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- PDB-6tvo: Human CRM1-RanGTP in complex with Leptomycin B -

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Basic information

Entry
Database: PDB / ID: 6tvo
TitleHuman CRM1-RanGTP in complex with Leptomycin B
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
KeywordsNUCLEAR PROTEIN / CRM1 / inhibitor / complex / Exportin 1
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of centrosome duplication / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette ...HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of centrosome duplication / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / regulation of protein export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nucleocytoplasmic transport / Maturation of hRSV A proteins / dynein intermediate chain binding / DNA metabolic process / mitotic sister chromatid segregation / protein localization to nucleus / spermatid development / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / sperm flagellum / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cajal body / mRNA export from nucleus / 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 / centriole / protein export from nucleus / viral process / Downregulation of TGF-beta receptor signaling / mitotic spindle organization / G protein activity / 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 / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / Separation of Sister Chromatids / GDP binding / melanosome / ribosome biogenesis / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / nuclear membrane / cadherin binding / ribonucleoprotein complex / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Exportin-1/5 ...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 / 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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Leptomycin B, bound form / Exportin-1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsShaikhqasem, A. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: J.Med.Chem. / Year: 2020
Title: Characterization of Inhibition Reveals Distinctive Properties for Human andSaccharomyces cerevisiaeCRM1.
Authors: Shaikhqasem, A. / Dickmanns, A. / Neumann, P. / Ficner, R.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 5, 2020Group: Database references / Derived calculations / Category: citation / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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
B: GTP-binding nuclear protein Ran
A: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8575
Polymers142,7492
Non-polymers1,1083
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-19 kcal/mol
Surface area50340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.290, 151.330, 234.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 20782.215 Da / Num. of mol.: 1 / 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
#2: Protein Exportin-1 / Karyopherin / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 121966.547 Da / Num. of mol.: 1 / Mutation: V430A, L431A, V432A
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
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-LMB / Leptomycin B, bound form / Leptomycin


Mass: 560.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H52O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal, antibiotic*YM
Has ligand of interestY

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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: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.02M sodium L-glutamate, 0.02M DL-alanine, 0.02M glycine, 0.02M DL-lysine HCl, 0.02 M DL-serine, 10%w/v PEG 8000, 20% v/v ethylene glycol, 0.1M bicine /Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.2→73.91 Å / Num. obs: 36131 / % possible obs: 99.5 % / Redundancy: 4.799 % / Biso Wilson estimate: 101.099 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.065 / Χ2: 1.077 / Net I/σ(I): 17.63 / Num. measured all: 173383 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.394.8850.9021.9627544570656380.7491.01498.8
3.39-3.624.8890.4224.0426276538153740.9180.47499.9
3.62-3.914.8650.2037.7324914513451210.9780.22899.7
3.91-4.294.7860.10513.4422791478247620.9930.11899.6
4.29-4.794.6890.0621.3119727423842070.9970.06899.3
4.79-5.534.8970.05125.5618537379837850.9980.05799.7
5.53-6.774.7670.04527.2315439324632390.9980.05199.8
6.77-9.564.5950.02148.03116762554254110.02499.5
9.56-73.914.4260.01671.056479148114640.9990.01898.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXV1.15refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NC1

3nc1


Resolution: 3.201→73.91 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.98
RfactorNum. reflection% reflection
Rfree0.2354 1813 5.02 %
Rwork0.2159 --
obs0.2169 36094 99.5 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 210.26 Å2 / Biso mean: 114.1921 Å2 / Biso min: 74.59 Å2
Refinement stepCycle: final / Resolution: 3.201→73.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9605 0 73 0 9678
Biso mean--115.61 --
Num. residues----1186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2011-3.28760.4131510.4194255799
3.2876-3.38440.33251430.34782611100
3.3844-3.49360.3191350.31742615100
3.4936-3.61850.33821450.31242606100
3.6185-3.76340.29731220.29132612100
3.7634-3.93460.28641420.25642621100
3.9346-4.1420.24531480.2262617100
4.142-4.40150.22321320.2138262799
4.4015-4.74130.22021320.1932264399
4.7413-5.21830.22561450.2013263499
5.2183-5.97320.25021410.22042647100
5.9732-7.52440.24651370.21452712100
7.5244-73.910.16161400.1545277999
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)
11.1273-0.0589-0.0020.4043-0.03650.9372-0.04110.12070.0842-0.00010.01970.0840.0409-0.02270.03050.9359-0.0409-0.03360.839-0.04530.9381-12.9799-19.2589-70.5221
21.9337-0.66860.43731.47431.03572.674-0.0236-0.014-0.2408-0.00110.13860.19750.3402-0.0656-0.08221.04-0.0822-0.06680.91830.02361.0613-11.8695-33.0201-76.3255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA8 - 1031
2X-RAY DIFFRACTION2chain BB6 - 180

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