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- PDB-2mbv: LMO4-LIM2 in complex with DEAF1 (404-418) -

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Basic information

Entry
Database: PDB / ID: 2mbv
TitleLMO4-LIM2 in complex with DEAF1 (404-418)
ComponentsFusion protein of LIM domain transcription factor LMO4 (77-147) and DEAF1 (404-418)
KeywordsTRANSCRIPTION / LMO4 / DEAF1 / embryonic development / cancer
Function / homology
Function and homology information


regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / spinal cord association neuron differentiation / regulation of mammary gland epithelial cell proliferation / spinal cord motor neuron differentiation / embryonic skeletal system development / regulation of cell fate specification / positive regulation of kinase activity / motor neuron axon guidance ...regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / spinal cord association neuron differentiation / regulation of mammary gland epithelial cell proliferation / spinal cord motor neuron differentiation / embryonic skeletal system development / regulation of cell fate specification / positive regulation of kinase activity / motor neuron axon guidance / ventricular septum development / cell leading edge / behavioral fear response / negative regulation of protein-containing complex assembly / regulation of cell migration / thymus development / neural tube closure / RNA polymerase II transcription regulatory region sequence-specific DNA binding / visual learning / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / transcription corepressor activity / DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Transcription factor DEAF-1 / Cysteine Rich Protein / Cysteine Rich Protein / SAND domain / SAND domain / SAND domain profile. / SAND domain / MYND finger / SAND-like domain superfamily / Zinc finger, MYND-type ...Transcription factor DEAF-1 / Cysteine Rich Protein / Cysteine Rich Protein / SAND domain / SAND domain / SAND domain profile. / SAND domain / MYND finger / SAND-like domain superfamily / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM domain transcription factor LMO4 / Deformed epidermal autoregulatory factor 1 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics, distance geometry
AuthorsJoseph, S. / Matthews, J.M. / Kwan, A.H.-Y. / Mackay, J.P. / Cubeddu, L. / Foo, P.
CitationJournal: To be Published
Title: Structural characterisation of LIM-only protein 4 (LMO4) in complex with Deformed Epidermal Autoregulatory Factor-1 (DEAF1)
Authors: Joseph, S. / Kwan, A.H. / Foo, P. / Cubeddu, L. / Mackay, J.P. / Matthews, J.M.
History
DepositionAug 6, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: 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_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_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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: Fusion protein of LIM domain transcription factor LMO4 (77-147) and DEAF1 (404-418)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2733
Polymers10,1421
Non-polymers1312
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fusion protein of LIM domain transcription factor LMO4 (77-147) and DEAF1 (404-418)


Mass: 10142.460 Da / Num. of mol.: 1
Fragment: LMO4 (UNP residues 77-147), DEAF1 (UNP residues 404-418)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lmo4 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P61969, UniProt: Q9Z1T5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1312D DQF-COSY
1412D 1H-1H TOCSY
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D HNCO
11113D HN(CA)CO
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 0.3-0.7 mM [U-99% 13C; U-99% 15N] DIC4, 20 mM acetic acid, 35 mM sodium chloride, 1 mM DTT, 0.067 mM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDIC4-1[U-99% 13C; U-99% 15N]0.3-0.71
20 mMacetic acid-21
35 mMsodium chloride-31
1 mMDTT-41
0.067 mMDSS-51
Sample conditionsIonic strength: 0.13 / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA0.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics, distance geometry
Software ordinal: 1
NMR constraintsNOE constraints total: 894 / NOE intraresidue total count: 450 / NOE long range total count: 227 / NOE medium range total count: 45 / NOE sequential total count: 172 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 43 / Protein psi angle constraints total count: 43
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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