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- PDB-6jnm: REF6 ZnF2-4-NAC004-mC3 complex -

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Basic information

Entry
Database: PDB / ID: 6jnm
TitleREF6 ZnF2-4-NAC004-mC3 complex
Components
  • DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
  • DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')
  • Lysine-specific demethylase REF6
KeywordsDNA BINDING PROTEIN/DNA / REF6 / zinc finger / 5mC / DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / response to diterpene / heat acclimation / protein localization to heterochromatin / sugar mediated signaling pathway / unidimensional cell growth / vegetative to reproductive phase transition of meristem ...regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / response to diterpene / heat acclimation / protein localization to heterochromatin / sugar mediated signaling pathway / unidimensional cell growth / vegetative to reproductive phase transition of meristem / regulation of photoperiodism, flowering / systemic acquired resistance / response to brassinosteroid / histone H3K27me2/H3K27me3 demethylase activity / leaf development / ethylene-activated signaling pathway / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / response to abscisic acid / Ino80 complex / abscisic acid-activated signaling pathway / response to mechanical stimulus / epigenetic regulation of gene expression / protein homooligomerization / response to heat / sequence-specific DNA binding / positive regulation of gene expression / regulation of DNA-templated transcription / protein homodimerization activity / zinc ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / zinc finger / Zinc finger C2H2 type domain profile. ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Lysine-specific demethylase REF6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsYao, Q.Q. / Wu, B.X. / Ma, J.B.
CitationJournal: Nat Commun / Year: 2019
Title: DNA methylation repels targeting of Arabidopsis REF6.
Authors: Qiu, Q. / Mei, H. / Deng, X. / He, K. / Wu, B. / Yao, Q. / Zhang, J. / Lu, F. / Ma, J. / Cao, X.
History
DepositionMar 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase REF6
D: DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')
C: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
B: Lysine-specific demethylase REF6
F: DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')
E: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,11812
Polymers38,7266
Non-polymers3926
Water3,027168
1
A: Lysine-specific demethylase REF6
D: DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')
C: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5596
Polymers19,3633
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-27 kcal/mol
Surface area8670 Å2
MethodPISA
2
B: Lysine-specific demethylase REF6
F: DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')
E: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5596
Polymers19,3633
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-26 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.516, 88.516, 72.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Lysine-specific demethylase REF6 / Jumonji domain-containing protein 12 / Lysine-specific histone demethylase REF6 / Protein RELATIVE ...Jumonji domain-containing protein 12 / Lysine-specific histone demethylase REF6 / Protein RELATIVE OF EARLY FLOWERING 6


Mass: 12026.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: REF6, JMJ12, PKDM9A, At3g48430, T29H11_50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STM3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: DNA chain DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')


Mass: 3639.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 5CM / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')


Mass: 3697.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3,350, 0.03 M citrate acid, 0.07 M Bis-Tris propane pH 7.6

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 35297 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 4.241
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 1.02 / Num. unique obs: 3546

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JNL

6jnl


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.905 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1666 5.1 %RANDOM
Rwork0.2 ---
obs0.201 31212 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 974 6 168 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0162622
X-RAY DIFFRACTIONr_bond_other_d0.0020.021924
X-RAY DIFFRACTIONr_angle_refined_deg2.0921.63736
X-RAY DIFFRACTIONr_angle_other_deg1.4134484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58620.52676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73815264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9561518
X-RAY DIFFRACTIONr_chiral_restr0.1140.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212242
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02592
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7222.82710
X-RAY DIFFRACTIONr_mcbond_other2.7132.815709
X-RAY DIFFRACTIONr_mcangle_it3.9274.192884
X-RAY DIFFRACTIONr_mcangle_other3.9264.197885
X-RAY DIFFRACTIONr_scbond_it3.3622.7451912
X-RAY DIFFRACTIONr_scbond_other3.3612.7451913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8374.0332853
X-RAY DIFFRACTIONr_long_range_B_refined6.3527.7213412
X-RAY DIFFRACTIONr_long_range_B_other6.35627.6033381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 40 -
Rwork0.282 963 -
obs--38.47 %

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