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- PDB-6jnn: REF6 ZnF2-4-NAC004-mC1 complex -

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Basic information

Entry
Database: PDB / ID: 6jnn
TitleREF6 ZnF2-4-NAC004-mC1 complex
Components
  • DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
  • DNA (5'-D(*TP*TP*(5CM)P*TP*CP*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 / ethylene-activated signaling pathway / leaf development / 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 profile. / Small domain found in the jumonji family of transcription factors / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / jmjN domain / JmjC domain, hydroxylase / zinc finger / Zinc finger C2H2 type domain profile. ...JmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / jmjN domain / JmjC domain, hydroxylase / 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: 2.6 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 1.1Apr 3, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2May 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 1.3Nov 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: Lysine-specific demethylase REF6
D: DNA (5'-D(*TP*TP*(5CM)P*TP*CP*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*(5CM)P*TP*CP*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')
I: DNA (5'-D(*TP*TP*(5CM)P*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')
H: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
L: DNA (5'-D(*TP*TP*(5CM)P*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')
K: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
N: Lysine-specific demethylase REF6
G: Lysine-specific demethylase REF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,23724
Polymers77,45212
Non-polymers78512
Water00
1
A: Lysine-specific demethylase REF6
D: DNA (5'-D(*TP*TP*(5CM)P*TP*CP*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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-28 kcal/mol
Surface area8860 Å2
MethodPISA
2
B: Lysine-specific demethylase REF6
F: DNA (5'-D(*TP*TP*(5CM)P*TP*CP*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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-30 kcal/mol
Surface area9040 Å2
MethodPISA
3
I: DNA (5'-D(*TP*TP*(5CM)P*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')
H: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
N: Lysine-specific demethylase REF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5596
Polymers19,3633
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-23 kcal/mol
Surface area8920 Å2
MethodPISA
4
L: DNA (5'-D(*TP*TP*(5CM)P*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')
K: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')
G: Lysine-specific demethylase REF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5596
Polymers19,3633
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-66 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.969, 70.969, 141.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22N
13A
23G
14D
24F
15D
25I
16D
26L
17C
27E
18C
28H
19C
29K
110B
210N
111B
211G
112F
212I
113F
213L
114E
214H
115E
215K
116I
216L
117H
217K
118N
218G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1265 - 1353
2010B1265 - 1353
1020A1265 - 1353
2020N1265 - 1353
1030A1265 - 1353
2030G1265 - 1353
1040D1 - 12
2040F1 - 12
1050D1 - 12
2050I1 - 12
1060D1 - 12
2060L1 - 12
1070C1 - 12
2070E1 - 12
1080C1 - 12
2080H1 - 12
1090C1 - 12
2090K1 - 12
10100B1265 - 1353
20100N1265 - 1353
10110B1265 - 1353
20110G1265 - 1353
10120F1 - 12
20120I1 - 12
10130F1 - 12
20130L1 - 12
10140E1 - 12
20140H1 - 12
10150E1 - 12
20150K1 - 12
10160I1 - 12
20160L1 - 12
10170H1 - 12
20170K1 - 12
10180N1265 - 1353
20180G1265 - 1353

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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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.: 4
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*(5CM)P*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')


Mass: 3639.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3,350, 0.15 M malic acid

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Data collection

DiffractionMean temperature: 100 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.537
11K, H, -L20.463
ReflectionResolution: 2.58→30 Å / Num. obs: 24572 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 13.69
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 2448

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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: 2.6→30 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.88 / SU B: 12.834 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1027 5.2 %RANDOM
Rwork0.251 ---
obs0.251 18614 85 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 54.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20 Å2
2---2.19 Å20 Å2
3---4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 1948 12 0 4900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0165222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.5937438
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6335352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76420.596151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.51515521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8191535
X-RAY DIFFRACTIONr_chiral_restr0.1040.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213368
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.2615.6871420
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.8328.5051768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9895.3273802
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.39697.12521655
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A55860.13
12B55860.13
21A49920.21
22N49920.21
31A49760.21
32G49760.21
41D20500.02
42F20500.02
51D17580.19
52I17580.19
61D19660.1
62L19660.1
71C23060.03
72E23060.03
81C22300.11
82H22300.11
91C22200.1
92K22200.1
101B49880.21
102N49880.21
111B50780.21
112G50780.21
121F17720.19
122I17720.19
131F19800.1
132L19800.1
141E22140.12
142H22140.12
151E22060.11
152K22060.11
161I17920.17
162L17920.17
171H22800.06
172K22800.06
181N52120.19
182G52120.19
LS refinement shellResolution: 2.58→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 11 -
Rwork0.386 550 -
obs--30.31 %

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