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- PDB-6o5k: Murine TRIM28 Bbox1 domain -

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Basic information

Entry
Database: PDB / ID: 6o5k
TitleMurine TRIM28 Bbox1 domain
ComponentsTranscription intermediary factor 1-beta
KeywordsTRANSCRIPTION / B-box KAP1 TIF1beta Krab-ZFP Co-repressor
Function / homology
Function and homology information


: / Generic Transcription Pathway / convergent extension involved in axis elongation / negative regulation of DNA demethylation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...: / Generic Transcription Pathway / convergent extension involved in axis elongation / negative regulation of DNA demethylation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromo shadow domain binding / SUMO transferase activity / protein sumoylation / epithelial to mesenchymal transition / positive regulation of DNA binding / heterochromatin / embryo implantation / positive regulation of DNA repair / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / positive regulation of protein binding / in utero embryonic development / protein autophosphorylation / transcription coactivator activity / protein kinase activity / protein phosphorylation / DNA repair / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSun, Y. / Keown, J.R. / Goldstone, D.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: J.Mol.Biol. / Year: 2019
Title: A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family.
Authors: Sun, Y. / Keown, J.R. / Black, M.M. / Raclot, C. / Demarais, N. / Trono, D. / Turelli, P. / Goldstone, D.C.
History
DepositionMar 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transcription intermediary factor 1-beta
B: Transcription intermediary factor 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7816
Polymers15,5192
Non-polymers2624
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-21 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.012, 51.459, 72.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 154 - 195 / Label seq-ID: 23 - 64

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Transcription intermediary factor 1-beta / TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-A-interacting protein / KRIP-1 / RING-type E3 ...TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-A-interacting protein / KRIP-1 / RING-type E3 ubiquitin transferase TIF1-beta / Tripartite motif-containing protein 28


Mass: 7759.448 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim28, Kap1, Krip1, Tif1b / Plasmid: pET-49+(b)-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: Q62318, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 38.33 % / Description: Rod-like
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 2.7 M Ammonium sulfate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→42.04 Å / Num. obs: 17060 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.072 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 14.2 % / Rmerge(I) obs: 3.95 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 817 / CC1/2: 0.391 / Rpim(I) all: 1.075 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSJan 10, 2014data reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.574 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20764 855 5 %RANDOM
Rwork0.18039 ---
obs0.18181 16157 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.632 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-0 Å2-0 Å2
2--0.84 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: 1 / Resolution: 1.6→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 0 4 44 714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.014715
X-RAY DIFFRACTIONr_bond_other_d0.0010.018580
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.683980
X-RAY DIFFRACTIONr_angle_other_deg0.9521.6541385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83621.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4115116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.554155
X-RAY DIFFRACTIONr_chiral_restr0.0590.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02123
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_it2.9482.51369
X-RAY DIFFRACTIONr_mcbond_other2.9412.505368
X-RAY DIFFRACTIONr_mcangle_it3.8473.757461
X-RAY DIFFRACTIONr_mcangle_other3.8463.761462
X-RAY DIFFRACTIONr_scbond_it3.2942.811346
X-RAY DIFFRACTIONr_scbond_other3.2892.815347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4934.102515
X-RAY DIFFRACTIONr_long_range_B_refined5.00929.766768
X-RAY DIFFRACTIONr_long_range_B_other4.93629.413758
X-RAY DIFFRACTIONr_rigid_bond_restr1.65231295
X-RAY DIFFRACTIONr_sphericity_free28.791523
X-RAY DIFFRACTIONr_sphericity_bonded21.50951303
Refine LS restraints NCS

Ens-ID: 1 / Number: 1207 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 60 -
Rwork0.332 1181 -
obs--99.92 %

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