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- PDB-2lxd: Backbone 1H, 13C, and 15N Chemical Shift Assignments for LMO2(LIM... -

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Basic information

Entry
Database: PDB / ID: 2lxd
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for LMO2(LIM2)-Ldb1(LID)
ComponentsRhombotin-2,LIM domain-binding protein 1
KeywordsTRANSCRIPTION / LIM / 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 / epithelial structure maintenance / head development / primitive erythrocyte differentiation / bHLH transcription factor binding / beta-catenin-TCF complex ...regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / head development / primitive erythrocyte differentiation / bHLH transcription factor binding / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / RUNX1 regulates transcription of genes involved in differentiation of HSCs / LIM domain binding / gastrulation with mouth forming second / anterior/posterior axis specification / embryonic hemopoiesis / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / positive regulation of cell adhesion / hair follicle development / regulation of cell migration / cerebellum development / transcription coregulator binding / positive regulation of transcription elongation by RNA polymerase II / neuron differentiation / Wnt signaling pathway / RNA polymerase II transcription regulator complex / : / 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 adhesion / chromatin binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / metal ion 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 / torsion angle dynamics, torsion angle dynamics
Model detailslowest energy, model1
AuthorsDastmalchi, S. / Wilkinson-White, L. / Kwan, A.H. / Gamsjaeger, R. / Mackay, J.P. / Matthews, J.M.
Citation
Journal: Protein Sci. / Year: 2012
Title: Solution structure of a tethered Lmo2(LIM2) /Ldb1(LID) complex.
Authors: Dastmalchi, S. / Wilkinson-White, L. / Kwan, A.H. / Gamsjaeger, R. / Mackay, J.P. / Matthews, J.M.
#1: Journal: Biomol.Nmr Assign. / Year: 2010
Title: 1H, 15N and 13C assignments of an intramolecular Lmo2-LIM2/Ldb1-LID complex
Authors: Wilkinson-White, L.E. / Dastmalchi, S. / Kwan, A.H. / Ryan, D.P. / Mackay, J.P. / Matthews, J.M.
History
DepositionAug 20, 2012Deposition site: BMRB / Processing site: PDBJ
SupersessionSep 12, 2012ID: 2L3K
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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.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
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: Rhombotin-2,LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9363
Polymers13,8051
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Rhombotin-2,LIM domain-binding protein 1 / Cysteine-rich protein TTG-2 / LIM domain only protein 2 / LMO-2 / T-cell translocation protein 2 / ...Cysteine-rich protein TTG-2 / LIM domain only protein 2 / LMO-2 / T-cell translocation protein 2 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / mLdb1 / Nuclear LIM interactor


Mass: 13805.416 Da / Num. of mol.: 1 / Fragment: UNP residues 84-156,UNP residues 226-375 / Mutation: C47S
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN OF RHOMBOTIN-2, LINKER, LIM DOMAIN-BINDING PROTEIN 1
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lmo2, Rbtn-2, Rbtn2, Rhom-2, Ldb1, Nli / Production host: Escherichia coli (E. coli) / 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 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CO)CA
1713D HNHA
1813D HBHA(CO)NH
1933D (H)CCH-TOCSY
11012D 1H-13C HSQC
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11322D 1H-1H TOCSY
11422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1865 uM [U-100% 13C; U-100% 15N] Flic-1, 17 uM DSS-2, 5 % D2O-3, 20 mM MES-4, 1 mM DTT-5, 95 % H2O-6, 150 mM NaCl-7, 95% H2O/5% D2O95% H2O/5% D2O
2630 uM Flic-8, 17 uM DSS-9, 1 mM DTT-10, 5 % D2O-11, 20 mM MES-12, 95 % H2O-13, 150 mM NaCl-14, 95% H2O/5% D2O95% H2O/5% D2O
3865 uM [U-100% 13C; U-100% 15N] Flic-15, 17 uM DSS-16, 100 % D2O-17, 20 mM MES-18, 1 mM DTT-19, 150 mM NaCl-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
865 uMFlic-1[U-100% 13C; U-100% 15N]1
17 uMDSS-21
5 %D2O-31
20 mMMES-41
1 mMDTT-51
95 %H2O-61
150 mMNaCl-71
630 uMFlic-82
17 uMDSS-92
1 mMDTT-102
5 %D2O-112
20 mMMES-122
95 %H2O-132
150 mMNaCl-142
865 uMFlic-15[U-100% 13C; U-100% 15N]3
17 uMDSS-163
100 %D2O-173
20 mMMES-183
1 mMDTT-193
150 mMNaCl-203
Sample conditionspH: 6.5 / Pressure: 1 atm / 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
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
TopSpin2.1.b9Bruker Biospincollection
TopSpin2.1.b9Bruker Biospinprocessing
TALOS2009.215.15.29Cornilescu, Delaglio and Baxdata analysis
CYANArefinement
CNSrefinement
RefinementMethod: torsion angle dynamics, torsion angle dynamics / Software ordinal: 1 / Details: CYANA, CNS
NMR constraintsNOE constraints total: 1066 / NOE intraresidue total count: 283 / NOE long range total count: 316 / NOE medium range total count: 138 / NOE sequential total count: 329
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.79 ° / Maximum upper distance constraint violation: 0.4 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.016 Å

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