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- PDB-5vwe: Solution NMR structure of the HMG domain of human FACT complex su... -

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Basic information

Entry
Database: PDB / ID: 5vwe
TitleSolution NMR structure of the HMG domain of human FACT complex subunit SSRP1
ComponentsFACT complex subunit SSRP1
KeywordsTRANSCRIPTION / Hitone chaperone / DNA replication / DNA damage response / human FACT complex / SSRP1 / NMR spectroscopy
Function / homology
Function and homology information


FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat ...FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / nucleosome binding / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / histone binding / DNA replication / Regulation of TP53 Activity through Phosphorylation / DNA repair / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
: / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH 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 ...: / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHu, Q. / Botuyan, M.V. / Mer, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
CitationJournal: To Be Published
Title: Solution NMR structure of the HMG domain of human FACT complex subunit SSRP1
Authors: Hu, Q. / Botuyan, M.V. / Mer, G.
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: FACT complex subunit SSRP1


Theoretical massNumber of molelcules
Total (without water)8,0501
Polymers8,0501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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 FACT complex subunit SSRP1 / Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin ...Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin transcription complex 80 kDa subunit / FACTp80 / Facilitates chromatin transcription complex subunit SSRP1 / Recombination signal sequence recognition protein 1 / Structure-specific recognition protein 1 / hSSRP1 / T160


Mass: 8050.128 Da / Num. of mol.: 1 / Fragment: unp residues 551-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSRP1, FACT80 / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q08945

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HBHA(CO)NH
161isotropic13D H(CCO)NH
171isotropic13D CCCH-TOCSY
181isotropic13D HNCO
191isotropic13D HCACO
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-100% 13C; U-100% 15N] Human SSRP1 HMG Domain, 50 mM Sodium phosphate buffer, 50 mM NaCl, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMHuman SSRP1 HMG Domain[U-100% 13C; U-100% 15N]1
50 mMSodium phosphate buffernatural abundance1
50 mMNaClnatural abundance1
Sample conditionsIonic strength: 50 mM NaCl mM / Label: Conditions_1 / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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