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- PDB-3lpy: Crystal structure of the RRM domain of CyP33 -

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Basic information

Entry
Database: PDB / ID: 3lpy
TitleCrystal structure of the RRM domain of CyP33
ComponentsPeptidyl-prolyl cis-trans isomerase E
KeywordsISOMERASE / RRM / CyP33 / MLL1 binding / 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 / 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 / intracellular membrane-bounded organelle / mRNA binding / Neutrophil degranulation / regulation of DNA-templated transcription / RNA binding / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Z. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression.
Authors: Wang, Z. / Song, J. / Milne, T.A. / Wang, G.G. / Li, H. / Allis, C.D. / Patel, D.J.
History
DepositionFeb 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5078
Polymers17,6462
Non-polymers8616
Water1,802100
1
A: Peptidyl-prolyl cis-trans isomerase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0153
Polymers8,8231
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4925
Polymers8,8231
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.833, 59.833, 50.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 8822.854 Da / Num. of mol.: 2 / Fragment: N-terminal RRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIE, CYP33 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UNP9, peptidylprolyl isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes-Na, 2.4 M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 5, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 13746 / Num. obs: 13240 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 33.2 Å2 / Rsym value: 0.067 / Net I/σ(I): 58.1
Reflection shellResolution: 2→2.08 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 1312 / Rsym value: 0.418 / % possible all: 98.9

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1153 -RANDOM
Rwork0.216 ---
all-13746 --
obs-13240 96.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 50 100 1396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.82
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.36
LS refinement shellResolution: 2→2.08 Å
RfactorNum. reflection% reflection
Rfree0.331 95 -
Rwork0.334 --
obs-1312 98.9 %

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