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- PDB-4m6b: Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2... -

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Basic information

Entry
Database: PDB / ID: 4m6b
TitleCrystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer
Components
  • Chimera protein of Histone H2B.1 and Histone H2A.Z
  • Helicase SWR1
KeywordsStructural Protein/Hydrolase / Chromatin remodeler / Histone binding / Structural Protein-Hydrolase complex
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / nuclear-transcribed mRNA catabolic process, non-stop decay / Swr1 complex / replication fork protection complex / recombinational repair / postreplication repair / ATP-dependent chromatin remodeler activity / silent mating-type cassette heterochromatin formation / helicase activity / euchromatin ...Condensation of Prophase Chromosomes / nuclear-transcribed mRNA catabolic process, non-stop decay / Swr1 complex / replication fork protection complex / recombinational repair / postreplication repair / ATP-dependent chromatin remodeler activity / silent mating-type cassette heterochromatin formation / helicase activity / euchromatin / chromatin DNA binding / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / DNA helicase / molecular adaptor activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / chromatin / structural molecule activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone, subunit A / Histone, subunit A / Histone H2B signature. ...domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Helicase conserved C-terminal domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B.1 / Helicase SWR1 / Histone H2A.Z
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHong, J.J. / Feng, H.Q. / Wang, F. / Ranjan, A. / Chen, J.H. / Jiang, J.S. / Girlando, R. / Xiao, T.S. / Wu, C. / Bai, Y.W.
CitationJournal: Mol.Cell / Year: 2014
Title: The Catalytic Subunit of the SWR1 Remodeler Is a Histone Chaperone for the H2A.Z-H2B Dimer.
Authors: Hong, J. / Feng, H. / Wang, F. / Ranjan, A. / Chen, J. / Jiang, J. / Ghirlando, R. / Xiao, T.S. / Wu, C. / Bai, Y.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Structure summary
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Chimera protein of Histone H2B.1 and Histone H2A.Z
C: Helicase SWR1
D: Chimera protein of Histone H2B.1 and Histone H2A.Z
F: Helicase SWR1


Theoretical massNumber of molelcules
Total (without water)54,3514
Polymers54,3514
Non-polymers00
Water3,369187
1
A: Chimera protein of Histone H2B.1 and Histone H2A.Z
C: Helicase SWR1


Theoretical massNumber of molelcules
Total (without water)27,1762
Polymers27,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-14 kcal/mol
Surface area10820 Å2
MethodPISA
2
D: Chimera protein of Histone H2B.1 and Histone H2A.Z
F: Helicase SWR1


Theoretical massNumber of molelcules
Total (without water)27,1762
Polymers27,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-14 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.667, 69.917, 101.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Chimera protein of Histone H2B.1 and Histone H2A.Z /


Mass: 21205.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c
Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C, HTZ1, H2AZ, HTA3, YOL012C, O2345
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codonplus(DE3)-RIPL / References: UniProt: P02293, UniProt: Q12692
#2: Protein Helicase SWR1


Mass: 5970.131 Da / Num. of mol.: 2 / Fragment: Swr1-Z domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SWR1, YDR334W, D9651.6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codonplus(DE3)-RIPL / References: UniProt: Q05471, DNA helicase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% (w/v) PEG 2000 MME, 100 mM HEPES, pH 7.5, 50 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 274 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 45391 / Num. obs: 43986 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.6 / % possible all: 75.6

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2224 -RANDOM
Rwork0.211 ---
all0.226 45621 --
obs0.226 43984 96.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 187 3398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_dihedral_angle_d20.272
X-RAY DIFFRACTIONc_improper_angle_d0.985
LS refinement shellResolution: 1.78→1.84 Å
RfactorNum. reflection% reflection
Rfree0.278 174 -
Rwork0.272 --
obs-3289 73 %

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