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- PDB-2n1d: Solution structure of the MRG15-MRGBP complex -

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Basic information

Entry
Database: PDB / ID: 2n1d
TitleSolution structure of the MRG15-MRGBP complex
Components
  • MRG/MORF4L-binding protein
  • Mortality factor 4-like protein 1
KeywordsPROTEIN BINDING / MRG domain / protein-protein interaction / Tip60-NuA4 complex / HAT complex
Function / homology
Function and homology information


: / regulation of double-strand break repair / regulation of growth / Sin3-type complex / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / double-strand break repair via homologous recombination / nucleosome / chromatin organization / HATs acetylate histones ...: / regulation of double-strand break repair / regulation of growth / Sin3-type complex / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / double-strand break repair via homologous recombination / nucleosome / chromatin organization / HATs acetylate histones / regulation of apoptotic process / regulation of cell cycle / nuclear speck / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm
Similarity search - Function
Chromatin modification-related protein Eaf7/MRGBP / Chromatin modification-related protein EAF7 / MRG domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Enzyme I; Chain A, domain 2 / RNA binding activity-knot of a chromodomain ...Chromatin modification-related protein Eaf7/MRGBP / Chromatin modification-related protein EAF7 / MRG domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Enzyme I; Chain A, domain 2 / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MRG/MORF4L-binding protein / Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsXie, T. / Zmysloski, A.M. / Zhang, Y. / Radhakrishnan, I.
CitationJournal: Structure / Year: 2015
Title: Structural Basis for Multi-specificity of MRG Domains.
Authors: Xie, T. / Zmyslowski, A.M. / Zhang, Y. / Radhakrishnan, I.
History
DepositionMar 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MRG/MORF4L-binding protein
B: Mortality factor 4-like protein 1


Theoretical massNumber of molelcules
Total (without water)26,1272
Polymers26,1272
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-24 kcal/mol
Surface area12970 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy, restraint violations, and RMS deviations from the ideal covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein MRG/MORF4L-binding protein / MRG-binding protein / Up-regulated in colon cancer 4 / Urcc4


Mass: 6284.072 Da / Num. of mol.: 1 / Fragment: UNP residues 69-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRGBP, C20orf20 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NV56
#2: Protein Mortality factor 4-like protein 1 / MORF-related gene 15 protein / Protein MSL3-1 / Transcription factor-like protein MRG15


Mass: 19842.713 Da / Num. of mol.: 1 / Fragment: UNP residues 194-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORF4L1, MRG15, FWP006, HSPC008, HSPC061, PP368 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1322D double half-filtered 1H-1H NOESY
1423D 15N,13C-filtered, 15N,13C-edited 1H-1H NOESY
1533D 1H-15N NOESY
1643D 1H-13C NOESY
1742D double half-filtered 1H-1H NOESY
1843D 15N,13C-filtered, 15N,13C-edited 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] protein 1, 0.8 mM protein 2, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] protein 1, 0.8 mM protein 2, 100% D2O100% D2O
30.9 mM protein 1, 0.9 mM [U-100% 13C; U-100% 15N] protein 2, 90% H2O/10% D2O90% H2O/10% D2O
40.9 mM protein 1, 0.9 mM [U-100% 13C; U-100% 15N] protein 2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1-1[U-100% 13C; U-100% 15N]1
0.8 mMentity_2-21
0.8 mMentity_1-3[U-100% 13C; U-100% 15N]2
0.8 mMentity_2-42
0.9 mMentity_1-53
0.9 mMentity_2-6[U-100% 13C; U-100% 15N]3
0.9 mMentity_1-74
0.9 mMentity_2-8[U-100% 13C; U-100% 15N]4
Sample conditionsIonic strength: 0.05 / pH: 6.9 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Agilent INOVA / Manufacturer: Agilent / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
FelixAccelrys Software Inc.processing
SparkyGoddarddata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy, restraint violations, and RMS deviations from the ideal covalent geometry
Conformers calculated total number: 80 / Conformers submitted total number: 20

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