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- PDB-2l1g: RDC refined solution structure of the THAP zinc finger of THAP1 i... -

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Basic information

Entry
Database: PDB / ID: 2l1g
TitleRDC refined solution structure of the THAP zinc finger of THAP1 in complex with its 16bp RRM1 DNA target
Components
  • DNA (5'-D(*GP*CP*TP*TP*GP*TP*GP*TP*GP*GP*GP*CP*AP*GP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*CP*TP*GP*CP*CP*CP*AP*CP*AP*CP*AP*AP*GP*C)-3')
  • THAP domain-containing protein 1
KeywordsTranscription/DNA / Zinc finger / Protein-DNA complex / DNA binding domain / Transcription factor / CCCH / Transcription-DNA complex
Function / homology
Function and homology information


endothelial cell proliferation / regulation of mitotic cell cycle / PML body / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...endothelial cell proliferation / regulation of mitotic cell cycle / PML body / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
THAP domain-containing protein 1 / THAP / THAP-type zinc finger superfamily / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile
Similarity search - Domain/homology
DNA / DNA (> 10) / THAP domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Rigid body docking, Semi flexible simulated annealing, Water refinement
Model detailslowest energy, model 1
AuthorsCampagne, S. / Gervais, V. / Saurel, O. / Milon, A.
CitationJournal: To be published
Title: RDC refined solution structure of the THAP zinc finger of THAP1 in complex with its 16bp RRM1 DNA target
Authors: Campagne, S. / Gervais, V. / Saurel, O. / Milon, A.
History
DepositionJul 28, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / 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_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.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_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

Downloads & links

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Assembly

Deposited unit
A: THAP domain-containing protein 1
B: DNA (5'-D(*GP*CP*TP*TP*GP*TP*GP*TP*GP*GP*GP*CP*AP*GP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*CP*TP*GP*CP*CP*CP*AP*CP*AP*CP*AP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0554
Polymers19,9893
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein THAP domain-containing protein 1 / RRM1


Mass: 10189.776 Da / Num. of mol.: 1 / Fragment: zinc finger domain / Mutation: C62S, C67S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9NVV9
#2: DNA chain DNA (5'-D(*GP*CP*TP*TP*GP*TP*GP*TP*GP*GP*GP*CP*AP*GP*CP*G)-3')


Mass: 4986.212 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Specific THAP1 binding sequence element found in the RRM1 gene promoter
#3: DNA chain DNA (5'-D(P*CP*GP*CP*TP*GP*CP*CP*CP*AP*CP*AP*CP*AP*AP*GP*C)-3')


Mass: 4813.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Specific THAP1 binding sequence element found in the RRM1 gene promoter
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCO
1413D (H)CCH-TOCSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1713D 1H-15N TOCSY
1813D H(CCO)NH
1922D 1H-1H NOESY
11022D 1H-1H TOCSY
11112D IPAP 15N HSQC
11212D 15N HSQC T1
11312D 15N HSQC T2
11412D 15N HSQC Heteronuclear NOE
11513D 1JC'CA HNCO IPAP
NMR detailsText: The structure was determined by a combination of NOE derived restraints, hydrogen bonds, dihedral angles and RDCs.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-100% 13C; U-100% 15N] THAP domain-1, 1mM RRM1-2, 90% H2O/10% D2O90% H2O/10% D2O
21mM THAP domain-3, 1mM RRM1-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTHAP domain-1[U-100% 13C; U-100% 15N]1
1 mMRRM1-21
1 mMTHAP domain-32
1 mMRRM1-42
Sample conditionsIonic strength: 0.03 / pH: 6.8 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XEASYKeller and Wuthrichdata analysis
XEASYKeller and Wuthrichchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
CNS1.21refinement
RefinementMethod: Rigid body docking, Semi flexible simulated annealing, Water refinement
Software ordinal: 1
Details: HADDOCK (it0), HADDOCK (it1), HADDOCK (water refinement) done with 49 1D(HN-N) RDCs and 49 1D(CACO) RDCs
NMR constraintsNOE constraints total: 2518 / NOE intraresidue total count: 517 / NOE long range total count: 39 / NOE medium range total count: 974 / NOE sequential total count: 974 / Hydrogen bond constraints total count: 136 / Protein phi angle constraints total count: 78 / Protein psi angle constraints total count: 78
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 17 / Representative conformer: 1

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