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- PDB-5dis: Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a... -

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Basic information

Entry
Database: PDB / ID: 5dis
TitleCrystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid FG-repeat containing fragment of Nup214
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214
  • Snurportin-1SPN1
KeywordsTRANSPORT PROTEIN / FG-repeats / Nucleoporin / Nup214 / Exportin
Function / homology
Function and homology information


cytoplasmic side of nuclear pore / RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of nucleocytoplasmic transport / RNA cap binding / regulation of centrosome duplication / RNA nuclear export complex / nuclear export signal receptor activity ...cytoplasmic side of nuclear pore / RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of nucleocytoplasmic transport / RNA cap binding / regulation of centrosome duplication / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / Nuclear Pore Complex (NPC) Disassembly / cellular response to mineralocorticoid stimulus / manchette / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / NLS-dependent protein nuclear import complex / regulation of protein export from nucleus / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / structural constituent of nuclear pore / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / Viral Messenger RNA Synthesis / nuclear localization sequence binding / DNA metabolic process / dynein intermediate chain binding / detection of maltose stimulus / maltose binding / maltose transport complex / SUMOylation of ubiquitinylation proteins / maltose transport / maltodextrin transmembrane transport / ribosomal subunit export from nucleus / Vpr-mediated nuclear import of PICs / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / SUMOylation of DNA replication proteins / carbohydrate transmembrane transporter activity / protein localization to nucleus / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ribosomal large subunit export from nucleus / carbohydrate transport / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / sperm flagellum / Cajal body / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / NPAS4 regulates expression of target genes / protein export from nucleus / centriole / viral process / ATP-binding cassette (ABC) transporter complex / SUMOylation of chromatin organization proteins / cell chemotaxis / Downregulation of TGF-beta receptor signaling / mitotic spindle organization / G protein activity / HCMV Late Events / male germ cell nucleus / RHO GTPases Activate Formins / Deactivation of the beta-catenin transactivating complex / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / MAPK6/MAPK4 signaling / Heme signaling / ISG15 antiviral mechanism / kinetochore / recycling endosome / small GTPase binding / HCMV Early Events / positive regulation of protein import into nucleus / protein import into nucleus
Similarity search - Function
Nuclear pore complex protein Nup214, phenylalanine-glycine (FG) domain / Nucleoporin Nup214 phenylalanine-glycine (FG) domain / Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Nuclear pore complex protein / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat ...Nuclear pore complex protein Nup214, phenylalanine-glycine (FG) domain / Nucleoporin Nup214 phenylalanine-glycine (FG) domain / Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Nuclear pore complex protein / 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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / D-amino Acid Aminotransferase; Chain A, domain 1 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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 / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / GUANOSINE-5'-TRIPHOSPHATE / PROLINE / Exportin-1 / Snurportin-1 / Maltose/maltodextrin-binding periplasmic protein / Nuclear pore complex protein Nup214 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMonecke, T. / Port, S.A. / Dickmanns, A. / Kehlenbach, R.H. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
Citation
Journal: Cell Rep / Year: 2015
Title: Structural and Functional Characterization of CRM1-Nup214 Interactions Reveals Multiple FG-Binding Sites Involved in Nuclear Export.
Authors: Port, S.A. / Monecke, T. / Dickmanns, A. / Spillner, C. / Hofele, R. / Urlaub, H. / Ficner, R. / Kehlenbach, R.H.
#1: Journal: To Be Published
Title: Combining dehydration, construct optimization and improved data collection to solve the crystal structure of a CRM1-RanGTP-SPN1-Nup214 quaternary export complex
Authors: Monecke, T. / Dickmanns, A. / Weiss, M.S. / Port, S.A. / Kehlenbach, R.H. / Ficner, R.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_audit_support / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_audit_support.funding_organization / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Exportin-1
B: GTP-binding nuclear protein Ran
C: Snurportin-1
D: Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,1829
Polymers224,0624
Non-polymers1,1205
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-79 kcal/mol
Surface area80960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.330, 248.970, 210.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Exportin-1 / Karyopherin / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 120395.742 Da / Num. of mol.: 1 / Fragment: UNP residues 5-1058
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPO1, CRM1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14980
#2: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 19812.088 Da / Num. of mol.: 1 / Fragment: UNP residues 8-179 / Mutation: Q69L
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
#3: Protein Snurportin-1 / SPN1 / RNA U transporter 1


Mass: 33276.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNUPN, RNUT1, SPN1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95149
#4: Protein Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214 / MBP / MMBP / Maltodextrin-binding protein / 214 kDa nucleoporin / Nucleoporin Nup214 / Protein CAN


Mass: 50577.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, NUP214, CAIN, CAN, KIAA0023 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P35658

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Sugars , 1 types, 1 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 16 molecules

#6: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% PEG 8000, 0.2M L-proline, 0.1M Tris pH 7.5, 4 mM D-maltose, 180 mM LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2014
RadiationMonochromator: Si111-DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.85→48.49 Å / Num. obs: 67922 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 80.01 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.062 / Χ2: 1.037 / Net I/σ(I): 15.52 / Num. measured all: 313050
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.85-2.954.10.8730.5712.0125297672161400.64491.4
2.95-3.050.9170.4652.7123638586455960.52895.4
3.05-3.250.9640.3074.4347205968496530.34499.7
3.25-3.830.9930.1279.848536918001179250.14399.6
3.83-4.120.9970.06318.3226990559955710.07199.5
4.12-4.410.9980.0522.8920152423242060.05699.4
4.41-4.70.9980.04226.5514986325832340.04799.3
4.7-140.9990.0333.056714515115149800.03499.1
14-170.9990.02347.2710692772690.02697.1
17-500.9990.02144.3911993683480.02594.6
5021

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GJX, 1ANF

3gjx

1anf


Resolution: 2.85→48.485 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.17 / Stereochemistry target values: ML
Details: Overall, the electron density map for MBP and especially its N-terminal lobe is of poor quality. This suggests that significant movement of MBP in the crystal lattice is possible, which is ...Details: Overall, the electron density map for MBP and especially its N-terminal lobe is of poor quality. This suggests that significant movement of MBP in the crystal lattice is possible, which is consistent with the overall elevated B-factors of the MBP residues. Hence, several parts of MBP are not defined in the electron density map. Since dissolved crystals analysed by SDS-PAGE clearly showed the presence of full-length MBP in order to retain structural integrity of the crystal lattice and the MBP, the residues were not omitted.
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 3392 5 %Random selection
Rwork0.2056 ---
obs0.2078 67814 98.16 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→48.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14907 0 72 12 14991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615303
X-RAY DIFFRACTIONf_angle_d0.92520716
X-RAY DIFFRACTIONf_dihedral_angle_d15.2635641
X-RAY DIFFRACTIONf_chiral_restr0.0372311
X-RAY DIFFRACTIONf_plane_restr0.0052634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.89070.46691300.40692444X-RAY DIFFRACTION91
2.8907-2.93380.42941300.36742459X-RAY DIFFRACTION92
2.9338-2.97970.41361300.33792466X-RAY DIFFRACTION91
2.9797-3.02850.42051380.31672630X-RAY DIFFRACTION96
3.0285-3.08070.35391390.30962670X-RAY DIFFRACTION100
3.0807-3.13670.32431430.29092723X-RAY DIFFRACTION100
3.1367-3.19710.34351420.2842681X-RAY DIFFRACTION100
3.1971-3.26230.38181410.27522704X-RAY DIFFRACTION99
3.2623-3.33320.32141420.26052691X-RAY DIFFRACTION100
3.3332-3.41070.321440.24192729X-RAY DIFFRACTION100
3.4107-3.4960.29881420.23172700X-RAY DIFFRACTION100
3.496-3.59050.29651400.22592679X-RAY DIFFRACTION99
3.5905-3.69610.25791430.21922701X-RAY DIFFRACTION99
3.6961-3.81540.27261420.21372705X-RAY DIFFRACTION100
3.8154-3.95170.24811420.20282703X-RAY DIFFRACTION100
3.9517-4.10980.21171450.18192738X-RAY DIFFRACTION99
4.1098-4.29680.20551420.17522704X-RAY DIFFRACTION99
4.2968-4.52310.21961440.16432725X-RAY DIFFRACTION100
4.5231-4.80630.22081420.16592700X-RAY DIFFRACTION99
4.8063-5.1770.20841430.17622721X-RAY DIFFRACTION99
5.177-5.69730.21071460.19192776X-RAY DIFFRACTION100
5.6973-6.520.25151460.21832756X-RAY DIFFRACTION100
6.52-8.2080.24151450.20252759X-RAY DIFFRACTION99
8.208-48.49240.19411510.16562858X-RAY DIFFRACTION98
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)
10.54050.07280.63810.64270.4211.78550.04210.0369-0.13520.25440.0240.05960.42460.0121-0.07260.6076-0.06110.10180.51720.00040.5555-11.0936-37.563212.6386
20.53550.0089-0.04840.5643-0.28470.08010.07250.5057-0.1885-0.5095-0.02-0.02530.79550.2582-0.02132.25540.2287-0.21611.7616-0.01181.422911.7443-81.4498-19.2643
35.9544-0.40051.47246.63660.60374.96270.05380.6320.1183-0.1770.1431-0.24260.26160.5822-0.16010.53340.04680.04130.53610.00740.35883.2415-34.91829.7787
43.594-2.5236-0.95135.76931.15034.3673-0.04340.68510.2861-1.15560.1464-0.2932-0.41910.3829-0.06531.0114-0.3497-0.00020.9265-0.03640.589-13.4557-32.2797-40.4504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain D
3X-RAY DIFFRACTION3chain B
4X-RAY DIFFRACTION4chain C

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