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- PDB-3mdf: Crystal structure of the RRM domain of Cyclophilin 33 -

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Basic information

Entry
Database: PDB / ID: 3mdf
TitleCrystal structure of the RRM domain of Cyclophilin 33
ComponentsPeptidyl-prolyl cis-trans isomerase E
KeywordsRNA BINDING PROTEIN / RRM domain / PHD finger / Cyp33 / MLL / Isomerase / mRNA processing / mRNA splicing / Nucleus / RNA-binding / Rotamase / Spliceosome
Function / homology
Function and homology information


poly(A) binding / U2-type catalytic step 2 spliceosome / cyclosporin A binding / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / 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 / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / 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 / intracellular membrane-bounded organelle / mRNA binding / 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 / RRM (RNA recognition motif) domain / 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 / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHom, R.A. / Chang, P.Y. / Roy, S. / Mussleman, C.A. / Glass, K.C. / Seleznevia, A.I. / Gozani, O. / Ismagilov, R.F. / Cleary, M.L. / Kutateladze, T.G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular mechanism of MLL PHD3 and RNA recognition by the Cyp33 RRM domain.
Authors: Hom, R.A. / Chang, P.Y. / Roy, S. / Musselman, C.A. / Glass, K.C. / Selezneva, A.I. / Gozani, O. / Ismagilov, R.F. / Cleary, M.L. / Kutateladze, T.G.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,8272
Polymers18,8272
Non-polymers00
Water2,594144
1
A: Peptidyl-prolyl cis-trans isomerase E


Theoretical massNumber of molelcules
Total (without water)9,4141
Polymers9,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase E


Theoretical massNumber of molelcules
Total (without water)9,4141
Polymers9,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.840, 40.520, 65.660
Angle α, β, γ (deg.)90.00, 127.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9413.567 Da / Num. of mol.: 2 / Fragment: RNA-RECOGNITION MOTIF (UNP residues:1-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIE, CYP33 / Plasmid: pET-28 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 / References: UniProt: Q9UNP9, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 291 K / pH: 7.6
Details: 0.1 M Hepes and 1.0 M tri-sodium dehydrate citrate pH 7.6, Microcapillary, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9786
DetectorType: MBC DETECTOR / Detector: NOIR1 / Date: Apr 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→26.2 Å / Num. obs: 15587 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 6.76 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.41 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
d*TREKdata scaling
BALBESphasing
CNS1.1refinement
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CVJ

1cvj


Resolution: 1.85→26.2 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2.1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2895 -RANDOM
Rwork0.21 ---
obs0.21 15587 99.9 %-
all-30165 --
Displacement parametersBiso mean: 27.66 Å2
Baniso -1Baniso -2Baniso -3
1-3.416 Å20 Å28.917 Å2
2---7.005 Å20 Å2
3---3.589 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-1.85 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.85→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 0 144 1448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.14
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.85→1.92 Å
RfactorNum. reflection% reflection
Rfree0.303 331 -
Rwork0.2767 --
obs--89.05 %

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