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- PDB-8itv: KL2.1 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 8itv
TitleKL2.1 in complex with CRM1-Ran-RanBP1
Components
  • CRM1 isoform 1
  • GTP-binding nuclear protein Ran
  • YRB1 isoform 1
KeywordsTRANSPORT PROTEIN / nuclear export inhibitor
Function / homology
Function and homology information


positive regulation of mitotic centrosome separation / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / import into nucleus / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein ...positive regulation of mitotic centrosome separation / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / import into nucleus / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NLS-bearing protein import into nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / viral process / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / centriole / GTPase activator activity / protein export from nucleus / mitotic spindle organization / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / nuclear envelope / melanosome / positive regulation of protein binding / mitotic cell cycle / G protein activity / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / cell division / GTPase activity / chromatin binding / nucleolus / GTP binding / chromatin / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
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 / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-TRIPHOSPHATE / NITRATE ION / : / YRB1 isoform 1 / CRM1 isoform 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: 2.3 Å
AuthorsSun, Q. / Jian, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: KL2.1 in complex with CRM1-Ran-RanBP1
Authors: Sun, Q. / Jian, L.
History
DepositionMar 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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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: YRB1 isoform 1
C: CRM1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,10936
Polymers155,9443
Non-polymers3,16433
Water12,250680
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.014, 106.014, 305.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 24399.055 Da / Num. of mol.: 1 / Mutation: Q69L, L182A
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 (E. coli) / References: UniProt: P62826
#2: Protein YRB1 isoform 1


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, GI526_G0000915 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PZB5
#3: Protein CRM1 isoform 1 / HLJ1_G0022020.mRNA.1.CDS.1 / Y55_G0022260.mRNA.1.CDS.1


Mass: 115224.461 Da / Num. of mol.: 1
Mutation: S27E , Q49E, A51V, del377-413, del441-461, D537G, T539C, V540E, K541Q, S553R, Q561E, A741T, Y1022C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, GI526_G0002640, PACBIOSEQ_LOCUS2878, PACBIOSEQ_LOCUS3002
Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PZI8

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Non-polymers , 9 types, 713 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: NO3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical ChemComp-Q73 / (3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoic acid


Mass: 490.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H46N2O5 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and ...Details: 0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 78260 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 0.997 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.80.56736470.2880.6690.310.6510.81595.4
2.34-2.384.30.55537880.3880.7480.2860.6280.84398.2
2.38-2.434.90.53838340.4820.8070.2580.5990.87199.4
2.43-2.485.70.52138420.5920.8620.230.5710.90799.6
2.48-2.536.90.48938950.750.9260.1960.5280.95499.9
2.53-2.598.50.47238690.8260.9510.1680.5020.9999.9
2.59-2.669.50.44138760.8770.9670.1470.4661.031100
2.66-2.7310.90.40238890.9080.9760.1240.4211.05299.9
2.73-2.8111.40.36738390.930.9820.110.3831.062100
2.81-2.911.50.32838980.950.9870.0990.3431.086100
2.9-311.30.28639180.9640.9910.0870.2991.07899.9
3-3.12120.24539030.9770.9940.0720.2561.05999.9
3.12-3.2611.90.20638830.9830.9960.0610.2151.04699.9
3.26-3.4412.40.17539350.9890.9970.0510.1821.058100
3.44-3.65120.14539500.9920.9980.0430.1511.026100
3.65-3.9312.40.12139290.9940.9990.0350.126199.9
3.93-4.3312.70.10439710.9950.9990.030.1080.975100
4.33-4.9512.50.09440010.9960.9990.0270.0980.964100
4.95-6.2412.40.140900.9950.9990.0290.1040.94999.9
6.24-5011.40.07443030.9970.9990.0230.0780.88399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.417 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22418 3949 5.1 %RANDOM
Rwork0.18624 ---
obs0.18815 74217 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.963 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10697 0 195 680 11572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01211111
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610727
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.64515017
X-RAY DIFFRACTIONr_angle_other_deg0.4111.57524692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19151329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.01551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.532102017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.21722
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212671
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022500
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8094.4035313
X-RAY DIFFRACTIONr_mcbond_other2.8094.4045314
X-RAY DIFFRACTIONr_mcangle_it4.4337.9066641
X-RAY DIFFRACTIONr_mcangle_other4.4337.9066642
X-RAY DIFFRACTIONr_scbond_it3.494.8795798
X-RAY DIFFRACTIONr_scbond_other3.4894.885799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7548.7528377
X-RAY DIFFRACTIONr_long_range_B_refined9.89452.548107
X-RAY DIFFRACTIONr_long_range_B_other9.88152.4547729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å
RfactorNum. reflection% reflection
Rfree0.321 286 -
Rwork0.326 5148 -
obs--95.55 %

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