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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 / Krueppel-associated box domain binding / epigenetic programming of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / embryonic placenta morphogenesis / : / suppression of viral release by host / genomic imprinting / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...Generic Transcription Pathway / convergent extension involved in axis elongation / Krueppel-associated box domain binding / epigenetic programming of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / embryonic placenta morphogenesis / : / suppression of viral release by host / genomic imprinting / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromo shadow domain binding / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / positive regulation of DNA repair / promoter-specific chromatin binding / RING-type E3 ubiquitin transferase / euchromatin / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / in utero embryonic development / transcription coactivator activity / protein kinase activity / innate immune response / DNA repair / 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 / 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: Yunyuan Sun / Jeremy R Keown / Moyra M Black / Charlène Raclot / Nicholas Demarais / Didier Trono / Priscilla Turelli / David C Goldstone /
Abstract: TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. ...TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. During early embryogenesis, TRIM28 mediates the transcriptional silencing of many endogenous retroviral elements and genomic imprinted sites. Silencing is initiated by the recruitment of TRIM28 to a target locus by members of the Krab-ZFP. Subsequently, TRIM28 functions as a scaffold protein to recruit chromatin modifying effectors featuring SETDB1, HP1 and the NuRD complex. Although many protein partners involved in silencing have been identified, the molecular basis of the protein interactions that mediate silencing remains largely unclear. In the present study, we identified the first Bbox domain (T28_B1 135-203) as a molecular interface responsible for the formation of higher-order oligomers of TRIM28. The structure of this domain reveals a new interface on the surface of the Bbox domain. Mutants disrupting the interface disrupt the formation of oligomers but have no observed effect on transcriptional silencing defining a single TRIM28 dimer as the functional unit for silencing. Using assembly-deficient mutants, we employed small-angle X-ray scattering and biophysical techniques to characterize binding to member of the Krab-ZFP family. This allows us to narrow and define the binding interface to the center of the coiled-coil region (residues 294-321) of TRIM28 and define mutants that abolish binding to the Krab-ZFP proteins.
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: _ / 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: _ / 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


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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