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- PDB-2lau: Solution structure of the THAP-zinc finger domain 1-81 from the c... -

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Basic information

Entry
Database: PDB / ID: 2lau
TitleSolution structure of the THAP-zinc finger domain 1-81 from the cell growth suppressor human THAP11 protein
ComponentsTHAP domain-containing protein 11
KeywordsTRANSCRIPTION / ZINC FINGER / PROTEIN-DNA COMPLEX / DNA BINDING DOMAIN / TRANSCRIPTION FACTOR / CCCH / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of mitochondrial transcription / electron transport chain / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin ...regulation of mitochondrial transcription / electron transport chain / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
THAP / 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
THAP domain-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsDurand, J. / Campagne, S. / Milon, A. / Gervais, V.
CitationJournal: To be Published
Title: Solution structure of the THAP domain from the cell growth suppressor human THAP11
Authors: Durand, J. / Campagne, S. / Milon, A. / Gervais, V.
History
DepositionMar 21, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: 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_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_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.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
Revision 1.2May 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: THAP domain-containing protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1932
Polymers9,1271
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)19 / 112structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein THAP domain-containing protein 11


Mass: 9127.448 Da / Num. of mol.: 1 / Fragment: THAP-type zinc finger region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THAP11, HRIHFB2206 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EK4
#2: 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1422D 1H-1H TOCSY
1522D DQF-COSY
1622D 1H-1H NOESY
1713D CBCA(CO)NH
1813D HNCO
1913D HNCA
11013D HN(CA)CB
11113D HBHA(CO)NH
11213D HN(CO)CA
11333D HNHA
11413D (H)CCH-TOCSY
11533D 1H-15N NOESY
11633D 1H-15N TOCSY
11713D 1H-13C NOESY aliphatic
11813D 1H-13C NOESY aromatic
11913D H(CCO)NH
12013D C(CO)NH
12113D HNHB
12232D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] THAP domain, 50 mM Tris-HCl, 30 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM THAP domain, 50 mM Tris-HCl, 30 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-99% 15N] THAP domain, 50 mM Tris-HCl, 30 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTHAP domain-1[U-99% 13C; U-99% 15N]1
50 mMTris-HCl-21
30 mMsodium chloride-31
5 mMDTT-41
0.7 mMTHAP domain-52
50 mMTris-HCl-62
30 mMsodium chloride-72
5 mMDTT-82
0.7 mMTHAP domain-9[U-99% 15N]3
50 mMTris-HCl-103
30 mMsodium chloride-113
5 mMDTT-123
Sample conditionsIonic strength: 30 / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE9502
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospinprocessing
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospinpeak picking
TopSpinBruker Biospindata analysis
TopSpinKeller and Wuthrichprocessing
TopSpinKeller and Wuthrichchemical shift assignment
TopSpinKeller and Wuthrichpeak picking
TopSpinKeller and Wuthrichdata analysis
CNS1.21Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1766 / NOE intraresidue total count: 0 / NOE long range total count: 672 / NOE medium range total count: 355 / NOE sequential total count: 739
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 112 / Conformers submitted total number: 19

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