.241 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 2000 2.28 %
Rwork0.1856 --
obs0.1865 87729 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.152→40.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10929 0 18 720 11667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211327
X-RAY DIFFRACTIONf_angle_d0.51515353
X-RAY DIFFRACTIONf_dihedral_angle_d14.9446887
X-RAY DIFFRACTIONf_chiral_restr0.0381748
X-RAY DIFFRACTIONf_plane_restr0.0031958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1516-2.20540.352450.25861957X-RAY DIFFRACTION30
2.2054-2.2650.2851010.24114304X-RAY DIFFRACTION66
2.265-2.33160.25311460.22326275X-RAY DIFFRACTION96
2.3316-2.40690.25151530.21466509X-RAY DIFFRACTION99
2.4069-2.49290.24121510.20446525X-RAY DIFFRACTION100
2.4929-2.59270.25641540.1996575X-RAY DIFFRACTION100
2.5927-2.71070.23511520.19776552X-RAY DIFFRACTION100
2.7107-2.85350.23481540.19246596X-RAY DIFFRACTION100
2.8535-3.03230.25131540.1946598X-RAY DIFFRACTION100
3.0323-3.26630.2041550.19266618X-RAY DIFFRACTION100
3.2663-3.59480.22611540.17796654X-RAY DIFFRACTION100
3.5948-4.11450.19731570.1616697X-RAY DIFFRACTION100
4.1145-5.18210.18781580.14746775X-RAY DIFFRACTION100
5.1821-40.24820.23381660.19117094X-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)
10.0280.0271-0.01020.0232-0.00920.0010.0590.014-0.02-0.01140.0242-0.1587-0.11330.11410.11480.0447-0.1870.070.1593-0.14020.30939.096348.415833.0789
20.0481-0.03130.01540.0207-0.01160.0072-0.0176-0.0217-0.02180.0157-0.0115-0.13360.0160.089-0.0695-0.02910.0168-0.03280.1835-0.08590.3258.027337.042337.1236
30.03170.0234-0.01970.029-0.0070.0124-0.03320.0169-0.0533-0.02950.0046-0.03230.0208-0.0155-0.0859-0.0354-0.0111-0.09280.1178-0.06490.2046-3.374538.39136.8091
40.0117-0.0245-0.02050.05840.05120.0450.0335-0.0097-0.0045-0.08980.00630.0225-0.0213-0.0524-0.0010.084-0.0082-0.01080.1565-0.02960.1231-7.015646.32237.6601
50.0203-0.01110.01150.0536-0.03110.02040.03110.07030.0505-0.02320.1089-0.026-0.1320.09560.01960.2323-0.11710.04550.1911-0.05020.16526.810962.373837.8827
60.0037-0.0064-0.00190.0122-0.00080.0024-0.00930.0253-0.0045-0.01110.02040.0224-0.0070.0600.3885-0.13230.14410.4348-0.05650.479810.664160.03467.5532
70.00820.01180.00050.0120.00030.00290.0313-0.01690.00540.02550.00980.0289-0.00010.007300.869-0.13480.00510.8059-0.03640.77732.438782.266550.1062
80.0060.0024-0.00680.0029-0.0080.04680.0024-0.0053-0.01380.0294-0.0378-0.0165-0.13150.1071-0.04790.5331-0.27560.22610.2347-0.03310.4267.202868.289921.5171
90.0050.00060.00840.00220.00630.02380.00420.01130.0582-0.0686-0.0068-0.0428-0.240.16940.00350.507-0.2550.18080.2341-0.02270.38787.797970.689212.462
100.0650.04060.00060.59730.24350.3442-0.0151-0.1769-0.16940.53160.259-0.86650.2060.6130.7044-0.08830.267-0.30060.19720.04790.37788.115925.419153.5275
110.3303-0.0031-0.11190.32280.1350.48390.11340.03840.08040.06660.0196-0.0069-0.2269-0.23270.57510.12480.00980.00510.2022-0.04170.0368-25.966154.216847.8721
120.1875-0.1040.06370.20910.04490.183-0.0537-0.01320.1124-0.06680.19660.0335-0.4724-0.30670.39160.23150.20110.1490.37760.03770.1045-26.288755.46054.3213
130.3728-0.20830.12610.1474-0.17790.3060.09240.0893-0.2567-0.08020.0610.18150.08140.04530.10070.1610.01480.01110.1845-0.05110.2369-8.84117.190414.5091
140.0001-0.00010.00020.0004-00.0004-0.00350.00280.0085-0.00860.0010.00540.00220.0066-00.95360.13960.01190.89630.02130.8963-38.978676.164826.8193
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 190 )
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 216 )
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 82 )
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 139 )
9X-RAY DIFFRACTION9chain 'B' and (resid 140 through 201 )
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 268 )
11X-RAY DIFFRACTION11chain 'C' and (resid 269 through 569 )
12X-RAY DIFFRACTION12chain 'C' and (resid 570 through 808 )
13X-RAY DIFFRACTION13chain 'C' and (resid 809 through 1052 )
14X-RAY DIFFRACTION14chain 'D' and (resid 459 through 464 )

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