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- PDB-7v9g: Native BEN4 domain of protein Bend3 with DNA -

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Basic information

Entry
Database: PDB / ID: 7v9g
TitleNative BEN4 domain of protein Bend3 with DNA
Components
  • BEN domain-containing protein 3
  • DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
  • DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of ATP metabolic process / rDNA binding / rDNA heterochromatin formation / negative regulation of transcription by RNA polymerase I / heterochromatin / protein homooligomerization / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
BEN domain-containing protein 3 / BEN domain / BEN domain / BEN domain profile. / BEN
Similarity search - Domain/homology
DNA / DNA (> 10) / BEN domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsZhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. ...Zhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. / Liu, C.P. / Zhang, Z. / Xu, R.M. / Zhu, B.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508900, 2017YFA0504202 China
National Science Foundation (NSF, China)31991162, 31521002 China
Chinese Academy of SciencesXDB 37010100 China
CitationJournal: Science / Year: 2022
Title: Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.
Authors: Zhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. / Liu, C.P. / Zhang, Z. / Xu, R.M. / Zhu, B.
History
DepositionAug 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BEN domain-containing protein 3
B: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
C: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
D: BEN domain-containing protein 3
E: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
F: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
G: BEN domain-containing protein 3
H: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
I: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
J: BEN domain-containing protein 3
K: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
L: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)93,35212
Polymers93,35212
Non-polymers00
Water00
1
A: BEN domain-containing protein 3
B: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
C: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
D: BEN domain-containing protein 3
E: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
F: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)46,6766
Polymers46,6766
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-81 kcal/mol
Surface area22640 Å2
MethodPISA
2
G: BEN domain-containing protein 3
H: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
I: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
J: BEN domain-containing protein 3
K: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
L: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)46,6766
Polymers46,6766
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-74 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.484, 200.484, 151.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 715 through 810)
21(chain D and resid 715 through 810)
31(chain G and resid 715 through 810)
41(chain J and resid 715 through 810)
12chain B
22chain E
32chain H
42chain K
13chain C
23chain F
33chain I
43chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROASNASN(chain A and resid 715 through 810)AA715 - 8104 - 99
21PROPROASNASN(chain D and resid 715 through 810)DD715 - 8104 - 99
31PROPROASNASN(chain G and resid 715 through 810)GG715 - 8104 - 99
41PROPROASNASN(chain J and resid 715 through 810)JJ715 - 8104 - 99
12DTDTDCDCchain BBB1 - 161 - 16
22DTDTDCDCchain EEE1 - 161 - 16
32DTDTDCDCchain HHH1 - 161 - 16
42DTDTDCDCchain KKK1 - 161 - 16
13DGDGDADAchain CCC1 - 161 - 16
23DGDGDADAchain FFF1 - 161 - 16
33DGDGDADAchain III1 - 161 - 16
43DGDGDADAchain LLL1 - 161 - 16

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
BEN domain-containing protein 3


Mass: 13536.790 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bend3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PAL0
#2: DNA chain
DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')


Mass: 4876.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')


Mass: 4925.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 4.7 Å3/Da / Density % sol: 73.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate/Citric acid pH 4.0, 200 mM Sodium citrate tribasic, and 17% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97884 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97884 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 23049 / % possible obs: 86.95 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.06 / Num. unique obs: 2480

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→41.78 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 1189 5.16 %
Rwork0.2385 21860 -
obs0.2403 23049 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.71 Å2 / Biso mean: 84.7131 Å2 / Biso min: 30.04 Å2
Refinement stepCycle: final / Resolution: 3.5→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 2600 0 0 6115
Num. residues----549
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1975X-RAY DIFFRACTION9.862TORSIONAL
12D1975X-RAY DIFFRACTION9.862TORSIONAL
13G1975X-RAY DIFFRACTION9.862TORSIONAL
14J1975X-RAY DIFFRACTION9.862TORSIONAL
21B624X-RAY DIFFRACTION9.862TORSIONAL
22E624X-RAY DIFFRACTION9.862TORSIONAL
23H624X-RAY DIFFRACTION9.862TORSIONAL
24K624X-RAY DIFFRACTION9.862TORSIONAL
31C624X-RAY DIFFRACTION9.862TORSIONAL
32F624X-RAY DIFFRACTION9.862TORSIONAL
33I624X-RAY DIFFRACTION9.862TORSIONAL
34L624X-RAY DIFFRACTION9.862TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.660.36271550.34512639279499
3.66-3.850.32681490.306926842833100
3.85-4.090.30261300.270826922822100
4.09-4.410.28131540.224327032857100
4.41-4.850.23821690.22427012870100
4.85-5.550.25061480.220727412889100
5.55-6.990.27241490.245227812930100
6.99-41.780.23511350.18962919305499

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