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- PDB-5zpu: LFS829 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 5zpu
TitleLFS829 in complex with CRM1-Ran-RanBP1
Components
  • Exportin-1,Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / nuclear export / complex / mutant / activation
Function / homology
Function and homology information


Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus ...Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / 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 / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / spindle pole body / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / viral process / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / protein export from nucleus / centriole / GTPase activator activity / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / G protein activity / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / G1/S transition of mitotic cell cycle / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / 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 / nucleolus / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / 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 domain / Ran binding protein RanBP1-like / 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 / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-D29 / 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: 2.6 Å
AuthorsSun, Q. / Lei, Y.
CitationJournal: To Be Published
Title: To be published
Authors: Sun, Q. / Lei, Y.
History
DepositionApr 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)159,1367
Polymers158,1783
Non-polymers9584
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-40 kcal/mol
Surface area56450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.438, 105.438, 303.907
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 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 / Plasmid: pGEX4t-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41920
#3: Protein Exportin-1,Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117442.812 Da / Num. of mol.: 1
Mutation: D537G, T539C, V540E, K541Q, Y1022C,D537G, T539C, V540E, K541Q, Y1022C
Source method: isolated from a genetically manipulated source
Details: Chain C comprises residues 1-376 and 414-1058 of Exportin-1 (UNP P30822) with residues 377-413 deleted.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGEX4t-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30822

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Non-polymers , 5 types, 314 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-D29 / (Z)-{[(3E)-4-{(R)-[3,5-bis(trifluoromethyl)phenyl]sulfinyl}but-3-en-1-yl]imino}methanethiol


Mass: 375.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11F6NOS2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.94 % / Mosaicity: 0.383 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50.01 Å / Num. obs: 54140 / % possible obs: 100 % / Redundancy: 42.5 % / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.059 / Rrim(I) all: 0.306 / Χ2: 1.027 / Net I/σ(I): 2.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2Rmerge(I) obsRrim(I) all
2.6-2.6439.226610.4210.230.567
2.64-2.6939.726470.430.2220.577
2.69-2.7439.926390.5210.2160.581
2.74-2.839.826670.5330.2070.598
2.8-2.8639.826580.6630.1950.609
2.86-2.9339.726730.7280.1850.623
2.93-339.626430.7950.1740.637
3-3.0837.926570.8460.1620.6680.992
3.08-3.1739.126860.9250.1430.6970.8870.899
3.17-3.2842.226750.9190.1230.7520.7990.808
3.28-3.3943.926740.9550.1040.8240.6870.695
3.39-3.5344.227040.9680.0880.9270.5860.593
3.53-3.6944.926800.9770.0741.0620.4980.503
3.69-3.8844.727050.9830.0641.220.4270.432
3.88-4.1342.626970.9850.0561.3820.3670.371
4.13-4.4546.527350.9920.0451.5240.3090.313
4.45-4.8948.427340.9930.0391.5930.2760.278
4.89-5.646.827780.9940.0381.6080.2620.264
5.6-7.0544.728090.9950.0351.4470.2360.238
7.05-5044.830180.9970.0251.8950.1670.169

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HAT

4hat


Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.124 / SU ML: 0.258 / SU R Cruickshank DPI: 0.7959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.796 / ESU R Free: 0.321
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 2737 5.1 %RANDOM
Rwork0.2245 ---
obs0.2262 51038 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.69 Å2 / Biso mean: 59.084 Å2 / Biso min: 25.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å2-0 Å2
2--1.06 Å20 Å2
3----2.11 Å2
Refinement stepCycle: final / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10807 0 57 310 11174
Biso mean--66.46 47.72 -
Num. residues----1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911112
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210447
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.96315044
X-RAY DIFFRACTIONr_angle_other_deg0.904324282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43451343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72325.038522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27152042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0351551
X-RAY DIFFRACTIONr_chiral_restr0.0680.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022192
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 191 -
Rwork0.386 3700 -
all-3891 -
obs--100 %

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