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- PDB-1wxl: Solution Structure of the HMG-box domain in the SSRP1 subunit of FACT -

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Basic information

Entry
Database: PDB / ID: 1wxl
TitleSolution Structure of the HMG-box domain in the SSRP1 subunit of FACT
ComponentsSingle-strand recognition protein
KeywordsDNA BINDING PROTEIN / FACT / SSRP1 / HMG
Function / homology
Function and homology information


regulation of chromatin organization => GO:1902275 / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / regulation of DNA binding / follicle cell of egg chamber development / FACT complex / chromatin => GO:0000785 ...regulation of chromatin organization => GO:1902275 / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / regulation of DNA binding / follicle cell of egg chamber development / FACT complex / chromatin => GO:0000785 / chromo shadow domain binding / nucleosomal DNA binding / positive regulation of actin filament polymerization / nucleosome binding / negative regulation of protein phosphorylation / : / histone binding / DNA replication / protein heterodimerization activity / DNA repair / nucleolus / RNA binding / nucleus / cytosol
Similarity search - Function
FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / High mobility group box domain ...FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FACT complex subunit Ssrp1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsKasai, N. / Tsunaka, Y. / Ohki, I. / Hirose, S. / Morikawa, K. / Tate, S.
CitationJournal: J.Biomol.Nmr / Year: 2005
Title: Solution structure of the HMG-box domain in the SSRP1 subunit of FACT
Authors: Kasai, N. / Tsunaka, Y. / Ohki, I. / Hirose, S. / Morikawa, K. / Tate, S.
History
DepositionJan 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-strand recognition protein


Theoretical massNumber of molelcules
Total (without water)8,6701
Polymers8,6701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Single-strand recognition protein / SSRP1 / SSRP / Chorion-factor 5


Mass: 8669.924 Da / Num. of mol.: 1 / Fragment: residues 5-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05344

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1322D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.2mM Protein U-15N,13C; 2mM Sodium Acetate buffer; 90% H2O,10% D2O90% H2O/10% D2O
22.2mM Protein U-15N,13C; 2mM Sodium Acetate buffer; 100% D2O100% D2O
Sample conditionsIonic strength: 0 / pH: 5.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6brukercollection
NMRPipeDelaglio et al.processing
CNS1.1Brunger et al.structure solution
PIPPGarrett et al.data analysis
CNS1.1Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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