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- PDB-2lm0: Solution structure of the AF4-AF9 complex -

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Basic information

Entry
Database: PDB / ID: 2lm0
TitleSolution structure of the AF4-AF9 complex
ComponentsAF4/FMR2 family member 1/Protein AF-9 chimera
KeywordsNUCLEAR PROTEIN / Intrinsically Disordered
Function / homology
Function and homology information


super elongation complex / modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex ...super elongation complex / modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / chromosome / histone binding / gene expression / regulation of gene expression / molecular adaptor activity / chromatin binding / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #290 / AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF-4 proto-oncoprotein N-terminal region / AF4 interaction motif / AFF4, C-terminal homology domain / : / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #290 / AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF-4 proto-oncoprotein N-terminal region / AF4 interaction motif / AFF4, C-terminal homology domain / : / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein AF-9 / AF4/FMR2 family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLeach, B.I. / Kuntimaddi, A. / Schmidt, C.R. / Cierpicki, T. / Johnson, S.A. / Bushweller, J.H.
CitationJournal: Structure / Year: 2013
Title: Leukemia Fusion Target AF9 Is an Intrinsically Disordered Transcriptional Regulator that Recruits Multiple Partners via Coupled Folding and Binding.
Authors: Leach, B.I. / Kuntimaddi, A. / Schmidt, C.R. / Cierpicki, T. / Johnson, S.A. / Bushweller, J.H.
History
DepositionNov 18, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AF4/FMR2 family member 1/Protein AF-9 chimera


Theoretical massNumber of molelcules
Total (without water)14,3411
Polymers14,3411
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 #1

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Components

#1: Protein AF4/FMR2 family member 1/Protein AF-9 chimera / ALL1-fused gene from chromosome 4 protein / Protein AF-4 / Protein FEL / Proto-oncogene AF4 / ALL1- ...ALL1-fused gene from chromosome 4 protein / Protein AF-4 / Protein FEL / Proto-oncogene AF4 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 14340.592 Da / Num. of mol.: 1 / Fragment: UNP residues 738-779, UNP residues 490-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Thioredoxin coding region removed by Nde1 cleavage
Gene: AFF1, AF4, FEL, MLLT2, PBM1, MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 DE3 / References: UniProt: P51825, UniProt: P42568

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of the AF9 AHD fused to AF4
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D (H)CCH-TOCSY
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1823D 1H-13C NOESY
1922D 1H-15N HSQC
11033D HNCO IPAP
11143D HNCO IPAP
11243D HNCO IPAP
11343D HNCO IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
19.3 mM Bis-Tris, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 400 uM [U-100% 13C; U-100% 15N] Protein, 95% H2O/5% D2O95% H2O/5% D2O
215.8 mM MES, 9.3 mM Bis-Tris, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 2 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
39.3 mM Bis-Tris, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 400 uM [U-100% 13C; U-100% 15N] Protein, 3.5 % (3-acrylamidopropyl)-trimethylammonium chloride, 3.5 % acrylic acid, 95% H2O/5% D2O95% H2O/5% D2O
49.3 mM Bis-Tris, 15.8 mM MES, 100 mM sodium chloride, 1 mM DTT, 5 % D-99% D2O, 400 uM [U-100% 13C; U-100% 15N] Protein, 3.5 % (3-acrylamidopropyl)-trimethylammonium chloride, 3.5 % acrylamide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
9.3 mMBis-Tris-11
15.8 mMMES-21
100 mMsodium chloride-31
1 mMDTT-41
5 %D2O-5D-99%1
400 uMProtein-6[U-100% 13C; U-100% 15N]1
15.8 mMMES-72
9.3 mMBis-Tris-82
100 mMsodium chloride-92
1 mMDTT-102
5 %D2O-11D-99%2
2 mMprotein-12[U-100% 13C; U-100% 15N]2
9.3 mMBis-Tris-133
15.8 mMMES-143
100 mMsodium chloride-153
1 mMDTT-163
5 %D2O-17D-99%3
400 uMProtein-18[U-100% 13C; U-100% 15N]3
3.5 %(3-acrylamidopropyl)-trimethylammonium chloride-193
3.5 %acrylic acid-203
9.3 mMBis-Tris-214
15.8 mMMES-224
100 mMsodium chloride-234
1 mMDTT-244
5 %D2O-25D-99%4
400 uMProtein-26[U-100% 13C; U-100% 15N]4
3.5 %(3-acrylamidopropyl)-trimethylammonium chloride-274
3.5 %acrylamide-284
Sample conditionsIonic strength: 100 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker US2BrukerUS28002

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.27Schwieters, Kuszewski, Tjandra and Clorerefinement
XPLOR-NIH2.27Schwieters, Kuszewski, Tjandra and Clorestructure solution
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Simulated annealing with RDCs
NMR constraintsNOE constraints total: 2168 / NOE intraresidue total count: 1042 / NOE long range total count: 306 / NOE medium range total count: 291 / NOE sequential total count: 529 / Protein phi angle constraints total count: 59 / Protein psi angle constraints total count: 57
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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