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- PDB-8hq5: G6 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 8hq5
TitleG6 in complex with CRM1-Ran-RanBP1
Components
  • CRM1 isoform 1
  • GTP-binding nuclear protein Ran
  • YRB1 isoform 1
KeywordsTRANSPORT PROTEIN / Active Ran / Complex / 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) / NLS-bearing protein import into nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA ...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) / NLS-bearing protein import into nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / 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 / nuclear pore / ribosomal subunit export from nucleus / 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 / positive regulation of protein binding / melanosome / nuclear envelope / 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 / GTP binding / chromatin / nucleolus / 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
GUANOSINE-5'-TRIPHOSPHATE / Chem-MBI / 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: 2.25 Å
AuthorsSun, Q. / Lei, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81502629 China
CitationJournal: To Be Published
Title: F1 in complex with CRM1-Ran-RanBP1
Authors: Sun, Q. / Lei, Y.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: 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)157,96022
Polymers155,9443
Non-polymers2,01619
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-147 kcal/mol
Surface area56870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.580, 105.580, 304.909
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 , 8 types, 615 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: Cl
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-MBI / 3-[(4-bromophenyl)carbonylamino]-4-[4-(5-chloranyl-2-methyl-phenyl)piperazin-1-yl]benzoic acid


Mass: 528.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23BrClN3O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
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: BL19U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→99.77 Å / Num. obs: 81028 / % possible obs: 98.3 % / Redundancy: 25.8 % / CC1/2: 1 / Net I/σ(I): 25
Reflection shellResolution: 2.25→2.39 Å / Num. unique obs: 13078 / CC1/2: 0.854

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→50.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.97 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20867 4006 5 %RANDOM
Rwork0.17538 ---
obs0.17703 76894 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.25→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10709 0 110 596 11415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311058
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710418
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.64314966
X-RAY DIFFRACTIONr_angle_other_deg1.2581.57724211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48951326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08223.64566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.196152025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7711551
X-RAY DIFFRACTIONr_chiral_restr0.0690.21457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022225
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_it2.1444.4285315
X-RAY DIFFRACTIONr_mcbond_other2.1424.4275314
X-RAY DIFFRACTIONr_mcangle_it3.2576.6336636
X-RAY DIFFRACTIONr_mcangle_other3.2586.6346637
X-RAY DIFFRACTIONr_scbond_it2.7884.8275743
X-RAY DIFFRACTIONr_scbond_other2.7874.8265742
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5067.0878331
X-RAY DIFFRACTIONr_long_range_B_refined7.35183.96546623
X-RAY DIFFRACTIONr_long_range_B_other7.29283.79646304
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.254→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 294 -
Rwork0.253 5616 -
obs--99.21 %
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)
12.20090.66910.74651.48190.83242.64290.0523-0.06740.14430.1234-0.0179-0.1022-0.20610.1999-0.03440.0969-0.0257-0.00020.0258-0.00560.0272-4.59557.05-32.41
23.44220.9386-0.87473.0248-0.95234.09690.07740.0106-0.0258-0.0843-0.0636-0.1574-0.10140.403-0.01380.1511-0.116-0.04380.2054-0.02740.097817.1160.257-18
30.463-0.1786-0.04550.4009-0.07280.81130.01770.01270.05740.042-0.01340.0198-0.07620.0075-0.00420.0843-0.0375-0.0060.02610.00460.0161-14.93539.997-30.937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 216
2X-RAY DIFFRACTION2B79 - 200
3X-RAY DIFFRACTION3C0 - 1051

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