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- PDB-2l4z: NMR structure of fusion of CtIP (641-685) to LMO4-LIM1 (18-82) -

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Basic information

Entry
Database: PDB / ID: 2l4z
TitleNMR structure of fusion of CtIP (641-685) to LMO4-LIM1 (18-82)
ComponentsDNA endonuclease RBBP8,LIM domain transcription factor LMO4
KeywordsHYDROLASE / METAL BINDING PROTEIN / LIM domain / protein-protein interaction / LIM-interaction domain / LMO4 / RBBP8/CtIP / LIM-only protein
Function / homology
Function and homology information


regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / DNA double-strand break processing involved in repair via single-strand annealing / spinal cord association neuron differentiation / BRCA1-C complex / blastocyst hatching / spinal cord motor neuron differentiation / single-stranded DNA endodeoxyribonuclease activity / DNA strand resection involved in replication fork processing ...regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / DNA double-strand break processing involved in repair via single-strand annealing / spinal cord association neuron differentiation / BRCA1-C complex / blastocyst hatching / spinal cord motor neuron differentiation / single-stranded DNA endodeoxyribonuclease activity / DNA strand resection involved in replication fork processing / regulation of cell fate specification / homologous recombination / HDR through MMEJ (alt-NHEJ) / Impaired BRCA2 binding to PALB2 / mitotic G2/M transition checkpoint / positive regulation of kinase activity / motor neuron axon guidance / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / ventricular septum development / Transcriptional Regulation by E2F6 / cell leading edge / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of protein-containing complex assembly / regulation of cell migration / transcription repressor complex / thymus development / meiotic cell cycle / neural tube closure / double-strand break repair via homologous recombination / G1/S transition of mitotic cell cycle / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Meiotic recombination / RNA polymerase II transcription regulator complex / transcription corepressor activity / chromosome / Processing of DNA double-strand break ends / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / Hydrolases; Acting on ester bonds / cell division / DNA repair / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
DNA endonuclease Ctp1, N-terminal / DNA endonuclease RBBP8-like / Tumour-suppressor protein CtIP N-terminal domain / DNA endonuclease activator Ctp1, C-terminal / DNA endonuclease activator SAE2/CtIP C-terminus / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...DNA endonuclease Ctp1, N-terminal / DNA endonuclease RBBP8-like / Tumour-suppressor protein CtIP N-terminal domain / DNA endonuclease activator Ctp1, C-terminal / DNA endonuclease activator SAE2/CtIP C-terminus / 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
LIM domain transcription factor LMO4 / DNA endonuclease RBBP8
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiew, C. / Stokes, P.H. / Kwan, A.H. / Matthews, J.M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Basis of the Interaction of the Breast Cancer Oncogene LMO4 with the Tumour Suppressor CtIP/RBBP8.
Authors: Stokes, P.H. / Liew, C.W. / Kwan, A.H. / Foo, P. / Barker, H.E. / Djamirze, A. / O'Reilly, V. / Visvader, J.E. / Mackay, J.P. / Matthews, J.M.
History
DepositionOct 22, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Jan 1, 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_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity_name_com.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jul 26, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / 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 / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_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_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.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _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: DNA endonuclease RBBP8,LIM domain transcription factor LMO4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3513
Polymers13,2201
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA endonuclease RBBP8,LIM domain transcription factor LMO4 / CtBP-interacting protein / CtIP / Retinoblastoma-binding protein 8 / RBBP-8 / Retinoblastoma- ...CtBP-interacting protein / CtIP / Retinoblastoma-binding protein 8 / RBBP-8 / Retinoblastoma-interacting protein and myosin-like / RIM / Sporulation in the absence of SPO11 protein 2 homolog / SAE2 / Breast tumor autoantigen / LIM domain only protein 4 / LMO-4


Mass: 13219.799 Da / Num. of mol.: 1 / Mutation: C52S,C64S
Source method: isolated from a genetically manipulated source
Details: The fusion protein of CtIP (UNP 641-685), LINKER (901-911) and LMO4 (UNP 18-82)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: RBBP8, CTIP, Lmo4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q99708, UniProt: P61969, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHIS FUSION PROTEIN HAS NON-SEQUENTIAL RESIDUE NUMBERING. THE RESIDUE 901 LINKS TO THE RESIDUE 685 ...THIS FUSION PROTEIN HAS NON-SEQUENTIAL RESIDUE NUMBERING. THE RESIDUE 901 LINKS TO THE RESIDUE 685 AND THE RESIDUE 18 LINKS TO THE RESIDUE 911, RESPECTIVELY.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: CtIP on N-terminus, followed by 11-residue linker, LMO4-LIM1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HBHA(CO)NH
1623D HNCO
1723D 1H-15N NOESY
1823D HNHA
1923D C(CO)NH
11033D (H)CCH-TOCSY
11133D CCH-TOCSY
11233D 1H-13C NOESY
11342D 1H-1H NOESY
11442D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1150 uM [U-15N] Fusion protein-1, 20 mM sodium phosphate-2, 150 mM sodium chloride-3, 1 mM DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
2500 uM [U-99% 13C; U-99% 15N] Fusion protein-5, 20 mM sodium phosphate-6, 150 mM sodium chloride-7, 1 mM DTT-8, 90% H2O/10% D2O90% H2O/10% D2O
3300 uM [U-99% 13C; U-99% 15N] Fusion protein-9, 20 mM sodium phosphate-10, 150 mM sodium chloride-11, 1 mM DTT-12, 100% D2O100% D2O
4500 uM Fusion protein-13, 20 mM sodium phosphate-14, 150 mM sodium chloride-15, 1 mM DTT-16, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uMFusion protein-1[U-15N]1
20 mMsodium phosphate-21
150 mMsodium chloride-31
1 mMDTT-41
500 uMFusion protein-5[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-62
150 mMsodium chloride-72
1 mMDTT-82
300 uMFusion protein-9[U-99% 13C; U-99% 15N]3
20 mMsodium phosphate-103
150 mMsodium chloride-113
1 mMDTT-123
500 uMFusion protein-134
20 mMsodium phosphate-144
150 mMsodium chloride-154
1 mMDTT-164
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 6 ambient 291 K
2150 6 ambient 281 K
3150 6 ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.1-2.1Brukercollection
Sparky3.114Goddarddata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2166 / NOE intraresidue total count: 1027 / NOE long range total count: 333 / NOE medium range total count: 236 / NOE sequential total count: 463 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 123 / Protein psi angle constraints total count: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

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