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- PDB-6x2m: Crystal Structure of unliganded CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 6x2m
TitleCrystal Structure of unliganded CRM1-Ran-RanBP1
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / Nuclear export / CRM1 / XPO1 / Exportin-1
Function / homology
Function and homology information


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 ...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 / GTP metabolic process / tRNA processing in the nucleus / 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 / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / U5 snRNA binding / spermatid development / viral process / U2 snRNA binding / U6 snRNA binding / positive regulation of protein binding / sperm flagellum / nuclear pore / mRNA export from nucleus / ribosomal subunit export from nucleus / U1 snRNA binding / ribosomal small subunit export from nucleus / centriole / GTPase activator activity / protein export from nucleus / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / recycling endosome / kinetochore / positive regulation of protein import into nucleus / small GTPase binding / protein import into nucleus / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / actin cytoskeleton organization / midbody / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / GTP binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.351 Å
AuthorsBaumhardt, J.M.
Funding support2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)
Welch Foundation
CitationJournal: Mol.Biol.Cell / Year: 2020
Title: Recognition of nuclear export signals by CRM1 carrying the oncogenic E571K mutation.
Authors: Baumhardt, J.M. / Walker, J.S. / Lee, Y. / Shakya, B. / Brautigam, C.A. / Lapalombella, R. / Grishin, N. / Chook, Y.M.
History
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,8586
Polymers158,2203
Non-polymers6393
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-42 kcal/mol
Surface area55670 Å2
Unit cell
Length a, b, c (Å)105.313, 105.313, 306.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 24456.105 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 / 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: 16320.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117442.812 Da / Num. of mol.: 1 / Mutation: 377-413 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Non-polymers , 4 types, 141 molecules

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


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17% (weight/vol) PEG3350, 100 mM Bis-Tris (pH 6.4), 200 mM ammonium nitrate, and 10 mM Spermine HCl

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→49.8 Å / Num. obs: 123060 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.59 / Net I/σ(I): 22.1
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 880 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hb2

4hb2


Resolution: 2.351→37.234 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 2941 3.34 %
Rwork0.2321 85005 -
obs0.2331 87946 64.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.58 Å2 / Biso mean: 34.6849 Å2 / Biso min: 1.27 Å2
Refinement stepCycle: final / Resolution: 2.351→37.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 0 138 10956
Biso mean---24.08 -
Num. residues----1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311314
X-RAY DIFFRACTIONf_angle_d0.52115358
X-RAY DIFFRACTIONf_chiral_restr0.0391752
X-RAY DIFFRACTIONf_plane_restr0.0031961
X-RAY DIFFRACTIONf_dihedral_angle_d14.866885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.351-2.38920.5177300.31688014
2.3892-2.43040.4361370.3177104117
2.4304-2.47460.3242400.339119619
2.4746-2.52220.3717480.3327135522
2.5222-2.57360.367560.3132170727
2.5736-2.62960.3336740.3177212034
2.6296-2.69070.3383900.3252271943
2.6907-2.7580.32161200.3271354856
2.758-2.83250.36771270.3223371859
2.8325-2.91590.33051460.3021394862
2.9159-3.00990.3311400.3056413966
3.0099-3.11750.31771500.3005440970
3.1175-3.24220.30321710.2855476476
3.2422-3.38970.29151950.257565489
3.3897-3.56830.3242140.2455623299
3.5683-3.79160.26042170.22636320100
3.7916-4.0840.26382150.2016258100
4.084-4.49440.21782190.18196305100
4.4944-5.14330.18512140.17946288100
5.1433-6.47450.23572230.219625199
6.4745-37.2340.18682150.1802615397
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)
10.3557-0.0396-0.09840.2056-0.15690.62560.06410.01370.21840.07040.101-0.135-0.22390.2220.0590.0822-0.00330.00890.3472-0.05180.194860.5886-5.921433.9521
20.40080.0997-0.00590.2012-0.06160.2927-0.0266-0.1217-0.0053-0.09030.1879-0.2064-0.18420.39190.00840.1937-0.032-0.01340.3248-0.05550.293763.0405-8.047734.4273
30.0030.0055-0.01410.1477-0.06310.031-0.1482-0.0994-0.1842-0.03280.0662-0.09790.12440.0356-0.06050.10340.02860.02060.1873-0.00370.275352.1189-18.571239.0472
40.2747-0.0692-0.25680.33850.14610.2143-0.11980.0575-0.0012-0.1049-0.05690.0679-0.0596-0.1967-0.00310.129-0.0414-0.02240.1741-0.03040.200947.2675-7.727536.8117
50.087-0.03920.02710.2877-0.21570.16360.03310.04940.20620.06110.19430.0294-0.43340.2140.19140.2819-0.19520.03410.3689-0.07060.333160.556710.282237.6419
60.00940.0060.00080.00850.00510.003-0.0508-0.0079-0.01960.0448-0.0343-0.0028-0.05520.0106-01.1189-0.06490.29361.386-0.08391.237175.918413.30884.8075
70.0185-0.01720.02130.0366-0.00290.0284-0.12150.03790.0915-0.1125-0.05230.201-0.07010.0747-00.5311-0.02710.01660.4847-0.14090.507357.06445.61559.1596
80.20390.10450.00320.1111-0.11120.15710.0641-0.10620.04540.1646-0.0029-0.1925-0.28810.3044-0.00280.6159-0.15570.10410.4186-0.07840.44260.588216.559221.454
90.09780.03-0.10160.19090.11940.1869-0.00550.14710.1291-0.39860.1771-0.031-0.62950.30510.10120.6707-0.28590.13020.3972-0.08470.428660.636917.617416.1693
100.77610.00980.40631.32640.20070.602-0.12-0.2304-0.21590.24590.1381-0.33590.14850.31750.00960.24490.1067-0.09070.41570.03860.388164.3449-27.828152.7687
111.4564-0.0705-0.32090.88110.67481.21950.0703-0.010.4014-0.1362-0.02120.0945-0.3576-0.26581.4606-0.19670.1366-0.2074-0.01290.1192-0.016426.1412.608837.4548
121.0082-0.2265-0.09120.66010.22040.6362-0.16710.2452-0.1552-0.23350.20810.0179-0.0817-0.13370.02630.3424-0.1244-0.00210.3576-0.02950.145337.2638-14.68472.2087
130.3591-0.29680.19940.4746-0.34230.44940.02490.3861-0.4488-0.43140.0270.0720.2851-0.04850.00010.2553-0.02970.03590.3534-0.07340.446548.3723-43.119921.7985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 31 )A9 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 91 )A32 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 111 )A92 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 158 )A112 - 158
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 189 )A159 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 199 )A190 - 199
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 216 )A200 - 216
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 121 )B78 - 121
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 200 )B122 - 200
10X-RAY DIFFRACTION10chain 'C' and (resid -1 through 245 )C-1 - 245
11X-RAY DIFFRACTION11chain 'C' and (resid 246 through 692 )C246 - 692
12X-RAY DIFFRACTION12chain 'C' and (resid 693 through 921 )C693 - 921
13X-RAY DIFFRACTION13chain 'C' and (resid 922 through 1052 )C922 - 1052

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