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- PDB-7cnd: NCI-1 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 7cnd
TitleNCI-1 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 / import into nucleus / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / manchette / nuclear export signal receptor activity / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding ...positive regulation of mitotic centrosome separation / import into nucleus / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / manchette / nuclear export signal receptor activity / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / NLS-bearing protein import into nucleus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / mitotic sister chromatid segregation / viral process / spermatid development / ribosomal large subunit export from nucleus / nuclear pore / sperm flagellum / positive regulation of protein binding / ribosomal subunit export from nucleus / 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 / recycling endosome / 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 / 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 / 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 / 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 / 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
Chem-G6U / GUANOSINE-5'-TRIPHOSPHATE / 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: 1.8 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: 2021
Title: Structure-Guided Design of the First Noncovalent Small-Molecule Inhibitor of CRM1.
Authors: Lei, Y. / An, Q. / Shen, X.F. / Sui, M. / Li, C. / Jia, D. / Luo, Y. / Sun, Q.
History
DepositionJul 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: YRB1 isoform 1
C: CRM1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,96623
Polymers155,9423
Non-polymers2,02420
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-109 kcal/mol
Surface area56060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.333, 105.333, 304.205
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-1108-

CL

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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


Mass: 115222.430 Da / Num. of mol.: 1
Mutation: S27E , Q49E, del377-413, del441-461, D537G, 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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PZI8

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Non-polymers , 8 types, 793 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-G6U / ~{N}-[(~{E})-3-[3,5-bis(trifluoromethyl)phenyl]sulfinylprop-2-enyl]-3-methyl-butan-1-amine


Mass: 387.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19F6NOS / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
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: NFPSS / Beamline: BL18U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 158384 / % possible obs: 100 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.032 / Rrim(I) all: 0.146 / Χ2: 0.689 / Net I/σ(I): 3.1 / Num. measured all: 3137828
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8318.61.36578170.320.321.4030.345100
1.83-1.8618.61.30177800.4640.3051.3370.349100
1.86-1.918.51.21978350.5680.2861.2530.36100
1.9-1.9418.51.10777710.6260.2591.1380.381100
1.94-1.9818.30.99778530.7770.2351.0250.382100
1.98-2.0317.50.87978250.8270.2120.9050.389100
2.03-2.0818.50.76778160.8920.180.7880.426100
2.08-2.1319.90.65878480.9380.1480.6750.429100
2.13-2.2200.5778680.9520.1280.5850.455100
2.2-2.2719.90.47378130.9680.1060.4850.515100
2.27-2.3519.70.39278850.9780.0880.4020.538100
2.35-2.4418.80.32878840.9850.0760.3360.59100
2.44-2.5519.70.27578720.990.0620.2820.662100
2.55-2.6920.90.23679300.9920.0520.2420.734100
2.69-2.86210.19379200.9940.0420.1970.831100
2.86-3.0820.70.15979430.9960.0350.1630.964100
3.08-3.3920.30.12980070.9970.0290.1331.147100
3.39-3.8822.30.10780350.9970.0230.111.138100
3.88-4.8821.20.08981240.9980.020.0921.119100
4.88-5022.80.06385580.9980.0130.0641.46499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M60

6m60


Resolution: 1.8→37.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.653 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 7983 5 %RANDOM
Rwork0.2016 ---
obs0.2031 150221 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.13 Å2 / Biso mean: 40.591 Å2 / Biso min: 21.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0 Å2
2--0.52 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.8→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10699 0 110 774 11583
Biso mean--58.27 45.94 -
Num. residues----1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311040
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710416
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.64214945
X-RAY DIFFRACTIONr_angle_other_deg1.2731.57624201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08351327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80623.628565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57152022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3841551
X-RAY DIFFRACTIONr_chiral_restr0.0640.21460
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212059
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022220
LS refinement shellResolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 584 -
Rwork0.413 10994 -
all-11578 -
obs--99.92 %
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)
11.96640.5413-0.64941.3333-0.78652.17320.0561-0.0452-0.0940.1365-0.0070.12560.1594-0.1799-0.04910.1278-0.03490.00820.0644-0.00420.02554.619-56.806-32.311
22.65540.98510.87872.65850.7953.71610.0789-0.05270.0881-0.0607-0.05530.03320.0353-0.2719-0.02360.1644-0.10130.06210.1996-0.00020.0752-16.946-59.916-17.387
30.4194-0.17420.01410.36340.09530.77010.00290.0333-0.04990.0488-0.014-0.01440.08180.00140.01120.1067-0.03940.00670.0578-0.00720.012414.97-39.848-30.874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 216
2X-RAY DIFFRACTION2B80 - 200
3X-RAY DIFFRACTION3C0 - 1502

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