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- PDB-8hug: F1 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 8hug
TitleF1 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-N59 / 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: 2.15 Å
AuthorsSun, Q. / Lei, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81502629 China
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of a Hidden Pocket beneath the NES Groove by Novel Noncovalent CRM1 Inhibitors.
Authors: Li, C. / Zhang, Q. / Huang, W. / Huang, L. / Long, Q. / Lei, Y. / Jia, D. / Yang, S. / Yang, Y. / Zhang, X. / Sun, Q.
History
DepositionDec 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)157,69116
Polymers155,9443
Non-polymers1,74713
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-60 kcal/mol
Surface area57150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.570, 105.570, 304.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1613-

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: 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 #1/H766 (bacteria) / 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 , 7 types, 604 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.: 4 / 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.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Chemical ChemComp-N59 / 4-[4-(3-chlorophenyl)piperazin-1-yl]-3-[(3-fluorophenyl)sulfonylamino]benzoic acid


Mass: 489.947 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21ClFN3O4S / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 54.71 %
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: Jan 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→30.84 Å / Num. obs: 93392 / % possible obs: 98.9 % / Redundancy: 25.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.02 / Rrim(I) all: 0.097 / Net I/σ(I): 21.5 / Num. measured all: 2352015 / Scaling rejects: 542
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.2127.21.71418739168910.810.3351.7462.5100
9.62-30.8418.80.0442264612050.9990.010.04547.797

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CND

7cnd


Resolution: 2.15→30.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 11.567 / SU ML: 0.142 / SU R Cruickshank DPI: 0.2122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 4692 5 %RANDOM
Rwork0.1867 ---
obs0.1886 88554 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.51 Å2 / Biso mean: 60.42 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å2-0 Å2
2--1.79 Å2-0 Å2
3----3.58 Å2
Refinement stepCycle: final / Resolution: 2.15→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10706 0 105 592 11403
Biso mean--76.98 67.65 -
Num. residues----1325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311069
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710408
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.64514974
X-RAY DIFFRACTIONr_angle_other_deg1.2951.57724188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34751326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24223.622566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.484152025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0911551
X-RAY DIFFRACTIONr_chiral_restr0.0720.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022232
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 355 -
Rwork0.262 6480 -
all-6835 -
obs--100 %
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)
12.50330.73050.6971.76090.86283.35320.035-0.08790.12670.1439-0.0205-0.1207-0.31570.3292-0.01440.0632-0.0466-0.00920.04860.01140.1001-4.703957.077-32.2929
23.95221.138-1.52122.9951-0.91755.85320.1097-0.0931-0.1238-0.1316-0.0867-0.0526-0.10290.627-0.0230.1761-0.1738-0.1090.27950.01950.248116.894760.1784-17.2401
30.476-0.2094-0.02820.4131-0.08921.0322-0.0160.00730.05150.0891-0.0090.0253-0.1040.02730.0250.0807-0.0317-0.01660.0181-0.00620.1674-14.994739.8421-30.793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 216
2X-RAY DIFFRACTION2B81 - 200
3X-RAY DIFFRACTION3C0 - 1503

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