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- PDB-5z8n: Crystal structure of Arabidopsis thaliana EBS C-terminal deletion... -

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Basic information

Entry
Database: PDB / ID: 5z8n
TitleCrystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide
Components
  • Chromatin remodeling protein EBS
  • H3K4me2 peptide
KeywordsGENE REGULATION / EBS / BAH / PHD / H3K4me2 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.1 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
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: H3K4me2 peptide
B: Chromatin remodeling protein EBS
Q: H3K4me2 peptide
C: Chromatin remodeling protein EBS
R: H3K4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,11112
Polymers72,7196
Non-polymers3926
Water0
1
A: Chromatin remodeling protein EBS
P: H3K4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3704
Polymers24,2402
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-4 kcal/mol
Surface area11310 Å2
MethodPISA
2
B: Chromatin remodeling protein EBS
Q: H3K4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3704
Polymers24,2402
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-7 kcal/mol
Surface area11400 Å2
MethodPISA
3
C: Chromatin remodeling protein EBS
R: H3K4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3704
Polymers24,2402
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.464, 75.696, 80.357
Angle α, β, γ (deg.)90.00, 115.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22646.762 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EBS, At4g22140, F1N20.240 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: F4JL28
#2: Protein/peptide H3K4me2 peptide


Mass: 1592.843 Da / Num. of mol.: 3 / 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.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES, pH 6.5, 40% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 14581 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 10.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.701 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z8L

5z8l


Resolution: 3.1→40.992 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.85
RfactorNum. reflection% reflection
Rfree0.2516 734 5.06 %
Rwork0.2126 --
obs0.2147 14500 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→40.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4538 0 6 0 4544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084643
X-RAY DIFFRACTIONf_angle_d1.36260
X-RAY DIFFRACTIONf_dihedral_angle_d18.5431733
X-RAY DIFFRACTIONf_chiral_restr0.056645
X-RAY DIFFRACTIONf_plane_restr0.005819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.1002-3.33950.38191490.29362702141798
3.3395-3.67530.29411560.2585273299
3.6753-4.20670.24151440.21452755100
4.2067-5.29820.22291310.18212786100
5.2982-40.99510.22941540.198279199
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)
16.4802-4.68421.18266.48210.69986.0194-0.1722-0.4202-0.86240.71690.74190.50181.372-0.543-0.22771.1823-0.150.09350.69830.16730.9535-37.3147-23.502290.7403
27.5046-4.7257-1.25553.13131.11965.1199-0.2705-1.26520.17310.16780.3592-0.864-0.58940.6316-0.22110.81-0.1277-0.1390.6956-0.01390.9926-34.3573-12.695886.5781
32.3556-0.5998-1.4276.7173-0.87145.2567-0.4334-0.23210.12860.9517-0.14140.0054-0.24210.12080.36640.48060.0494-0.0450.6160.04540.7173-29.3435-19.840685.4633
47.3411-2.485-2.31385.88592.92794.6652-0.0488-0.23430.8269-0.55150.3273-0.6289-1.08710.5921-0.13070.5816-0.0523-0.08420.5845-0.06220.7489-34.47321.725276.9176
55.4725-5.93660.32126.51930.48133.4264-0.5789-0.4041-1.13881.11190.48910.70250.162-0.320.15970.7559-0.05210.0290.4618-0.03410.8611-39.4102-9.830483.4862
66.5008-3.1698-0.25447.70960.32599.2467-0.9150.13710.46270.20570.22150.30570.2375-0.52360.91950.58840.04240.02640.4559-0.02260.6366-41.0059-2.279276.6409
72.2351-2.8085-0.4156.527-0.44072.1226-0.09640.0563-0.05770.15330.35740.34140.40720.0650.24140.6067-0.0653-0.11320.5151-0.01660.8951-46.31249.621969.823
82.9271-0.65780.93765.1617-2.22583.5059-0.3091-0.26560.01210.13010.27970.2023-0.3715-0.0390.25170.7322-0.0057-0.13740.5681-0.08791.0508-56.374816.820673.161
93.1477-1.97013.05174.3837-3.95424.0423-1.3688-0.2328-0.6358-0.0515-0.2221-0.95020.40760.58250.65070.6027-0.0457-0.10510.7162-0.08450.8969-62.168320.013870.057
103.2737-3.7232-1.38254.24671.88834.3606-0.63281.65090.91240.71640.20321.77681.9904-2.4479-0.17840.6113-0.27960.0770.98420.06890.7954-57.60438.693976.4
113.4034-1.0007-2.36196.69450.76665.8591-0.4463-0.0638-0.82730.4590.2416-0.59140.6005-0.46950.09930.5020.0202-0.11910.6253-0.1120.7546-59.6314-33.306877.9383
123.24732.66040.12247.80050.20152.9458-0.2166-0.84541.299-0.65040.3767-2.9614-0.8305-0.0377-0.18350.5482-0.0213-0.19830.8902-0.13081.4588-56.5395-22.284475.4224
136.6684-4.0946-0.09283.38921.92193.29450.2924-0.1283-0.0868-0.04520.0124-0.1350.0474-0.4301-0.46680.6119-0.1730.15040.6049-0.00880.5986-57.6078-26.556570.7367
143.85710.7468-0.65558.72283.01848.71510.1626-0.6081.6313-1.1330.32350.0259-0.98650.6197-0.34540.6369-0.05780.11960.51070.00571.0739-65.0284-8.060878.1456
156.085-2.2194-2.58527.41963.33126.4194-0.0021-0.40570.59340.3540.2806-0.80810.72080.3902-0.3680.83070.00910.0330.5468-0.0360.6925-58.7788-24.870577.2325
164.9091-2.5116-1.31036.81522.73177.15460.1911-2.0738-1.11151.6659-0.03610.72230.66130.15030.52260.84990.08120.2840.67670.16680.692-71.8348-17.667590.8229
177.3999-3.8412-1.42485.96910.82526.56770.27880.87780.7178-0.2081-0.26290.3484-1.26270.28070.10660.5676-0.06160.00680.59920.03410.6729-70.4464-11.050974.9766
184.698-1.662-1.37658.1557.99059.70970.0754-0.62490.0668-1.2542-0.1184-0.5216-1.5491-0.23280.18650.7496-0.0515-0.03820.4670.09050.8297-78.84270.540884.1208
198.1664-4.1187-1.51575.48573.20364.8520.2926-0.19630.79121.05120.1364-0.11440.08870.11810.21820.6359-0.0645-0.05450.4755-0.08560.6485-78.8717-2.081793.5111
205.9985-4.3611-1.83597.9240.16692.636-1.3429-1.89440.31052.63771.632-1.5954-1.48161.7872-0.17341.07190.2292-0.08060.9106-0.27890.6841-73.78612.5469102.6098
215.5967-5.70655.3958.5539-4.07165.95810.35730.19930.0112-1.1729-0.4094-0.1387-0.76990.2377-0.03460.91720.1716-0.05810.58770.08230.7144-86.4166.042299.3878
228.8089-4.83770.82536.1996-2.3127.09290.80510.54270.38831.2145-1.25270.40951.70940.060.0530.9019-0.0650.1730.5807-0.19590.7777-76.6402-8.117497.2863
238.12982.60314.23479.38193.39073.60150.00090.106-0.6132-0.11270.2067-2.077-0.53170.5604-0.2680.955-0.0180.03060.7808-0.20380.8474-73.9226-43.1481103.204
244.5257-0.3832-0.74972.66992.92563.30620.17720.6767-0.7941-0.5385-0.50030.6258-0.6251-0.01670.24370.81250.0606-0.05120.75390.08060.8104-80.7921-42.1435101.3951
253.07831.2191-0.52965.24393.48423.59690.17510.36190.171-1.1063-0.03730.0094-1.1150.47720.11020.9568-0.0891-0.05460.68350.04850.6365-78.5565-32.4745103.4043
261.6219-0.3176-0.09555.69084.14677.28080.0734-0.00720.2715-0.02950.02750.2254-0.34570.0167-0.09430.6794-0.0728-0.04250.46810.07260.6449-80.4416-17.6508123.6847
278.4263-5.4977-1.2054.84583.04014.2711.60611.18481.19350.50620.7386-1.14140.8919-0.165-2.01561.1246-0.07590.13490.5121-0.01890.6052-74.6813-20.5437128.7899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 141 )
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 161 )
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 183 )
9X-RAY DIFFRACTION9chain 'A' and (resid 184 through 197 )
10X-RAY DIFFRACTION10chain 'P' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 39 )
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 58 )
13X-RAY DIFFRACTION13chain 'B' and (resid 59 through 73 )
14X-RAY DIFFRACTION14chain 'B' and (resid 74 through 95 )
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 111 )
16X-RAY DIFFRACTION16chain 'B' and (resid 112 through 125 )
17X-RAY DIFFRACTION17chain 'B' and (resid 126 through 143 )
18X-RAY DIFFRACTION18chain 'B' and (resid 144 through 153 )
19X-RAY DIFFRACTION19chain 'B' and (resid 154 through 173 )
20X-RAY DIFFRACTION20chain 'B' and (resid 174 through 185 )
21X-RAY DIFFRACTION21chain 'B' and (resid 186 through 197 )
22X-RAY DIFFRACTION22chain 'Q' and (resid 1 through 7 )
23X-RAY DIFFRACTION23chain 'C' and (resid 15 through 48 )
24X-RAY DIFFRACTION24chain 'C' and (resid 49 through 59 )
25X-RAY DIFFRACTION25chain 'C' and (resid 60 through 111 )
26X-RAY DIFFRACTION26chain 'C' and (resid 112 through 197 )
27X-RAY DIFFRACTION27chain 'R' and (resid 1 through 7 )

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