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- PDB-1y7q: Mammalian SCAN domain dimer is a domain-swapped homologue of the ... -

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Basic information

Entry
Database: PDB / ID: 1y7q
TitleMammalian SCAN domain dimer is a domain-swapped homologue of the HIV capsid C-terminal domain
ComponentsZinc finger protein 174
KeywordsTRANSCRIPTION / SCAN domain / retroviral capsid C-terminal domain / dimer / C2H2 zinc finger associated
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / actin cytoskeleton / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II ...sequence-specific double-stranded DNA binding / actin cytoskeleton / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Zinc finger protein 174 / DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger ...Zinc finger protein 174 / DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Zinc finger protein 174
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing torsion angle dynamics
AuthorsIvanov, D. / Stone, J.R. / Maki, J.L. / Collins, T. / Wagner, G.
CitationJournal: Mol.Cell / Year: 2005
Title: Mammalian SCAN Domain Dimer Is a Domain-Swapped Homolog of the HIV Capsid C-Terminal Domain
Authors: Ivanov, D. / Stone, J.R. / Maki, J.L. / Collins, T. / Wagner, G.
History
DepositionDec 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger protein 174
B: Zinc finger protein 174


Theoretical massNumber of molelcules
Total (without water)23,2532
Polymers23,2532
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Zinc finger protein 174 / / AW-1 / Zinc finger and SCAN domain containing protein 8


Mass: 11626.498 Da / Num. of mol.: 2 / Fragment: SCAN domain, residues 37-132 / Mutation: P100E, P111L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF174, ZSCAN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15697

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM SCAN domain, U-15N,13C25 mM Na phosphate, pH 6.5, 200 mM NaCl, 1 mM DTT
22 mM SCAN domain, U-15N,2D25 mM Na phosphate, pH 6.5, 200 mM NaCl, 1 mM DTT
32 mM SCAN domain, unlabeled25 mM Na phosphate, pH 6.5, 200 mM NaCl, 1 mM DTT
Sample conditionsIonic strength: 200mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian UNITYPLUSVarianUNITYPLUS7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Hermann, T.,Guntert, P., Wuthrich, K.structure solution
NMRPipe0.04Delaglio, F.processing
CYANA1.0.6Hermann, T.,Guntert, P., Wuthrich, K.refinement
RefinementMethod: distance geometry simulated annealing torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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