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- PDB-2l1l: NMR Solution Structure of the Phi0 PKI NES Peptide in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 2l1l
TitleNMR Solution Structure of the Phi0 PKI NES Peptide in Complex with CRM1-RanGTP
Components
  • Exportin-1
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsNUCLEAR PROTEIN / Nuclear Export / PKI NES / CRM1 / RanGTP
Function / homology
Function and homology information


cellular response to triglyceride / cellular response to salt / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cAMP-dependent protein kinase activity / nuclear export signal receptor activity / regulation of centrosome duplication / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA ...cellular response to triglyceride / cellular response to salt / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cAMP-dependent protein kinase activity / nuclear export signal receptor activity / regulation of centrosome duplication / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / negative regulation of cAMP/PKA signal transduction / NEP/NS2 Interacts with the Cellular Export Machinery / cAMP-dependent protein kinase inhibitor activity / nucleocytoplasmic transport / negative regulation of protein import into nucleus / protein kinase A catalytic subunit binding / Maturation of hRSV A proteins / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / mRNA export from nucleus / Cajal body / ribosomal subunit export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / regulation of G2/M transition of mitotic cell cycle / ribosomal small subunit export from nucleus / NPAS4 regulates expression of target genes / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein export from nucleus / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / Deactivation of the beta-catenin transactivating complex / Heme signaling / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / kinetochore / small GTPase binding / Separation of Sister Chromatids / nuclear envelope / ribosome biogenesis / nuclear membrane / DNA-binding transcription factor binding / response to xenobiotic stimulus / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
de novo design (two linked rop proteins) - #250 / 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 ...de novo design (two linked rop proteins) - #250 / 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 / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / de novo design (two linked rop proteins) / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Exportin-1 / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMadl, T. / Sattler, M.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.
Authors: Guttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Structural analysis of large protein complexes using solvent paramagnetic relaxation enhancements.
Authors: Madl, T. / Guttler, T. / Gorlich, D. / Sattler, M.
History
DepositionJul 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase inhibitor alpha
B: Exportin-1


Theoretical massNumber of molelcules
Total (without water)17,5622
Polymers17,5622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2749.015 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRM1, PKIA, PRKACN1, XPO1 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P61925
#2: Protein Exportin-1 / Exp1 / Chromosome region maintenance 1 protein homolog / CRM1


Mass: 14813.308 Da / Num. of mol.: 1
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N CRINEPT
1212D 1H-13C HMQC
1313D 13C ed NOESY-HMQC
1413D 15C ed NOESY-HMQC
1512D 13C-13C TOCSY
1612D 13C-13C NOESY

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Sample preparation

DetailsContents: 200 uM [U-13C; U-15N; U-2H; ILV-1H] Phi0 PKI-NES-1, 200 uM [U-13C; U-15N; U-2H; ILV-1H, Ala-1H/12C/14N] Phi0 PKI-NES-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMPhi0 PKI-NES-1[U-13C; U-15N; U-2H; ILV-1H]1
200 uMPhi0 PKI-NES-2[U-13C; U-15N; U-2H; ILV-1H, Ala-1H/12C/14N]1
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
ARIA1.2Linge, O'Donoghue and Nilgesgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
SparkyGoddardpeak picking
NMRPipeCornilescu, Delaglio and Baxprocessing
TopSpinBruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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