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- PDB-6lqe: Crystal structure of Arabidopsis ARID5 PHD finger in complex with... -

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Basic information

Entry
Database: PDB / ID: 6lqe
TitleCrystal structure of Arabidopsis ARID5 PHD finger in complex with H3K4me3 peptide
Components
  • 15-mer peptide from Histone H3.2
  • AT-rich interactive domain-containing protein 4
KeywordsGENE REGULATION / ARID5 / PHD finger / histone
Function / homology
Function and homology information


chromocenter / plastid / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
AT-rich interactive domain-containing protein 4 / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. ...AT-rich interactive domain-containing protein 4 / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / 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
Histone H3.1 / AT-rich interactive domain-containing protein 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLiu, R. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31622032 China
CitationJournal: Plant Cell / Year: 2020
Title: Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis.
Authors: Tan, L.M. / Liu, R. / Gu, B.W. / Zhang, C.J. / Luo, J. / Guo, J. / Wang, Y. / Chen, L. / Du, X. / Li, S. / Shao, C.R. / Su, Y.N. / Cai, X.W. / Lin, R.N. / Li, L. / Chen, S. / Du, J. / He, X.J.
History
DepositionJan 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Derived calculations / Category: citation / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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: AT-rich interactive domain-containing protein 4
P: 15-mer peptide from Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9204
Polymers9,7892
Non-polymers1312
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-10 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.922, 27.922, 124.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-903-

HOH

21A-904-

HOH

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Components

#1: Protein AT-rich interactive domain-containing protein 4 / ARID5 PHD finger / ARID domain-containing protein 4


Mass: 8181.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARID4, At3g43240, F7K15.90 / Plasmid: pSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6NQ79
#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.: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate, pH 4.6, 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 4421 / % possible obs: 99.8 % / Redundancy: 22.3 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.023 / Rrim(I) all: 0.108 / Χ2: 1.401 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9321.51.0052060.8830.221.031.048100
1.93-1.9720.50.5732140.9910.1250.5870.706100
1.97-2.0122.20.5482210.9820.1170.5610.546100
2.01-2.0521.80.5151940.9810.1110.5270.602100
2.05-2.0921.40.5442140.9830.1220.5581.308100
2.09-2.1424.50.3162150.9940.0640.3220.812100
2.14-2.19240.3342100.9880.0670.3410.752100
2.19-2.25240.3612120.9980.0750.3691.339100
2.25-2.3223.70.2442310.9970.050.2490.995100
2.32-2.3922.90.1971990.9960.0420.2010.99100
2.39-2.4821.90.1722140.9990.0380.1761.148100
2.48-2.5823.20.1662190.9940.0350.171.2399.1
2.58-2.723.80.1632060.9960.0340.1671.48100
2.7-2.8423.20.1292440.9990.0270.1321.414100
2.84-3.0224.10.1132070.9980.0230.1151.745100
3.02-3.2521.30.0982270.9980.0220.1011.984100
3.25-3.5823.10.0962330.9980.020.0982.361100
3.58-4.0922.40.0872320.9990.0190.0892.431100
4.09-5.1619.80.0732340.9990.0170.0752.37999.2
5.16-5017.80.0782890.9980.0190.082.46599

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→31.128 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.68 / Phase error: 30.02
RfactorNum. reflection% reflection
Rfree0.2409 329 4.45 %
Rwork0.201 --
obs0.2026 4356 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.58 Å2 / Biso mean: 51.0149 Å2 / Biso min: 32.55 Å2
Refinement stepCycle: final / Resolution: 1.9→31.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms478 0 2 5 485
Biso mean--43.53 45.66 -
Num. residues----63
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007487
X-RAY DIFFRACTIONf_angle_d1.107657
X-RAY DIFFRACTIONf_chiral_restr0.04167
X-RAY DIFFRACTIONf_plane_restr0.00585
X-RAY DIFFRACTIONf_dihedral_angle_d14.993171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9005-2.39420.30841780.23863520
2.3942-310.2211510.1923548
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)
10.1882-0.15210.19590.28320.07750.36720.17860.54141.0153-0.1119-0.007-0.3765-0.40740.12360.0010.45240.04290.02080.3360.05550.441311.157511.7774-19.1919
20.3231-0.1948-0.00960.15620.11410.23740.4865-0.13860.21110.0638-0.1075-0.6492-0.56380.6820.00680.5563-0.13150.05130.3492-0.03310.479910.97413.8201-11.5154
33.43360.0328-1.07430.35160.64021.9660.5599-0.4684-0.2914-0.60880.15560.88970.4084-0.20530.07380.5973-0.1575-0.08110.30970.10050.47828.23493.3375-6.4151
40.39760.61950.34581.06180.02241.4172-0.0714-0.94360.6160.04610.4341-0.0148-0.60720.1333-0.00250.459-0.09860.0430.5181-0.04730.38038.087612.4963-3.6808
54.3037-1.0665-0.63540.730.98512.11030.68481.47141.1715-0.5185-0.68790.4669-1.041-0.02460.25070.93610.03420.21970.27770.04970.65043.653517.8059-15.1794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 675 through 687 )A675 - 687
2X-RAY DIFFRACTION2chain 'A' and (resid 688 through 702 )A688 - 702
3X-RAY DIFFRACTION3chain 'A' and (resid 703 through 710 )A703 - 710
4X-RAY DIFFRACTION4chain 'A' and (resid 711 through 729 )A711 - 729
5X-RAY DIFFRACTION5chain 'P' and (resid 1 through 8 )P1 - 8

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