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- PDB-5tgc: Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP -

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Basic information

Entry
Database: PDB / ID: 5tgc
TitleStructure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP
Components
  • Actin-like protein ARP9
  • Actin-related protein 7
  • Regulator of Ty1 transposition protein 102
KeywordsSTRUCTURAL PROTEIN / Chromatin remodeling complexes / Actin-related protein / ATP-binding site / Nuclear actin
Function / homology
Function and homology information


RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / NuA4 histone acetyltransferase complex / chromosome segregation ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / NuA4 histone acetyltransferase complex / chromosome segregation / transcription elongation by RNA polymerase II / chromatin organization / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Regulator of Ty1 transposition protein 102 / Actin-like protein ARP9 / Actin-related protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.245 Å
AuthorsTuregun, B. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01_GM073791 United States
CitationJournal: Commun Biol / Year: 2018
Title: Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase.
Authors: Turegun, B. / Baker, R.W. / Leschziner, A.E. / Dominguez, R.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 7
B: Actin-like protein ARP9
C: Regulator of Ty1 transposition protein 102
D: Actin-related protein 7
E: Actin-like protein ARP9
F: Regulator of Ty1 transposition protein 102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,24311
Polymers252,9416
Non-polymers1,3035
Water00
1
A: Actin-related protein 7
B: Actin-like protein ARP9
C: Regulator of Ty1 transposition protein 102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1706
Polymers126,4703
Non-polymers6993
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Actin-related protein 7
E: Actin-like protein ARP9
F: Regulator of Ty1 transposition protein 102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0745
Polymers126,4703
Non-polymers6032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21540 Å2
ΔGint-138 kcal/mol
Surface area80350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.387, 87.982, 105.430
Angle α, β, γ (deg.)109.030, 104.640, 96.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETATPATPchain AAA - G0 - 5011
21LEULEUATPATPchain DDD - J3 - 5014
12ALAALASO4SO4chain BBB - I2 - 5022
22PROPROSO4SO4chain EEE - K3 - 5013
13METMETARGARGchain CCC1 - 902 - 91
23METMETASPASPchain FFF1 - 882 - 89

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Actin-related protein 7 / Actin-like protein ARP7 / Chromatin structure-remodeling complex protein ARP7 / SWI/SNF complex component ARP7


Mass: 55433.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARP7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12406
#2: Protein Actin-like protein ARP9 / Chromatin structure-remodeling complex protein ARP9 / SWI/SNF complex component ARP9


Mass: 53131.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARP9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05123
#3: Protein Regulator of Ty1 transposition protein 102


Mass: 17904.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RTT102 / Production host: Escherichia coli (E. coli) / References: UniProt: P53330
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / Details: 0.17M Ammonium Sulfate, 20% PEG 3350, 17 mM EDTA / PH range: 6 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.245→39.366 Å / Num. obs: 40398 / % possible obs: 96.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Rsym value: 0.087 / Net I/σ(I): 11.2
Reflection shellResolution: 3.25→3.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.418 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
SAINTv8.34adata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I6M, chains A,B,D

4i6m


Resolution: 3.245→39.366 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3219 1940 5.01 %
Rwork0.2756 36805 -
obs0.2779 38745 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.41 Å2 / Biso mean: 70.1963 Å2 / Biso min: 31.75 Å2
Refinement stepCycle: final / Resolution: 3.245→39.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14131 0 101 0 14232
Biso mean--63.93 --
Num. residues----1750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414502
X-RAY DIFFRACTIONf_angle_d0.9419640
X-RAY DIFFRACTIONf_chiral_restr0.0362188
X-RAY DIFFRACTIONf_plane_restr0.0042486
X-RAY DIFFRACTIONf_dihedral_angle_d15.2555435
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4497X-RAY DIFFRACTION16.296TORSIONAL
12D4497X-RAY DIFFRACTION16.296TORSIONAL
21B4331X-RAY DIFFRACTION16.296TORSIONAL
22E4331X-RAY DIFFRACTION16.296TORSIONAL
31C678X-RAY DIFFRACTION16.296TORSIONAL
32F678X-RAY DIFFRACTION16.296TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2453-3.32650.45841220.4082328245084
3.3265-3.41630.42641380.39052624276296
3.4163-3.51680.42231400.37392630277096
3.5168-3.63020.39091370.34072625276296
3.6302-3.75990.41281400.34812640278096
3.7599-3.91030.36241350.33472608274396
3.9103-4.08810.32261400.30062648278897
4.0881-4.30340.34131400.29072666280697
4.3034-4.57260.33561390.25442644278397
4.5726-4.92510.26791410.23032665280697
4.9251-5.41960.30151410.24062675281698
5.4196-6.20120.3031420.26052695283798
6.2012-7.80280.29911430.24292684282799
7.8028-39.36910.21131420.17822673281597

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