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- PDB-2lua: Solution structure of CXC domain of MSL2 -

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Basic information

Entry
Database: PDB / ID: 2lua
TitleSolution structure of CXC domain of MSL2
ComponentsProtein male-specific lethal-2
KeywordsDNA BINDING PROTEIN / Metal binding
Function / homology
Function and homology information


dosage compensation complex / histone H2B ubiquitin ligase activity / X chromosome located dosage compensation complex, transcription activating / HATs acetylate histones / protein-RNA adaptor activity / MSL complex / dosage compensation by hyperactivation of X chromosome / sex-chromosome dosage compensation / chromatin-protein adaptor activity / lncRNA binding ...dosage compensation complex / histone H2B ubiquitin ligase activity / X chromosome located dosage compensation complex, transcription activating / HATs acetylate histones / protein-RNA adaptor activity / MSL complex / dosage compensation by hyperactivation of X chromosome / sex-chromosome dosage compensation / chromatin-protein adaptor activity / lncRNA binding / nuclear chromosome / X chromosome / transcription factor binding / protein autoubiquitination / molecular condensate scaffold activity / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin protein ligase activity / chromosome / protein ubiquitination / chromatin binding / DNA binding / metal ion binding
Similarity search - Function
E3 ubiquitin-protein ligase Msl2, zinc RING finger / E3 ubiquitin-protein ligase Msl2, CXC domain / E3 ubiquitin-protein ligase MSL2 / CXC domain of E3 ubiquitin-protein ligase MSL2 / zinc RING finger of MSL2 / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase Msl2, zinc RING finger / E3 ubiquitin-protein ligase Msl2, CXC domain / E3 ubiquitin-protein ligase MSL2 / CXC domain of E3 ubiquitin-protein ligase MSL2 / zinc RING finger of MSL2 / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase msl-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsFeng, Y. / Ye, K. / Zheng, S. / Wang, J.
CitationJournal: Plos One / Year: 2012
Title: Solution Structure of MSL2 CXC Domain Reveals an Unusual Zn(3)Cys(9) Cluster and Similarity to Pre-SET Domains of Histone Lysine Methyltransferases.
Authors: Zheng, S. / Wang, J. / Feng, Y. / Wang, J. / Ye, K.
History
DepositionJun 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Protein male-specific lethal-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8494
Polymers5,6531
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein male-specific lethal-2


Mass: 5652.500 Da / Num. of mol.: 1 / Fragment: CXC domain / Mutation: C49G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: msl-2, CG3241 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P50534
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D C(CO)NH
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N TOCSY
11013D CCH-TOCSY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11313D 1H-15N NOESY
11421D Cd113
11522D 1H-113Cd HSQC
11622D 1H-113Cd HMQC-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.5 mM [U-13C; U-15N] protein, 50 mM potassium phosphate, 0.01% w/v DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM protein, 3 mM Cd113 ZINC ION, 50 mM potassium phosphate, 0.01% w/v DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-13C; U-15N]0.5-1.51
50 mMpotassium phosphate-21
0.01 w/vDSS-31
1 mMentity_1-52
3 mMZINC ION-6Cd1132
50 mMpotassium phosphate-72
0.01 w/vDSS-82
Sample conditionsIonic strength: 0.05 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAVANCE4002

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
NMRViewJohnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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