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- PDB-2jox: Embryonic Neural Inducing Factor Churchill is not a DNA-Binding Z... -

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Basic information

Entry
Database: PDB / ID: 2jox
TitleEmbryonic Neural Inducing Factor Churchill is not a DNA-Binding Zinc Finger Protein: Solution Structure Reveals a Solvent-Exposed beta-Sheet and Zinc Binuclear Cluster
ComponentsChurchill protein
KeywordsTRANSCRIPTION / PROTEIN / ZINC
Function / homology
Function and homology information


multicellular organism development / positive regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
Transcription activator, Churchill / Transcription activator, Churchill / Churchill superfamily / Churchill protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsLee, B.M. / Buck-Koehntop, B.A. / Martinez-Yamout, M.A. / Gottesfeld, J.M. / Dyson, H. / Wright, P.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Embryonic Neural Inducing Factor Churchill Is not a DNA-binding Zinc Finger Protein: Solution Structure Reveals a Solvent-exposed beta-Sheet and Zinc Binuclear Cluster
Authors: Lee, B.M. / Buck-Koehntop, B.A. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionApr 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.deposit_site / _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 1.4May 8, 2024Group: Database references / Category: 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: Churchill protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3604
Polymers12,1641
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Churchill protein


Mass: 12163.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHURC1, C14orf52, CHCH / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUH1
#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 HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D (HCA)CO(CA)NH
1913D C(CO)NH
11013D (H)CCH-COSY
11113D CBCGCD
11213D CBCGCE
11313D HNHB
11413D HACAHB-COSY
11512D 1H-1H NOESY
11613D 1H-15N NOESY
11713D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] Churchill, 25 mM Tris, 100 mM NaCl, 2 mM DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMChurchill[U-13C; U-15N]1
25 mMTris1
100 mMNaCl1
2 mMDTT1
Sample conditionsIonic strength: 40 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX8003
Bruker DMXBrukerDMX9004
Bruker DRXBrukerDRX7505

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Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
NMRView5Johnson, One Moon Scientificdata analysis
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2351 / NOE intraresidue total count: 429 / NOE long range total count: 1344 / NOE medium range total count: 813 / NOE sequential total count: 550 / Protein chi angle constraints total count: 71 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 31 / Protein psi angle constraints total count: 30
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0.84 ° / Maximum upper distance constraint violation: 0.15 Å

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