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- PDB-8p2p: Polymeric form of the BTB domain of human ZBTB18 -

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Basic information

Entry
Database: PDB / ID: 8p2p
TitlePolymeric form of the BTB domain of human ZBTB18
ComponentsZinc finger and BTB domain-containing protein 18
KeywordsTRANSCRIPTION / Transcription regulation / BTB domain / polymerisation
Function / homology
Function and homology information


heterochromatin / skeletal muscle tissue development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...heterochromatin / skeletal muscle tissue development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.15 Å
AuthorsCoste, F. / Mance, L. / Pukalo, Z. / Suskiewicz, M.J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Mol.Cell / Year: 2024
Title: Dynamic BTB-domain filaments promote clustering of ZBTB proteins.
Authors: Mance, L. / Bigot, N. / Zhamungui Sanchez, E. / Coste, F. / Martin-Gonzalez, N. / Zentout, S. / Biliskov, M. / Pukalo, Z. / Mishra, A. / Chapuis, C. / Arteni, A.A. / Lateur, A. / Goffinont, ...Authors: Mance, L. / Bigot, N. / Zhamungui Sanchez, E. / Coste, F. / Martin-Gonzalez, N. / Zentout, S. / Biliskov, M. / Pukalo, Z. / Mishra, A. / Chapuis, C. / Arteni, A.A. / Lateur, A. / Goffinont, S. / Gaudon, V. / Talhaoui, I. / Casuso, I. / Beaufour, M. / Garnier, N. / Artzner, F. / Cadene, M. / Huet, S. / Castaing, B. / Suskiewicz, M.J.
History
DepositionMay 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Refinement description / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / refine_ls_restr_ncs / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Zinc finger and BTB domain-containing protein 18
A: Zinc finger and BTB domain-containing protein 18
C: Zinc finger and BTB domain-containing protein 18
D: Zinc finger and BTB domain-containing protein 18
E: Zinc finger and BTB domain-containing protein 18
F: Zinc finger and BTB domain-containing protein 18
G: Zinc finger and BTB domain-containing protein 18
H: Zinc finger and BTB domain-containing protein 18


Theoretical massNumber of molelcules
Total (without water)143,9488
Polymers143,9488
Non-polymers00
Water00
1
B: Zinc finger and BTB domain-containing protein 18
A: Zinc finger and BTB domain-containing protein 18


Theoretical massNumber of molelcules
Total (without water)35,9872
Polymers35,9872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Zinc finger and BTB domain-containing protein 18
D: Zinc finger and BTB domain-containing protein 18


Theoretical massNumber of molelcules
Total (without water)35,9872
Polymers35,9872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Zinc finger and BTB domain-containing protein 18
F: Zinc finger and BTB domain-containing protein 18


Theoretical massNumber of molelcules
Total (without water)35,9872
Polymers35,9872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Zinc finger and BTB domain-containing protein 18
H: Zinc finger and BTB domain-containing protein 18


Theoretical massNumber of molelcules
Total (without water)35,9872
Polymers35,9872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.908, 188.908, 139.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 84 or resid 91 through 119))
d_2ens_1(chain "B" and (resid 3 through 84 or resid 91 through 119))
d_3ens_1(chain "C" and (resid 3 through 84 or resid 91 through 119))
d_4ens_1(chain "D" and (resid 3 through 84 or resid 91 through 119))
d_5ens_1(chain "E" and (resid 3 through 84 or resid 91 through 119))
d_6ens_1(chain "F" and (resid 3 through 84 or resid 91 through 119))
d_7ens_1(chain "G" and resid 3 through 119)
d_8ens_1(chain "H" and (resid 3 through 84 or resid 91 through 119))

NCS domain segments:

Ens-ID: ens_1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PHEPHEAB3 - 843 - 84
d_12ASPASPAB91 - 11991 - 119
d_21PHEPHEBA3 - 843 - 84
d_22ASPASPBA91 - 11991 - 119
d_31PHEPHECC3 - 843 - 84
d_32ASPASPCC91 - 11991 - 119
d_41PHEPHEDD3 - 843 - 84
d_42ASPASPDD91 - 11991 - 119
d_51PHEPHEEE3 - 843 - 84
d_52ASPASPEE91 - 11991 - 119
d_61PHEPHEFF3 - 843 - 84
d_62ASPASPFF91 - 11991 - 119
d_71PHEPHEGG3 - 1193 - 119
d_81PHEPHEHH3 - 843 - 84
d_82ASPASPHH91 - 11991 - 119

NCS oper:
IDCodeMatrixVector
1given(0.010587562567, -0.994799910402, -0.101296800458), (-0.995020318729, -0.0205217188744, 0.097536784705), (-0.0991083691473, 0.0997596978674, -0.990063398903)24.548053332, 33.7854660662, -86.0172314845
2given(-0.784173409184, 0.21441465444, -0.582321578074), (-0.203533729322, 0.797624390616, 0.567775794238), (0.586213344575, 0.563756762669, -0.581835223399)-17.6148819919, 42.2290826404, -82.1873579547
3given(-0.180026439631, 0.685783188736, 0.705189264723), (-0.860153352737, 0.238042456742, -0.451078705508), (-0.477207178077, -0.687777003712, 0.547024773074)22.3271035042, 16.1133492444, 1.99253935753
4given(-0.027890529972, -0.27501171264, -0.961036251267), (-0.283780609724, -0.919676160709, 0.271411725924), (-0.958483533444, 0.280293270228, -0.0523927359694)-10.0445110226, 95.81537665, -37.737129958
5given(0.390831658158, -0.0662749357892, 0.918073116842), (0.869447852233, 0.354017424556, -0.344575239038), (-0.302177178537, 0.932887611664, 0.195983817635)62.434153391, 32.1914594148, -46.5055526019
6given(0.500747218819, -0.13455211011, 0.85507189903), (-0.795697211532, -0.460441294923, 0.39352225031), (0.340761163287, -0.877433498103, -0.337627436683)32.6825511585, 96.7891153021, -9.73729562152
7given(0.0376344059083, -0.404191067208, -0.913900012409), (0.431334452238, 0.831534680129, -0.350000951505), (0.901406812601, -0.381024483376, 0.205635846253)-33.6894023574, 28.7451893914, -0.833121410032

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Components

#1: Protein
Zinc finger and BTB domain-containing protein 18 / 58 kDa repressor protein / Transcriptional repressor RP58 / Translin-associated zinc finger protein ...58 kDa repressor protein / Transcriptional repressor RP58 / Translin-associated zinc finger protein 1 / TAZ-1 / Zinc finger protein 238 / Zinc finger protein C2H2-171


Mass: 17993.477 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB18, RP58, TAZ1, ZNF238 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99592
Has protein modificationN

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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: 4.31 Å3/Da / Density % sol: 71.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MgCl2, EtOH, imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 4.15→57.36 Å / Num. obs: 18588 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 212.64 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.041 / Net I/σ(I): 8.9
Reflection shellResolution: 4.15→4.22 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 886 / CC1/2: 0.628 / Rpim(I) all: 0.472 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
PHASERphasing
Cootmodel building
PHENIX1.2refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.15→57.36 Å / SU ML: 0.8558 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 53.9325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3599 938 5.05 %
Rwork0.3451 17634 -
obs0.3458 18572 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.19 Å2
Refinement stepCycle: LAST / Resolution: 4.15→57.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 0 0 4760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284775
X-RAY DIFFRACTIONf_angle_d0.62586676
X-RAY DIFFRACTIONf_chiral_restr0.0364924
X-RAY DIFFRACTIONf_plane_restr0.0042962
X-RAY DIFFRACTIONf_dihedral_angle_d4.46631010
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.998274641186
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.667606503928
ens_1d_4DX-RAY DIFFRACTIONTorsion NCS0.829438224589
ens_1d_5EX-RAY DIFFRACTIONTorsion NCS1.03404699738
ens_1d_6FX-RAY DIFFRACTIONTorsion NCS1.07439096669
ens_1d_7GX-RAY DIFFRACTIONTorsion NCS1.19984102497
ens_1d_8HX-RAY DIFFRACTIONTorsion NCS1.15033329141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.15-4.370.4381430.43662490X-RAY DIFFRACTION99.96
4.37-4.640.44151370.41812510X-RAY DIFFRACTION100
4.64-50.46261360.44212507X-RAY DIFFRACTION100
5-5.50.46521360.4762505X-RAY DIFFRACTION100
5.5-6.30.47241160.4592538X-RAY DIFFRACTION100
6.3-7.930.35571270.37492543X-RAY DIFFRACTION100
7.93-57.360.29251430.2562541X-RAY DIFFRACTION99.37

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