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- PDB-5ytb: RanY197A in complex with RanBP1-CRM1 -

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Basic information

Entry
Database: PDB / ID: 5ytb
TitleRanY197A in complex with RanBP1-CRM1
Components
  • Exportin-1,Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / Active Ran / Complex
Function / homology
Function and homology information


tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / Transcriptional and post-translational regulation of MITF-M expression and activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / manchette / cellular response to mineralocorticoid stimulus ...tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / Transcriptional and post-translational regulation of MITF-M expression and activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / protein localization to kinetochore / SUMOylation of RNA binding proteins / U4 snRNA binding / protein localization to nucleolus / spindle pole body / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / MAPK6/MAPK4 signaling / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / spermatid development / U5 snRNA binding / viral process / U2 snRNA binding / U6 snRNA binding / positive regulation of protein binding / sperm flagellum / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / U1 snRNA binding / 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 / G1/S transition of mitotic cell cycle / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / actin cytoskeleton organization / midbody / ubiquitin-dependent protein catabolic process / 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 / perinuclear region of cytoplasm / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-TRIPHOSPHATE / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSun, Q. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC81502629 China
CitationJournal: To Be Published
Title: RanY197A in complex with RanBP1-CRM1
Authors: Sun, Q. / Zhang, Y.
History
DepositionNov 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ran-specific GTPase-activating protein 1
C: Exportin-1,Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,54818
Polymers157,2963
Non-polymers1,25215
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-111 kcal/mol
Surface area55950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.285, 105.285, 305.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 24364.010 Da / Num. of mol.: 1 / Mutation: Y197A
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 Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16249.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli (E. coli) / References: UniProt: P41920
#3: Protein Exportin-1,Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 116682.086 Da / Num. of mol.: 1 / Mutation: D537G, T539C, V540E, K541Q, Y1022C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli (E. coli) / References: UniProt: P30822

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Non-polymers , 7 types, 244 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNatural mutation at this position

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG 3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 77397 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.028 / Rrim(I) all: 0.099 / Χ2: 0.974 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.3-2.3412.238220.8410.3140.833100
2.34-2.3813.637610.8960.2620.831000.9340.97
2.38-2.4313.838160.9430.2260.8471000.8130.844
2.43-2.4813.737870.9460.1880.8541000.6710.697
2.48-2.5313.638110.9580.1620.8531000.5780.6
2.53-2.5913.538170.9670.1360.8581000.4840.503
2.59-2.6613.238220.9740.1220.8861000.4270.444
2.66-2.7312.438030.9790.1030.9861000.350.365
2.73-2.8113.138420.9820.0880.9871000.3090.322
2.81-2.913.638190.9890.0690.971000.2450.255
2.9-313.738390.9920.0560.9681000.2010.209
3-3.1213.538440.9950.0461.0241000.1640.171
3.12-3.261338490.9950.0391.0851000.1350.14
3.26-3.4412.638610.9970.0311.0941000.1060.111
3.44-3.6513.738760.9970.0261.1081000.0950.098
3.65-3.9313.539040.9970.0251.0821000.090.093
3.93-4.3312.938990.9980.0221.0341000.0760.079
4.33-4.9513.339570.9980.021.0461000.0720.074
4.95-6.241340090.9970.0211.0641000.0740.077
6.24-5012.142590.9980.0181.05499.90.0580.061

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 16.554 / SU ML: 0.173 / SU R Cruickshank DPI: 0.1851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.211
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 3852 5 %RANDOM
Rwork0.1886 ---
obs0.1906 72664 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 161.9 Å2 / Biso mean: 66.292 Å2 / Biso min: 34.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å2-0 Å2-0 Å2
2--1.94 Å20 Å2
3----3.87 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10863 0 70 229 11162
Biso mean--67.27 55.3 -
Num. residues----1347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911134
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210488
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.96415065
X-RAY DIFFRACTIONr_angle_other_deg0.937324375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76551343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10225.057522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.552152042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8091551
X-RAY DIFFRACTIONr_chiral_restr0.0690.21723
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022185
X-RAY DIFFRACTIONr_rigid_bond_restr2.473321622
X-RAY DIFFRACTIONr_sphericity_free12.4915125
X-RAY DIFFRACTIONr_sphericity_bonded4.855521525
LS refinement shellResolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 280 -
Rwork0.271 5335 -
all-5615 -
obs--99.98 %
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)
10.25580.2626-0.24090.3912-0.12940.8280.032-0.0083-0.054-0.01720.02030.0251-0.10350.1508-0.05240.0305-0.0235-0.01080.1413-0.03840.15495.036348.254632.7442
20.67970.3086-0.0731.73570.83452.22470.0762-0.0939-0.096-0.1985-0.06290.0971-0.40710.2482-0.01330.1976-0.10190.04450.0795-0.02480.07887.586270.255317.9103
30.38280.0989-0.12780.25320.09050.2839-0.0150.0227-0.0324-0.02240.0430.0044-0.0551-0.0347-0.0280.01990.0184-0.00160.08770.00960.0823-12.0338.15431.0482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 216
2X-RAY DIFFRACTION2B80 - 200
3X-RAY DIFFRACTION3C-1 - 1052

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