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- PDB-1j2o: Structure of FLIN2, a complex containing the N-terminal LIM domai... -

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Basic information

Entry
Database: PDB / ID: 1j2o
TitleStructure of FLIN2, a complex containing the N-terminal LIM domain of LMO2 and ldb1-LID
ComponentsFusion of Rhombotin-2 and LIM domain-binding protein 1
KeywordsMETAL BINDING PROTEIN / LIM domain / LIM-interaction-domain (LID)
Function / homology
Function and homology information


histone H3-K4 acetylation / cellular component assembly / negative regulation of erythrocyte differentiation / mesendoderm development / regulation of kinase activity / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / head development / epithelial structure maintenance / primitive erythrocyte differentiation ...histone H3-K4 acetylation / cellular component assembly / negative regulation of erythrocyte differentiation / mesendoderm development / regulation of kinase activity / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / head development / epithelial structure maintenance / primitive erythrocyte differentiation / bHLH transcription factor binding / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / regulation of transcription elongation by RNA polymerase II / RUNX1 regulates transcription of genes involved in differentiation of HSCs / LIM domain binding / gastrulation with mouth forming second / anterior/posterior axis specification / cellular response to thyroid hormone stimulus / regulation of focal adhesion assembly / embryonic hemopoiesis / cell leading edge / somatic stem cell population maintenance / hair follicle development / positive regulation of cell adhesion / cerebellum development / regulation of cell migration / transcription coregulator binding / neuron differentiation / Wnt signaling pathway / RNA polymerase II transcription regulator complex / protein self-association / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cell differentiation / cell adhesion / negative regulation of DNA-templated transcription / chromatin / chromatin binding / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / nucleoplasm / metal ion binding / identical protein binding / nucleus
Similarity search - Function
LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Cysteine Rich Protein / Cysteine Rich Protein / 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
Rhombotin-2 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, automated noe assignment of ambiguous NOES
AuthorsDeane, J.E. / Mackay, J.P. / Kwan, A.H. / Sum, E.Y. / Visvader, J.E. / Matthews, J.M.
Citation
Journal: EMBO J. / Year: 2003
Title: Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4
Authors: Deane, J.E. / Mackay, J.P. / Kwan, A.H. / Sum, E.Y. / Visvader, J.E. / Matthews, J.M.
#1: Journal: PROTEIN ENG. / Year: 2001
Title: Design, production and characterization of FLIN2 and FLIN4: the engineering of intramolecular ldb1:LMO complexes.
Authors: Deane, J.E. / Visvader, J.E. / Mackay, J.P. / Matthews, J.M.
History
DepositionJan 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 of Rhombotin-2 and LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7353
Polymers12,6041
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with favorable non-bond energy
Representative

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Components

#1: Protein Fusion of Rhombotin-2 and LIM domain-binding protein 1 / FLIN2


Mass: 12604.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein is a fusion of the N-terminal LIM domain of LMO2 (residues 26-87) followed by an eleven residue linker (GGSGGHMGSGG) than the LID domain from ldb1 (residues 300-339). Originally ...Details: Protein is a fusion of the N-terminal LIM domain of LMO2 (residues 26-87) followed by an eleven residue linker (GGSGGHMGSGG) than the LID domain from ldb1 (residues 300-339). Originally expressed as a fusion with GST. GST portion removed by treatment with thrombin.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LMO2, Ldb1 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25801, UniProt: P70662
#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 NOESY
1223D 15N-separated NOESY
133HNHA
NMR detailsText: Backbone and Side-chain assignment made using standard 2D and 3D experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
1FLIN2 0.5mM, NaCl 50mM, dTris-HCL 20mM, pH 7.0, Dithiothreitol 1mM, TSP95% H20, 5% D20
2Uniformly 15-N labelled FLIN2 0.5mM, NaCl 50mM, dTris-HCL 20mM, pH 7.0, Dithiothreitol 1mM, DSS95% H20, 5% D20
3Uniformly 13-C/15-N labelled 0.5mM, NaCl 50mM, NaH2P04/Na2HPO4 20mM, pH 7.0, Dithiothreitol 1mM, DSS95% H20, 5% D20
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert et al.data analysis
XwinNMR2.5Brukerprocessing
XEASY1.3.13Bartels et al.data analysis
TALOSCornilescu et al.data analysis
ARIA1.1.2Nilges et al.structure solution
CNS1.1Brunger et al.structure solution
CNS1.1refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, automated noe assignment of ambiguous NOES
Software ordinal: 1
Details: The structures are based on 1690 NOE contraints (including 50 ambiguous constraints) and 134 torsion angle restaints
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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