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- PDB-7zez: Trimolecular complex Cyp33-RRMdelta alpha : MLL1-PHD3 : H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 7zez
TitleTrimolecular complex Cyp33-RRMdelta alpha : MLL1-PHD3 : H3K4me3
Components
  • Histone H3
  • Isoform 3 of Peptidyl-prolyl cis-trans isomerase E
  • MLL cleavage product N320
KeywordsTRANSCRIPTION / RRM / RNA BINDING PROTEIN-STRUCTURAL PROTEIN COMPLEX / HISTONE 3 / H3K4me3 / EPIGENETIC / MLL1 Transcription regulation / infant leukemia
Function / homology
Function and homology information


protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / poly(A) binding / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / poly(A) binding / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / U2-type catalytic step 2 spliceosome / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / cyclosporin A binding / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PKMTs methylate histone lysines / mRNA splicing, via spliceosome / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Transcriptional regulation of granulopoiesis / nucleosome / protein folding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / methylation / protein-containing complex assembly / secretory granule lumen / ficolin-1-rich granule lumen / nuclear speck / protein heterodimerization activity / intracellular membrane-bounded organelle / mRNA binding / apoptotic process / chromatin binding / Neutrophil degranulation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus ...Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / 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 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / RNA-binding domain superfamily / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Histone H3 / Histone-lysine N-methyltransferase 2A / Peptidyl-prolyl cis-trans isomerase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Peptidyl-prolyl cis-trans isomerase E
B: MLL cleavage product N320
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3265
Polymers19,1953
Non-polymers1312
Water00
1


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

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Components

#1: Protein Isoform 3 of Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 10349.721 Da / Num. of mol.: 1 / Fragment: RRM (UNP RESIDUES 1-90)
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
#2: Protein MLL cleavage product N320 / N-terminal cleavage product of 320 kDa / p320


Mass: 7437.360 Da / Num. of mol.: 1 / Fragment: PHD ZINC FINGER (UNP RESIDUES 1564-1627)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Plasmid: PTYB11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03164
#3: Protein/peptide Histone H3


Mass: 1407.620 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TAIL (UNP RESIDUES 2-14) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: B4E380
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC aliphatic
1184isotropic12D 1H-13C HSQC aliphatic
1175isotropic12D 1H-13C HSQC aliphatic
133isotropic12D 1H-13C HSQC aromatic
1204isotropic12D 1H-13C HSQC aromatic
1195isotropic12D 1H-13C HSQC aromatic
142isotropic13D 1H-15N NOESY
153isotropic13D 1H-13C NOESY aliphatic
1104isotropic13D 1H-13C NOESY aliphatic
195isotropic13D 1H-13C NOESY aliphatic
163isotropic13D 1H-13C NOESY aromatic
1124isotropic13D 1H-13C NOESY aromatic
1115isotropic13D 1H-13C NOESY aromatic
173isotropic13D F3-FILTERED- F2-EDITED 13C NOESY
1144isotropic13D F3-FILTERED- F2-EDITED 13C NOESY
1135isotropic13D F3-FILTERED- F2-EDITED 13C NOESY
183isotropic12D F2- FILTERED NOESY
1164isotropic12D F2- FILTERED NOESY
1155isotropic12D F2- FILTERED NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution21 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O15N90% H2O/10% D2O
solution31 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 90% H2O/10% D2O13C15N90% H2O/10% D2O
solution41 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O13C15N_Cyp33100% D2O
solution51 mM PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O13C15N_MLL1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E[U-100% 15N]2
1 mMHISTONE-LYSINE N-METHYLTRANSFERASE 2A[U-100% 15N]2
1 mMHISTONE H3natural abundance2
40 mMsodium chloridenatural abundance2
40 mMsodium phosphatenatural abundance2
50 uMzinc chloridenatural abundance2
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E[U-100% 13C; U-100% 15N]3
1 mMHISTONE-LYSINE N-METHYLTRANSFERASE 2A[U-100% 13C; U-100% 15N]3
1 mMHISTONE H3natural abundance3
40 mMsodium chloridenatural abundance3
40 mMsodium phosphatenatural abundance3
10 uMzinc chloridenatural abundance3
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E[U-100% 13C; U-100% 15N]4
1 mMHISTONE-LYSINE N-METHYLTRANSFERASE 2Anatural abundance4
1 mMHISTONE H3natural abundance4
40 mMsodium chloridenatural abundance4
40 mMsodium phosphatenatural abundance4
10 uMzinc chloridenatural abundance4
1 mMPEPTIDYL-PROLYL CIS-TRANS ISOMERASE Enatural abundance5
1 mMHISTONE-LYSINE N-METHYLTRANSFERASE 2A[U-100% 13C; U-100% 15N]5
1 mMHISTONE H3natural abundance5
40 mMsodium chloridenatural abundance5
40 mMsodium phosphatenatural abundance5
10 uMzinc chloridenatural abundance5
Sample conditionsIonic strength: 80 mM / Label: standard / pH: 7 / Pressure: AMBIENT Pa / Temperature: 310.15 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
AmberCASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMANrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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