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- PDB-5yro: RanL182A in complex with RanBP1-CRM1 -

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Basic information

Entry
Database: PDB / ID: 5yro
TitleRanL182A 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


Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / pre-miRNA export from nucleus / RNA nuclear export complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus ...Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / pre-miRNA export from nucleus / RNA nuclear export complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / protein localization to kinetochore / spindle pole body / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / NLS-bearing protein import into nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / RNA export from nucleus / 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 / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / U5 snRNA binding / viral process / U2 snRNA binding / U6 snRNA binding / ribosomal subunit export from nucleus / mRNA export from nucleus / nuclear pore / U1 snRNA binding / ribosomal small subunit export from nucleus / centriole / GTPase activator activity / mitotic spindle organization / protein export from nucleus / Transcriptional regulation by small RNAs / recycling endosome / kinetochore / small GTPase binding / G1/S transition of mitotic cell cycle / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / nuclear envelope / melanosome / positive regulation of protein binding / mitotic cell cycle / G protein activity / 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 / cell division / GTPase activity / chromatin binding / nucleolus / GTP binding / chromatin / 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 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
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 / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsSun, Q. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC81502629 China
CitationJournal: To Be Published
Title: RanL182A in complex with RanBP1-CRM1
Authors: Sun, Q. / Zhang, Y.
History
DepositionNov 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)158,97212
Polymers158,1043
Non-polymers8689
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-79 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.259, 105.259, 307.425
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: 24414.025 Da / Num. of mol.: 1 / Mutation: 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 Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16320.687 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: 117369.766 Da / Num. of mol.: 1 / Mutation: D537G, T539C, V540E, K541Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (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 , 6 types, 131 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.: 2 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNatural mutation Y1022C

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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: 2.75 Å3/Da / Density % sol: 55.31 %
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: 0.97921 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.396→50 Å / Num. obs: 65435 / % possible obs: 94.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.07 / Rrim(I) all: 0.179 / Χ2: 0.973 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.4-2.448.932330.410.79495.4
2.44-2.49932240.4970.8194.9
2.49-2.539.132100.5310.81795.20.855
2.53-2.59932350.6380.82295.10.775
2.59-2.649.131980.6860.84694.90.636
2.64-2.79.232550.7670.8795.20.502
2.7-2.779.232020.8070.88694.50.402
2.77-2.859.332280.8480.933950.336
2.85-2.939.332470.9010.9994.70.2450.7630.805
2.93-3.029.332300.9171.03494.80.2040.6310.666
3.02-3.139.332220.9391.0894.80.1480.4560.481
3.13-3.269.332500.9541.07195.10.1180.3620.383
3.26-3.419.232870.9511.07595.20.0880.2670.283
3.41-3.589.232650.9691.095950.0720.2180.231
3.58-3.81933040.9731.07795.50.0620.1810.193
3.81-4.18.832920.9711.06695.20.0540.1560.166
4.1-4.528.533300.9671.062950.0530.1430.154
4.52-5.178.333720.9681.03495.60.050.1310.141
5.17-6.518.534040.9751.06995.30.0440.1210.13
6.51-507.934470.9791.0390.20.0510.1350.145

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HB4

4hb4


Resolution: 2.396→40.531 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.27
RfactorNum. reflection% reflection
Rfree0.2446 3319 5.11 %
Rwork0.2072 --
obs0.2091 65001 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.27 Å2 / Biso mean: 68.9331 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.396→40.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10877 0 48 122 11047
Biso mean--72.76 56.12 -
Num. residues----1348
Refinement TLS params.Method: refined / Origin x: -7.3278 Å / Origin y: 42.6367 Å / Origin z: 30.5355 Å
111213212223313233
T0.4173 Å2-0.0276 Å2-0.0188 Å2-0.4913 Å2-0.0057 Å2--0.4565 Å2
L0.5835 °20.1006 °2-0.1073 °2-0.6074 °20.0484 °2--0.5124 °2
S-0.0682 Å °0.03 Å °0.0136 Å °-0.0577 Å °0.0814 Å °-0.0425 Å °-0.0916 Å °0.05 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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