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- PDB-5znp: Crystal structure of PtSHL in complex with an H3K4me3 peptide -

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Basic information

Entry
Database: PDB / ID: 5znp
TitleCrystal structure of PtSHL in complex with an H3K4me3 peptide
Components
  • 15-mer peptide from Histone H3.2
  • SHORT LIFE family protein
KeywordsGENE REGULATION / BAH / PHD / SHL / plant / H3K4me3 / epigenetics
Function / homology
Function and homology information


chromocenter / plastid / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / extracellular region / metal ion binding / nucleus ...chromocenter / plastid / structural constituent of chromatin / nucleosome / 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
BAH domain-containing protein / Histone H3.1
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLv, X. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0503200 China
CitationJournal: Nat Commun / Year: 2018
Title: Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL.
Authors: Qian, S. / Lv, X. / Scheid, R.N. / Lu, L. / Yang, Z. / Chen, W. / Liu, R. / Boersma, M.D. / Denu, J.M. / Zhong, X. / Du, J.
History
DepositionApr 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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: SHORT LIFE family protein
B: SHORT LIFE family protein
P: 15-mer peptide from Histone H3.2
Q: 15-mer peptide from Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2578
Polymers52,9964
Non-polymers2624
Water39622
1
A: SHORT LIFE family protein
P: 15-mer peptide from Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6294
Polymers26,4982
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-7 kcal/mol
Surface area11520 Å2
MethodPISA
2
B: SHORT LIFE family protein
Q: 15-mer peptide from Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6294
Polymers26,4982
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-7 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.340, 91.909, 114.370
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 SHORT LIFE family protein


Mass: 24890.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0004s16700g, POPTR_004G159900v3 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: B9H0V2
#2: Protein/peptide 15-mer peptide from Histone H3.2 / H3(1-15)K4me3 peptide / Histone H3.1


Mass: 1607.877 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12194 / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1151 / Rsym value: 0.77 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6N, 1W4S

2f6n

1w4s


Resolution: 2.8→45.955 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33
RfactorNum. reflection% reflection
Rfree0.2932 574 4.78 %
Rwork0.2495 --
obs0.2515 12004 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 4 22 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053201
X-RAY DIFFRACTIONf_angle_d1.0664316
X-RAY DIFFRACTIONf_dihedral_angle_d16.2951218
X-RAY DIFFRACTIONf_chiral_restr0.04436
X-RAY DIFFRACTIONf_plane_restr0.005571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08170.39491450.32772786X-RAY DIFFRACTION99
3.0817-3.52750.33871390.27912816X-RAY DIFFRACTION100
3.5275-4.44370.27131410.22922868X-RAY DIFFRACTION100
4.4437-45.96070.26341490.23292960X-RAY DIFFRACTION99
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)
17.2081-3.3010.87137.7727-0.60092.93940.1450.0575-0.312-0.1403-0.2805-0.2515-0.096-0.19510.10110.3304-0.05060.02330.3988-0.06690.4675.7631-18.17511.2826
27.2338-2.3785-0.55825.048-0.78211.47790.32270.3208-0.7677-0.2258-0.32570.6622-0.0272-0.1495-0.06710.33940.0468-0.02230.4842-0.06610.5836-9.2621-17.925713.4856
39.0102-5.4779-2.69965.18480.99182.49970.25710.24060.2016-0.07-0.24010.191-0.3068-0.3426-0.00560.3578-0.0246-0.09020.4549-0.05420.3572-12.832-9.659416.8643
43.504-0.82081.33796.8343-2.25436.80550.17871.04671.6537-0.8886-1.44670.8117-2.04090.0112-0.00860.59260.1128-0.06590.7624-0.12170.9236-23.71493.146615.0104
58.5248-1.5556-0.92096.979-5.51825.31121.0045-1.28761.3252-0.9479-0.421.552-1.0488-0.8942-0.33870.60060.28620.0241.1562-0.13821.65-31.2315.449617.8713
64.8227-0.92230.43558.50750.85225.0388-1.3737-1.77151.17180.22880.0259-1.0984-1.7578-0.9607-0.28680.92690.3227-0.11221.3021-0.04211.2451-32.586812.365813.4943
75.94475.43240.20775.08161.30797.6690.3447-0.5421-1.61910.0325-0.1887-1.7575-0.7572-0.1818-0.17470.50190.0645-0.05740.62730.0510.92359.4437.761347.0922
88.25151.9667-1.06365.74890.15870.1860.2891-0.9192-0.73910.5388-0.6406-0.7209-0.68460.09150.09260.507-0.1008-0.03450.4529-0.0280.5287-2.34419.699747.513
99.11012.02890.5713.61512.10741.28380.0486-0.27840.15950.1341-0.3240.14780.2456-0.23180.28430.3884-0.0617-0.010.49020.00860.4819-10.70314.235541.8314
105.74491.66711.14874.34574.02793.93490.62990.8251-0.8760.2955-0.6520.31161.01750.3119-0.01090.38850.03460.08480.4768-0.12030.8337-13.2093-4.072639.8259
112.90672.23663.44984.36820.00993.46120.2299-0.33520.307-0.20560.0570.32810.8794-1.0835-0.16710.4837-0.08780.15660.781-0.1490.7965-27.7489-7.903234.0419
126.0183-3.46210.50684.2949-2.15395.79320.7659-1.5967-0.81870.823-1.51320.14232.2913-1.2453-0.63111.5352-0.7538-0.13951.20420.20880.7838-34.9224-22.585338.7846
134.79220.9231-1.54196.5891-1.12596.9010.47781.74230.36630.03570.82570.5441-0.35850.3738-1.12611.14360.0229-0.06531.09980.05940.7622-15.51824.05879.8043
142.5848-2.0451-0.59834.2542-3.53086.325-0.1592-1.04680.34870.3033-1.0149-0.05332.1314-0.08351.46060.7727-0.18580.13860.81340.15350.8987-20.8138-16.655442.6341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 169 )
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 187 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 110 )
10X-RAY DIFFRACTION10chain 'B' and (resid 111 through 127 )
11X-RAY DIFFRACTION11chain 'B' and (resid 128 through 169 )
12X-RAY DIFFRACTION12chain 'B' and (resid 170 through 187 )
13X-RAY DIFFRACTION13chain 'P' and (resid 3 through 10 )
14X-RAY DIFFRACTION14chain 'Q' and (resid 1 through 9 )

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