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- PDB-6x2o: Crystal Structure of unliganded CRM1(E571K)-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 6x2o
TitleCrystal Structure of unliganded CRM1(E571K)-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


positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / spindle pole body / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / ribosomal subunit export from nucleus / nuclear pore / U1 snRNA binding / centriole / protein export from nucleus / 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 / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / G1/S transition of mitotic cell cycle / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / 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 / cytoplasm / cytosol
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 / 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: 2.551 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,7665
Polymers158,2203
Non-polymers5472
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.293, 105.293, 306.480
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)
Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117442.875 Da / Num. of mol.: 1 / Mutation: E582K
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 , 3 types, 298 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 273 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: 2.55→50 Å / Num. obs: 57265 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.078 / Rrim(I) all: 0.209 / Χ2: 0.982 / Net I/σ(I): 3.9 / Num. measured all: 409472
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.597.51.74228020.5390.6821.8730.7899.9
2.59-2.647.41.54328320.5780.6061.6610.809100
2.64-2.697.31.26928010.5790.5061.3691.189100
2.69-2.757.31.18528000.6860.4711.2770.809100
2.75-2.817.21.01728160.7240.4051.0960.845100
2.81-2.8770.81428240.8150.3290.880.802100
2.87-2.946.40.69428140.8370.2940.7550.80799.8
2.94-3.027.20.61328240.880.2440.6610.804100
3.02-3.117.50.48928340.9320.1910.5260.83100
3.11-3.217.50.43728280.9360.1710.470.847100
3.21-3.337.40.34728300.9490.1370.3740.98799.9
3.33-3.467.30.29328290.9610.1160.3151.21999.8
3.46-3.627.30.20228730.9840.080.2180.942100
3.62-3.816.70.18328430.9850.0750.1981.33999.9
3.81-4.0570.14828790.9860.060.161.44599.8
4.05-4.367.50.09428840.9950.0360.1011.001100
4.36-4.87.30.07729060.9960.030.0830.995100
4.8-5.4970.07129120.9960.0290.0770.84199.8
5.49-6.926.90.0729690.9960.0280.0750.74299.8
6.92-506.50.0431650.9930.0170.0431.64399.3

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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
Resolution: 2.551→43.391 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1999 3.76 %
Rwork0.2211 51152 -
obs0.2224 53151 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 355.54 Å2 / Biso mean: 46.1521 Å2 / Biso min: 15.15 Å2
Refinement stepCycle: final / Resolution: 2.551→43.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10827 0 0 296 11123
Biso mean---32.65 -
Num. residues----1344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411234
X-RAY DIFFRACTIONf_angle_d0.5615236
X-RAY DIFFRACTIONf_chiral_restr0.0421737
X-RAY DIFFRACTIONf_plane_restr0.0041941
X-RAY DIFFRACTIONf_dihedral_angle_d14.3666823
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.551-2.61430.2839760.2821195850
2.6143-2.6850.36541040.2941265169
2.685-2.7640.36281340.2922340988
2.764-2.85320.32951430.2698366095
2.8532-2.95510.30851470.2823380098
2.9551-3.07340.30541520.26883870100
3.0734-3.21330.27021530.25663895100
3.2133-3.38260.26651520.23893918100
3.3826-3.59440.29821520.23593883100
3.5944-3.87180.2191540.21243934100
3.8718-4.26110.21291550.18593950100
4.2611-4.8770.20391550.1693969100
4.877-6.14180.20921570.20674029100
6.1418-43.3910.24741650.195422699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.46490.07210.09540.24520.23410.2079-0.0157-0.0058-0.0519-0.15850.14840.22740.2857-0.3182-0.00010.3033-0.0381-0.00680.41580.05160.339-9.8881-48.9008339.5469
20.1362-0.04920.01510.09950.05410.03480.0683-0.04150.2462-0.0115-0.0160.2041-0.1011-0.16830.00010.24430.0119-0.00120.3440.03910.4275-9.4629-37.2019343.8071
30.0375-0.0806-0.02030.16710.04930.0147-0.0783-0.21770.1914-0.0946-0.0657-0.0244-0.34770.0628-0.00290.23670.03540.00150.35-0.01450.36490.5662-34.1138345.3822
40.2931-0.15110.22260.164-0.1290.186-0.0831-0.0643-0.13250.03320.0179-0.09780.09290.2402-0.11980.1756-0.0210.01850.24730.02710.25775.4074-44.9457343.2955
50.2474-0.3445-0.11510.49860.16740.04660.0503-0.00290.02770.22570.17580.05550.4032-0.25620.18060.379-0.1545-0.04090.53850.08640.3599-7.7978-63.015344.0491
60.0109-0.00220.00150.0095-0.00680.0044-0.10180.02280.11620.0692-0.0705-0.10910.13210.0334-01.069-0.2586-0.2711.69230.08751.1817-23.1017-65.9879311.3625
70.0553-0.0109-0.06370.1126-0.01340.0746-0.1422-0.0733-0.1882-0.1771-0.0209-0.42390.1089-0.01460.00170.6361-0.0679-0.06340.59950.13950.4657-4.2922-58.2618315.6165
80.12630.076-0.07070.14850.09120.1910.0027-0.3532-0.05610.11740.19210.0920.3211-0.2667-0.00020.7451-0.0975-0.09370.53490.09530.5516-5.8932-70.4107329.3242
90.54950.04480.11860.36-0.0460.3083-0.01830.00350.1433-0.41790.150.02660.5428-0.39720.04050.6569-0.1628-0.1130.48520.0730.4867-9.1931-67.817324.9355
100.03370.03720.01020.04180.00420.01460.3540.2078-0.1561-0.43460.0129-0.11610.66460.36770.00290.9987-0.143-0.0670.6207-0.06970.5965-4.3817-78.2746318.2845
111.1908-0.34060.11820.6466-0.25710.4507-0.0312-0.19790.02820.10280.05410.0781-0.034-0.11540.00010.273-0.00610.03590.3757-0.01630.31613.868-36.5507358.9947
120.06780.0775-0.24030.1733-0.13360.6326-0.04630.0418-0.215-0.2132-0.0021-0.12970.4130.40480.13420.53290.16560.07240.5882-0.09930.443333.614-63.0496324.3487
130.3918-0.147-0.24970.70620.44540.8247-0.04390.1450.1641-0.19420.1446-0.02440.070.074200.4073-0.0614-0.03210.46510.04680.37311.4709-27.8201315.7026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 66 )A9 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 91 )A67 - 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 97 )B78 - 97
9X-RAY DIFFRACTION9chain 'B' and (resid 98 through 180 )B98 - 180
10X-RAY DIFFRACTION10chain 'B' and (resid 181 through 200 )B181 - 200
11X-RAY DIFFRACTION11chain 'C' and (resid -1 through 514 )C-1 - 514
12X-RAY DIFFRACTION12chain 'C' and (resid 515 through 692 )C515 - 692
13X-RAY DIFFRACTION13chain 'C' and (resid 693 through 1052 )C693 - 1052

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