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- PDB-7zev: Free form of extended Cyp33-RRM -

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Basic information

Entry
Database: PDB / ID: 7zev
TitleFree form of extended Cyp33-RRM
ComponentsPeptidyl-prolyl cis-trans isomerase E
KeywordsTRANSCRIPTION / RRM / RNA BINDING PROTEIN-STRUCTURAL PROTEIN COMPLEX / HISTONE 3 / H3K4me3 / EPIGENETIC / MLL1 Transcription regulation / infant leukemia
Function / homology
Function and homology information


poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Transcription-Coupled Nucleotide Excision Repair (TC-NER) ...poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA splicing, via spliceosome / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein folding / secretory granule lumen / ficolin-1-rich granule lumen / nuclear speck / mRNA binding / intracellular membrane-bounded organelle / Neutrophil degranulation / regulation of DNA-templated transcription / RNA binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / RNA recognition motif / RNA recognition motif ...Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBlatter, M. / Allain, F. / Meylan, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Sci Adv / Year: 2023
Title: RNA binding induces an allosteric switch in Cyp33 to repress MLL1-mediated transcription.
Authors: Blatter, M. / Meylan, C. / Clery, A. / Giambruno, R. / Nikolaev, Y. / Heidecker, M. / Solanki, J.A. / Diaz, M.O. / Gabellini, D. / Allain, F.H.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase E


Theoretical massNumber of molelcules
Total (without water)13,1901
Polymers13,1901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 13189.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIE, CYP33 / Plasmid: PTYB12 / Details (production host): NdeI plus XhoI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNP9, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC aliphatic
132isotropic12D 1H-13C HSQC aromatic
141isotropic13D 1H-15N NOESY
152isotropic13D 1H-13C NOESY aliphatic
162isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O15N90% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O13C15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E[U-100% 15N]1
40 mMsodium chloridenatural abundance1
40 mMsodium phosphatenatural abundance1
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E[U-100% 13C; U-100% 15N]2
40 mMsodium chloridenatural abundance2
40 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 80 mM / Label: standard / pH: 7 / Pressure: AMBIENT Pa / Temperature: 303.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber10Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3.96Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 250 / Conformers submitted total number: 20

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