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- PDB-3wee: Structure of the full-length yeast Arp7-Arp9 Heterodimer -

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Basic information

Entry
Database: PDB / ID: 3wee
TitleStructure of the full-length yeast Arp7-Arp9 Heterodimer
Components
  • Actin-like protein ARP9
  • Actin-related protein 7
KeywordsTRANSCRIPTION REGULATOR / Actin / chromatin / remodeling / RSC complex / SWI-SNF complex / nucleus / ARP / Actin-related protein / Actin-like protein
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 / nucleosome disassembly / RSC-type complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / anatomical structure morphogenesis / transcription elongation by RNA polymerase II ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / nucleosome disassembly / RSC-type complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / anatomical structure morphogenesis / 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
Actin; Chain A, domain 4 - #60 / 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 ...Actin; Chain A, domain 4 - #60 / 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
Actin-like protein ARP9 / Actin-related protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsLobsiger, J. / Richmond, T.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the full-length yeast Arp7-Arp9 heterodimer.
Authors: Lobsiger, J. / Hunziker, Y. / Richmond, T.J.
History
DepositionJul 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Dec 18, 2019Group: Database references / Derived calculations / Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-like protein ARP9
B: Actin-related protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0067
Polymers110,4012
Non-polymers6065
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-77 kcal/mol
Surface area42500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.774, 103.774, 184.451
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Actin-like protein ARP9 / Chromatin structure-remodeling complex protein ARP9 / SWI/SNF complex component ARP9


Mass: 54829.801 Da / Num. of mol.: 1 / Mutation: M1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARP9, SWP59, YM9973.07, YMR033W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q05123
#2: Protein Actin-related protein 7 / Actin-like protein ARP7 / Chromatin structure-remodeling complex protein ARP7 / SWI/SNF complex component ARP7


Mass: 55570.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARP7, SWP61, YP9367.14, YPR034W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q12406
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM

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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: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2M sodium/potassium phosphate, 100mM CAPS/NaOH, pH 10.5, 200mM lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00608 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2012
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00608 Å / Relative weight: 1
ReflectionResolution: 3.1→29.732 Å / Num. all: 21509 / Num. obs: 21509 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9 % / Biso Wilson estimate: 63.84 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.1
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3098 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→29.73 Å / SU ML: 0.34 / σ(F): 1.38 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 2004 9.33 %Random
Rwork0.1993 ---
all0.2012 21472 --
obs0.2012 21472 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.26 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6721 0 34 0 6755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076896
X-RAY DIFFRACTIONf_angle_d1.1129331
X-RAY DIFFRACTIONf_dihedral_angle_d14.1932585
X-RAY DIFFRACTIONf_chiral_restr0.0761051
X-RAY DIFFRACTIONf_plane_restr0.0051180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.1001-3.21070.34241960.292919271927
3.2107-3.33910.24541980.258819141914
3.3391-3.49090.26311940.225118921892
3.4909-3.67460.23661990.214419321932
3.6746-3.90440.24992010.210119241924
3.9044-4.20510.20971960.19219241924
4.2051-4.62680.18121990.17419461946
4.6268-5.29310.20052050.172619491949
5.2931-6.65640.24462000.194619821982
6.6564-29.73360.1822160.17920782078
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.49910.6024-0.29391.0324-0.31741.3679-0.206-0.54150.57210.58770.22120.0191-0.76430.3089-0.00140.71580.063-0.00020.7601-0.16260.7047-14.6196109.914834.8225
22.35811.1181-0.97081.9403-0.83232.4554-0.0722-0.43860.03450.1820.0209-0.3872-0.05670.3883-0.00340.40980.04510.03320.5599-0.07440.471-11.5024102.50825.7001
30.3980.1187-0.2880.3551-0.1670.25310.2410.58860.8497-0.16020.12430.048-0.19740.448501.0436-0.25170.26210.9452-0.13111.17290.7391122.81861.42
40.7131-0.7283-0.56421.28160.47251.5468-0.05330.32310.1806-0.09160.1827-0.2058-0.11120.0686-00.4353-0.01630.09210.50850.03780.447-17.258107.38134.1999
5-0.0007-0.00960.01380.1514-0.03080.6420.1048-0.22470.2176-0.23680.1875-1.1491-1.32850.93220.00870.9865-0.0670.14570.93070.08620.7469-31.9522115.5011-23.181
60.8704-0.5795-0.50540.7640.07040.4764-0.0605-0.23530.42960.6006-0.22920.333-0.4384-0.5802-00.7474-0.04210.06110.68910.02290.7383-29.2979109.68256.5245
70.6698-0.6140.23470.5706-0.15530.3242-0.1139-0.7118-0.08320.41830.02920.2429-0.1124-0.070600.7190.06840.03620.75840.04380.4703-28.81799.855335.7939
80.60680.14080.71221.32880.33231.144-0.16890.0393-0.18250.17220.0601-0.12950.05950.1465-00.52720.04190.15410.46910.02730.6392-19.653880.452315.7767
92.4999-0.1003-0.36921.5189-0.2131.953-0.18150.2123-0.4679-0.06630.0251-0.08950.34030.0177-0.00050.5916-0.0090.20970.37-0.09810.5868-24.957875.11187.6216
101.85030.1920.18650.531-0.2111.9477-0.10190.4466-0.3069-0.3485-0.04470.26660.4523-0.251800.6423-0.10410.1160.6928-0.23690.7382-45.853378.4451-6.7572
110.74370.2024-0.50360.3099-0.26220.5013-0.1660.0221-0.48580.07240.03060.04160.1889-0.0864-0.00020.638-0.08920.19540.5258-0.02350.7406-42.669969.830716.4209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 6:45 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 46:224 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 225:289 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 290:362 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 363:394 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 395:423 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 424:467 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 4:44 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 45:242 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 243:390 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 391:468 )

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