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- PDB-1m3v: FLIN4: Fusion of the LIM binding domain of Ldb1 and the N-termina... -

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Basic information

Entry
Database: PDB / ID: 1m3v
TitleFLIN4: Fusion of the LIM binding domain of Ldb1 and the N-terminal LIM domain of LMO4
Componentsfusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO4
KeywordsMETAL BINDING PROTEIN / LIM domain / fusion protein / LMO proteins / Ldb1
Function / homology
Function and homology information


regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / primitive erythrocyte differentiation / head development / beta-catenin-TCF complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / primitive erythrocyte differentiation / head development / beta-catenin-TCF complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / epithelial structure maintenance / LIM domain binding / gastrulation with mouth forming second / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / hair follicle development / positive regulation of cell adhesion / regulation of cell migration / cerebellum development / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulator complex / Wnt signaling pathway / neuron differentiation / transcription regulator complex / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / chromatin / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsDeane, J.E. / Mackay, J.P. / Kwan, A.H.Y. / 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: J.Biomol.NMR / Year: 2002
Title: 1H, 15N and 13C assignments of FLIN4, an intramolecular LMO4:ldb1 complex.
Authors: Deane, J.E. / Visvader, J.E. / Mackay, J.P. / Matthews, J.M.
#2: 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. / Sum, E. / Mackay, J.P. / Lindeman, G.J. / Visvader, J.E. / Matthews, J.M.
History
DepositionJun 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6May 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: fusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1483
Polymers13,0181
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein fusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO4 / FLIN4


Mass: 13017.508 Da / Num. of mol.: 1 / Mutation: C37S, C49S
Source method: isolated from a genetically manipulated source
Details: Fusion protein comprises LIM domain transcription factor LMO4 (residues 16-86) via glycine-rich linker (GGSGGHMGSGG), LIM domain-binding protein 1 (residues 300-339).
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: 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
1212D TOCSY
131DQF-COSY
1423D 15N-separated NOESY
153HNHA
163HNCA
173HN(CO)CA
183HN(CA)CB
193CBCA(CO)NH
1103(H)CCH-TOCSY
NMR detailsText: This structure was solved using triple resonance NMR techniques. In addition to the experiments listed above HNCO, HN(CA)CO, CC(CO)NH-TOCSY and HCC(CO)NH-TOCSY were also used for backbone and ...Text: This structure was solved using triple resonance NMR techniques. In addition to the experiments listed above HNCO, HN(CA)CO, CC(CO)NH-TOCSY and HCC(CO)NH-TOCSY were also used for backbone and side chain assignments.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM FLIN4, 20mM NaH2PO4, pH7.0, 50mM NaCl, 1mM DTT, 20uM d4-TSP95% H2O/5% D2O
20.5mM [15N]-FLIN4, 20mM NaH2PO4, pH7.0, 50mM NaCl, 1mM DTT, 20uM d4-TSP95% H2O/5% D2O
31.0mM [13C,15N]-FLIN4, 20mM NaH2PO4, pH7.0, 50mM NaCl, 1mM DTT, 20uM d4-TSP95% H2O/5% D2O
Sample conditionspH: 7 / 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
XwinNMR2.5Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
DYANA1.5Guntert et alrefinement
ARIA1.1.2Linge et alstructure solution
TALOS98.040.21.02Cornilescu et alstructure solution
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: Structure calculations were performed using ARIA 1.1. Final structures are based on 1804 unambiguous and 81 ambiguous NOE-derived distance restraints and 112 angle constraints from coupling ...Details: Structure calculations were performed using ARIA 1.1. Final structures are based on 1804 unambiguous and 81 ambiguous NOE-derived distance restraints and 112 angle constraints from coupling constant data and predictions from chemical shift analysis using TALOS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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