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- PDB-5z8l: crystal structure of Arabidopsis thaliana EBS in complex with an ... -

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Basic information

Entry
Database: PDB / ID: 5z8l
Titlecrystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide
Components
  • Chromatin remodeling protein EBS
  • H3K27me3 peptide
KeywordsGENE REGULATION / EBS / BAH / PHD / H3K27me3 / histone reader
Function / homology
Function and homology information


negative regulation of long-day photoperiodism, flowering / regulation of photoperiodism, flowering / seed germination / flower development / chromocenter / plastid / negative regulation of gene expression, epigenetic / molecular function inhibitor activity / methylated histone binding / post-embryonic development ...negative regulation of long-day photoperiodism, flowering / regulation of photoperiodism, flowering / seed germination / flower development / chromocenter / plastid / negative regulation of gene expression, epigenetic / molecular function inhibitor activity / methylated histone binding / post-embryonic development / structural constituent of chromatin / nucleosome / transcription cis-regulatory region binding / protein heterodimerization activity / chromatin binding / DNA binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chromatin remodeling protein EBS / Histone H3.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.005 Å
AuthorsYang, Z. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0503200 China
CitationJournal: Nat. Genet. / Year: 2018
Title: EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.
Authors: Yang, Z. / Qian, S. / Scheid, R.N. / Lu, L. / Chen, X. / Liu, R. / Du, X. / Lv, X. / Boersma, M.D. / Scalf, M. / Smith, L.M. / Denu, J.M. / Du, J. / Zhong, X.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromatin remodeling protein EBS
P: H3K27me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1684
Polymers28,0372
Non-polymers1312
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-8 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.247, 60.299, 98.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromatin remodeling protein EBS / / Protein EARLY BOLTING IN SHORT DAYS


Mass: 26493.152 Da / Num. of mol.: 1 / Mutation: K201A,K202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EBS, At4g22140, F1N20.240 / Plasmid: pSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: F4JL28
#2: Protein/peptide H3K27me3 peptide


Mass: 1543.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.91 Å3/Da / Density % sol: 35.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M sodium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.2827 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14980 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 51
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 5.6 / Rsym value: 0.797 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.005→49.019 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.22 / Phase error: 24.82
RfactorNum. reflection% reflection
Rfree0.2301 753 5.03 %
Rwork0.2012 --
obs0.2026 14932 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.005→49.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 2 108 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091710
X-RAY DIFFRACTIONf_angle_d1.2032303
X-RAY DIFFRACTIONf_dihedral_angle_d14.875642
X-RAY DIFFRACTIONf_chiral_restr0.074242
X-RAY DIFFRACTIONf_plane_restr0.005297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0055-2.07710.26591480.25842487144196
2.0771-2.16030.25811210.25462644100
2.1603-2.25860.26321550.2242657100
2.2586-2.37770.28061250.23432627100
2.3777-2.52670.26241330.22692653100
2.5267-2.72170.26981500.22612630100
2.7217-2.99560.2861520.22032647100
2.9956-3.4290.21311690.20792593100
3.429-4.31970.19581380.16652652100
4.3197-49.03360.19341000.17862676100
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)
12.6126-0.08420.15514.291-0.96355.96890.2327-0.3226-0.0490.1652-0.11810.28830.1572-0.5464-0.18030.2635-0.05170.00530.3245-0.07320.280712.295637.177539.2568
25.66280.5579-2.15641.43080.49862.82420.08810.23-0.0239-0.0367-0.0647-0.03330.0104-0.1077-0.03530.21130.0209-0.05070.14080.0060.160729.969833.290424.2584
33.32610.8823.28212.16440.89234.1302-0.047-0.77910.1519-0.97580.68220.2104-0.73171.5069-0.61311.13830.00540.21530.67740.1050.647637.746738.278410.1989
40.4417-0.13020.21770.0452-0.06610.1075-0.2720.14410.0354-0.0349-0.10020.11-0.2345-0.08080.30051.19230.1039-0.13731.2586-0.25551.037627.82833.3658.7877
52.520.94431.6452.2643.72146.12330.5711-0.8158-0.32031.6448-0.8547-0.03550.6159-0.87040.31370.8914-0.1887-0.02580.54580.07970.459416.260923.928241.9838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 220 )
5X-RAY DIFFRACTION5chain 'P' and (resid 23 through 30 )

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