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- PDB-5chl: Structural basis of H2A.Z recognition by YL1 histone chaperone co... -

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Basic information

Entry
Database: PDB / ID: 5chl
TitleStructural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1 chromatin remodeling complex
Components
  • Histone H2A.Z
  • Vacuolar protein sorting-associated protein 72 homologVacuole
KeywordsCHAPERONE / remodeling complex / histone
Function / homology
Function and homology information


: / : / NuA4 histone acetyltransferase complex / heterochromatin organization / RNA polymerase II core promoter sequence-specific DNA binding / nucleosomal DNA binding / heterochromatin / cellular response to estradiol stimulus / euchromatin / chromatin DNA binding ...: / : / NuA4 histone acetyltransferase complex / heterochromatin organization / RNA polymerase II core promoter sequence-specific DNA binding / nucleosomal DNA binding / heterochromatin / cellular response to estradiol stimulus / euchromatin / chromatin DNA binding / structural constituent of chromatin / nucleosome / chromatin organization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleus
Similarity search - Function
Vps72/YL1 family / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Histone, subunit A / Histone, subunit A / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain ...Vps72/YL1 family / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Histone, subunit A / Histone, subunit A / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2A.Z / Vacuolar protein sorting-associated protein 72 homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.892 Å
AuthorsShan, S. / Liang, X. / Pan, L. / Wu, C. / Zhou, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structural basis of H2A.Z recognition by SRCAP chromatin-remodeling subunit YL1
Authors: Liang, X. / Shan, S. / Pan, L. / Zhao, J. / Ranjan, A. / Wang, F. / Zhang, Z. / Huang, Y. / Feng, H. / Wei, D. / Huang, L. / Liu, X. / Zhong, Q. / Lou, J. / Li, G. / Wu, C. / Zhou, Z.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 72 homolog
B: Histone H2A.Z


Theoretical massNumber of molelcules
Total (without water)29,7472
Polymers29,7472
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-3 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.047, 108.047, 58.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-109-

HOH

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Components

#1: Protein Vacuolar protein sorting-associated protein 72 homolog / Vacuole / Protein YL-1


Mass: 8585.671 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: YL-1, CG4621 / Cell line (production host): BL21(RIPL) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VKM6
#2: Protein Histone H2A.Z / / H2A/z


Mass: 21161.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AFZ, H2AZ / Cell line (production host): BL21(RIPL) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.19 mM CYMAL-7, 0.1 M HEPES, pH 7.5, 40% Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.892→50 Å / Num. obs: 28027 / % possible obs: 99.9 % / Redundancy: 8.8 % / Net I/σ(I): 23.3

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.892→29.967 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1400 5.01 %
Rwork0.2003 --
obs0.2018 27960 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→29.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 0 147 2064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011944
X-RAY DIFFRACTIONf_angle_d1.0962618
X-RAY DIFFRACTIONf_dihedral_angle_d16.114734
X-RAY DIFFRACTIONf_chiral_restr0.077293
X-RAY DIFFRACTIONf_plane_restr0.004344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8916-1.95920.27841160.23912541X-RAY DIFFRACTION96
1.9592-2.03760.28361320.22842609X-RAY DIFFRACTION100
2.0376-2.13030.23781360.21112616X-RAY DIFFRACTION100
2.1303-2.24260.24371630.19362606X-RAY DIFFRACTION100
2.2426-2.3830.22491520.20092611X-RAY DIFFRACTION100
2.383-2.56690.271400.20982660X-RAY DIFFRACTION100
2.5669-2.82510.22281390.20412663X-RAY DIFFRACTION100
2.8251-3.23340.22291390.212688X-RAY DIFFRACTION100
3.2334-4.07220.21031310.19152718X-RAY DIFFRACTION100
4.0722-29.97060.22771520.19032848X-RAY DIFFRACTION100

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