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- PDB-3nby: Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex -

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Basic information

Entry
Database: PDB / ID: 3nby
TitleCrystal structure of the PKI NES-CRM1-RanGTP nuclear export complex
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Snurportin-1SPN1
KeywordsGTP-binding protein/transport protein / protein transport / GTP-binding protein-transport protein complex
Function / homology
Function and homology information


Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Heme signaling / Cyclin A/B1/B2 associated events during G2/M transition / HuR (ELAVL1) binds and stabilizes mRNA / RNA import into nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion ...Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Heme signaling / Cyclin A/B1/B2 associated events during G2/M transition / HuR (ELAVL1) binds and stabilizes mRNA / RNA import into nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RHO GTPases Activate Formins / Separation of Sister Chromatids / RNA cap binding / regulation of centrosome duplication / MAPK6/MAPK4 signaling / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / regulation of protein export from 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 / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / ribosomal subunit export from nucleus / regulation of protein catabolic process / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / protein localization to nucleus / ribosomal large subunit export from nucleus / sperm flagellum / Cajal body / mRNA export from nucleus / nuclear pore / protein export from nucleus / centriole / viral process / 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 / kinetochore / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / ribosome biogenesis / mitotic cell cycle / nuclear envelope / snRNP Assembly / positive regulation of protein binding / midbody / actin cytoskeleton organization / nuclear membrane / DNA-binding transcription factor binding / cadherin binding / ribonucleoprotein complex / protein heterodimerization activity / cell division / protein domain specific binding / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / chromatin / GTP binding / nucleolus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / 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 ...Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / 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 / DNA ligase/mRNA capping enzyme / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / 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 / Importin-alpha, importin-beta-binding domain / IBB domain profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / 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 / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Snurportin-1 / GTP-binding nuclear protein Ran / Exportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.42 Å
AuthorsGuttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.
Authors: Guttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Snurportin-1
C: GTP-binding nuclear protein Ran
A: Exportin-1
E: Snurportin-1
F: GTP-binding nuclear protein Ran
D: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,67210
Polymers369,5776
Non-polymers1,0954
Water0
1
B: Snurportin-1
C: GTP-binding nuclear protein Ran
A: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,3365
Polymers184,7883
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-59 kcal/mol
Surface area64890 Å2
MethodPISA
2
E: Snurportin-1
F: GTP-binding nuclear protein Ran
D: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,3365
Polymers184,7883
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-54 kcal/mol
Surface area64570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.090, 223.726, 163.064
Angle α, β, γ (deg.)90.00, 100.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999999, -0.001217, 0.00046), (-0.001217, -0.999999, -0.000787), (0.000461, 0.000786, -1)35.959999, -213.886993, -5.16338
2given(0.999999, -0.000806, -0.001455), (-0.000806, -1, 0.000348), (-0.001455, -0.000347, -0.999999)35.987499, -213.906006, -5.33234
3given(0.999984, -0.00513, -0.002501), (-0.005134, -0.999985, -0.001663), (-0.002492, 0.001676, -0.999995)35.5191, -213.822998, -5.00412

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Components

#1: Protein Snurportin-1 / SPN1 / RNA U transporter 1


Mass: 41228.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: PKIA (GeneID: 5569) SNUPN (GeneID: 10073), RNUT1, SNUPN, SPN1
Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: O95149
#2: Protein GTP-binding nuclear protein Ran / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4 / Androgen receptor-associated protein 24


Mass: 20192.484 Da / Num. of mol.: 2 / Mutation: Q69L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARA24, OK/SW-cl.81, RAN, RAN (GeneID: 5901) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P62826
#3: Protein Exportin-1 / Karyopherin / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123367.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crm1, Xpo1, Xpo1 (GeneID: 103573) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q6P5F9
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1 M Tris/HCl pH range 8.08-8.30, 10-14% (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2005 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionHighest resolution: 3.42 Å / Num. obs: 57482 / % possible obs: 83.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.606 Å2 / Rmerge F obs: 0.267 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.203 / Net I/σ(I): 5.68 / Num. measured all: 169861

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3GJX

3gjx


Resolution: 3.42→38.632 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.54 / Isotropic thermal model: Overall / σ(F): 2 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3145 3408 5 %
Rwork0.2578 --
obs0.2607 57482 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.082 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2832 Å20 Å21.6947 Å2
2--3.5419 Å2-0 Å2
3----0.2587 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.51 Å
Luzzati d res low-8 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.42→38.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24018 0 66 0 24084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325652
X-RAY DIFFRACTIONf_angle_d1.54533344
X-RAY DIFFRACTIONf_dihedral_angle_d18.8889153
X-RAY DIFFRACTIONf_chiral_restr0.0913752
X-RAY DIFFRACTIONf_plane_restr0.0064237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.46890.36811330.29912694X-RAY DIFFRACTION100
3.4689-3.52060.36411430.27332668X-RAY DIFFRACTION100
3.5206-3.57560.34761480.26312722X-RAY DIFFRACTION100
3.5756-3.63410.32421470.26162682X-RAY DIFFRACTION100
3.6341-3.69680.34281390.28192689X-RAY DIFFRACTION100
3.6968-3.76390.39591340.28442712X-RAY DIFFRACTION100
3.7639-3.83630.32371460.2772687X-RAY DIFFRACTION100
3.8363-3.91450.36511490.28082682X-RAY DIFFRACTION100
3.9145-3.99950.31161390.26742739X-RAY DIFFRACTION100
3.9995-4.09250.36881370.25052667X-RAY DIFFRACTION100
4.0925-4.19470.28211400.24932727X-RAY DIFFRACTION100
4.1947-4.3080.33871450.23982671X-RAY DIFFRACTION100
4.308-4.43460.28351430.24092690X-RAY DIFFRACTION100
4.4346-4.57750.28741430.2272709X-RAY DIFFRACTION100
4.5775-4.74080.27251440.22772697X-RAY DIFFRACTION100
4.7408-4.93020.27741350.2382685X-RAY DIFFRACTION100
4.9302-5.15410.30861440.25332735X-RAY DIFFRACTION100
5.1541-5.42520.33991450.2562682X-RAY DIFFRACTION100
5.4252-5.76410.31461420.25882687X-RAY DIFFRACTION100
5.7641-6.20740.29961440.25592692X-RAY DIFFRACTION100
6.2074-6.8290.2951380.24742711X-RAY DIFFRACTION99
6.829-7.81010.27311430.23812698X-RAY DIFFRACTION99
7.8101-9.81310.25411440.21332717X-RAY DIFFRACTION99
9.8131-38.63420.25861430.26292725X-RAY DIFFRACTION99

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