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- PDB-2mv7: Solution NMR structure of DOT1L in complex with AF9 (DOT1L-AF9) -

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Basic information

Entry
Database: PDB / ID: 2mv7
TitleSolution NMR structure of DOT1L in complex with AF9 (DOT1L-AF9)
Components
  • Histone-lysine N-methyltransferase, H3 lysine-79 specific
  • Protein AF-9
KeywordsProtein Binding/Transferase / MIXED LINEAGE LEUKEMIA / LEUKEMIA / Protein Binding-Transferase complex
Function / homology
Function and homology information


modification-dependent protein binding / regulation of stem cell division / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / segment specification / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / histone H3 methyltransferase activity ...modification-dependent protein binding / regulation of stem cell division / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / segment specification / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / anterior/posterior pattern specification / histone methyltransferase activity / hematopoietic stem cell differentiation / heterochromatin formation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / telomere organization / transcription elongation factor complex / DNA damage checkpoint signaling / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / PKMTs methylate histone lysines / chromosome / gene expression / histone binding / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / molecular adaptor activity / transcription coactivator activity / intracellular membrane-bounded organelle / DNA repair / chromatin binding / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / YEATS / YEATS superfamily / YEATS family ...AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein AF-9 / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, SIMULATED ANNEALING, SIMULATED ANNEALING
Model detailslowest energy, model1
AuthorsKuntimaddi, A. / Bushweller, J.H.
CitationJournal: Cell Rep / Year: 2015
Title: Degree of Recruitment of DOT1L to MLL-AF9 Defines Level of H3K79 Di- and Tri-methylation on Target Genes and Transformation Potential.
Authors: Kuntimaddi, A. / Achille, N.J. / Thorpe, J. / Lokken, A.A. / Singh, R. / Hemenway, C.S. / Adli, M. / Zeleznik-Le, N.J. / Bushweller, J.H.
History
DepositionSep 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 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 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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: Protein AF-9
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific


Theoretical massNumber of molelcules
Total (without water)10,8142
Polymers10,8142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 8147.218 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 500-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PETDUET-1 / Gene: AF9, MLLT3, YEATS3 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 DE3 / References: UniProt: P42568
#2: Protein/peptide Histone-lysine N-methyltransferase, H3 lysine-79 specific / DOT1-like protein / Histone H3-K79 methyltransferase / H3-K79-HMTase / Lysine N-methyltransferase 4


Mass: 2667.113 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 877-900
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PETDUET-1 / Gene: DOT1L, KIAA1814, KMT4 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 DE3
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase

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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 C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D (H)CCH-TOCSY
1913D HNHA
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11333D HNCO IPAP
11413D HNCO IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
1750 uM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 uM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
2750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O95% H2O/5% D2O
3750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLIC ACID, 750 mM [U-100% 13C; U-100% 15N] PROTEIN AF, 750 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC, 9.3 mM BIS-TRIS, 15.8 mM MES, 100 mM SODIUM CHLORIDE, 1 mM DTT, 3.5 % (3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE, 3.5 % ACRYLAMIDE, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
750 uMPROTEIN AF-9-1[U-100% 13C; U-100% 15N]1
750 uMHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC-2[U-100% 13C; U-100% 15N]1
9.3 mMBIS-TRIS-31
15.8 mMMES-41
100 mMSODIUM CHLORIDE-51
1 mMDTT-61
750 mMPROTEIN AF-9-7[U-100% 13C; U-100% 15N]2
750 mMHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC-8[U-100% 13C; U-100% 15N]2
9.3 mMBIS-TRIS-92
15.8 mMMES-102
100 mMSODIUM CHLORIDE-112
1 mMDTT-122
3.5 %(3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE-132
3.5 %ACRYLIC ACID-142
750 mMPROTEIN AF-9-15[U-100% 13C; U-100% 15N]2
750 mMHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC-16[U-100% 13C; U-100% 15N]2
9.3 mMBIS-TRIS-172
15.8 mMMES-182
100 mMSODIUM CHLORIDE-192
1 mMDTT-202
3.5 %(3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE-212
3.5 %ACRYLAMIDE-222
750 mMPROTEIN AF-9-23[U-100% 13C; U-100% 15N]3
750 mMHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC-24[U-100% 13C; U-100% 15N]3
9.3 mMBIS-TRIS-253
15.8 mMMES-263
100 mMSODIUM CHLORIDE-273
1 mMDTT-283
3.5 %(3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE-293
3.5 %ACRYLIC ACID-303
750 mMPROTEIN AF-9-31[U-100% 13C; U-100% 15N]3
750 mMHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC-32[U-100% 13C; U-100% 15N]3
9.3 mMBIS-TRIS-333
15.8 mMMES-343
100 mMSODIUM CHLORIDE-353
1 mMDTT-363
3.5 %(3-ACRYLAMIDOPROPYL)-TRIMETHYLAMMONIUM CHLORIDE-373
3.5 %ACRYLAMIDE-383
Sample conditionsIonic strength: 100 / pH: 6.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE6001
VARIAN INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR_NIH_2.34SCHWIETERS, KUSZEWSKI, TJrefinement
X-PLOR_NIH_2.34SCHWIETERS, KUSZEWSKI, TJstructure solution
CYANA_2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
SparkyGoddardstructure solution
SparkyGoddardpeak picking
SparkyGoddardrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxcollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
MOLMOLKoradi, Billeter and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
VnmrJVariancollection
RefinementMethod: simulated annealing, SIMULATED ANNEALING, SIMULATED ANNEALING
Software ordinal: 1
Details: FIRST ROUND OF STRUCTURE CALCULATION/REFINEMENT WAS CONDUCTED WITH DISTANCE AND DIHEDRAL ANGLE RESTRAINTS ONLY USING HIGH TEMPERATURE ANNEALING. FINAL ROUND OF REFINEMENT INCLUDED RDCS USING ...Details: FIRST ROUND OF STRUCTURE CALCULATION/REFINEMENT WAS CONDUCTED WITH DISTANCE AND DIHEDRAL ANGLE RESTRAINTS ONLY USING HIGH TEMPERATURE ANNEALING. FINAL ROUND OF REFINEMENT INCLUDED RDCS USING LOW TEMPERATURE ANNEALING., FIRST ROUND WITH DISTANCE AND DIHEDRAL ANGLE RESTRAINTS ONLY WITH HIGH TEMPERATURE ANNEALING., FINAL ROUND OF REFINEMENT WITH RDCS WITH LOW TEMPERATURE ANNEALING.
NMR constraintsNOE constraints total: 1667 / NOE intraresidue total count: 821 / NOE long range total count: 230 / NOE medium range total count: 216 / NOE sequential total count: 400
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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