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- PDB-2miu: Structure of FHL2 LIM adaptor and its Interaction with Ski -

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Basic information

Entry
Database: PDB / ID: 2miu
TitleStructure of FHL2 LIM adaptor and its Interaction with Ski
ComponentsFour and a half LIM domains protein 2
KeywordsPROTEIN BINDING / FHL2 / LIM domain
Function / homology
Function and homology information


atrial cardiac muscle cell development / ventricular cardiac muscle cell development / bHLH transcription factor binding / heart trabecula formation / negative regulation of calcineurin-NFAT signaling cascade / transcription factor binding / response to hormone / transcription coregulator activity / PPARA activates gene expression / Z disc ...atrial cardiac muscle cell development / ventricular cardiac muscle cell development / bHLH transcription factor binding / heart trabecula formation / negative regulation of calcineurin-NFAT signaling cascade / transcription factor binding / response to hormone / transcription coregulator activity / PPARA activates gene expression / Z disc / osteoblast differentiation / transcription corepressor activity / focal adhesion / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
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
Four and a half LIM domains protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, Y. / Sun, Y. / Medrano, E.E. / Tian, X. / Weiss, M.A.
CitationJournal: To be Published
Title: Structure of FHL2 LIM adaptor and its Interaction with Ski
Authors: Yang, Y. / Sun, Y. / Medrano, E.E. / Tian, X. / Weiss, M.A.
History
DepositionDec 20, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: 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_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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: Four and a half LIM domains protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6814
Polymers11,4851
Non-polymers1963
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 / 100structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Four and a half LIM domains protein 2 / FHL-2 / LIM domain protein DRAL / Skeletal muscle LIM-protein 3 / SLIM-3


Mass: 11484.961 Da / Num. of mol.: 1 / Fragment: LIM domain (UNP residues 1-98)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FHL2, DRAL, SLIM3 / Plasmid: pGEX-5X-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14192
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D C(CO)NH
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D HNCO
1913D 1H-13C NOESY
11013D 1H-15N NOESY

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 50 mM sodium chloride, 0.5-0.8 mM [U-13C; U-15N] protein, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein-1[U-13C; U-15N]0.5-0.81
50 mMsodium phosphate-21
50 mMsodium chloride-31
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
PIPPGarrettdata analysis
Insight IIAccelrys Software Inc.data analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
XwinNMRBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1903 / NOE intraresidue total count: 577 / NOE long range total count: 481 / NOE medium range total count: 360 / NOE sequential total count: 485
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

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