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- PDB-6h3a: Crystal structure of the KAP1 RBCC domain in complex with the SMA... -

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Basic information

Entry
Database: PDB / ID: 6h3a
TitleCrystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain.
Components
  • SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
  • Transcription intermediary factor 1-beta
KeywordsLIGASE / TRIM28 / transcriptional co-repressor / CUE domain / Ubuiquitin
Function / homology
Function and homology information


convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / suppression of viral release by host / regulation of DNA recombination / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromosome separation / genomic imprinting / chromo shadow domain binding / DNA double-strand break processing ...convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / suppression of viral release by host / regulation of DNA recombination / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromosome separation / genomic imprinting / chromo shadow domain binding / DNA double-strand break processing / nucleosome array spacer activity / ATP-dependent chromatin remodeler activity / Generic Transcription Pathway / SUMO transferase activity / DNA methylation-dependent constitutive heterochromatin formation / nuclear replication fork / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / SUMOylation of transcription cofactors / positive regulation of DNA repair / ubiquitin binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / RNA polymerase II transcription regulator complex / positive regulation of protein import into nucleus / HCMV Early Events / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / site of double-strand break / DNA helicase / proteasome-mediated ubiquitin-dependent protein catabolic process / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / transcription coactivator activity / protein kinase activity / chromatin remodeling / innate immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / Ubiquitin system component CUE / CUE domain profile. / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / Ubiquitin system component CUE / CUE domain profile. / 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. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Helicase conserved C-terminal domain / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription intermediary factor 1-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.505 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Lim, M. / Williams, H.L. / Svejstrup, J.Q. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: Structure / Year: 2019
Title: A Ubiquitin-Binding Domain that Binds a Structural Fold Distinct from that of Ubiquitin.
Authors: Lim, M. / Newman, J.A. / Williams, H.L. / Masino, L. / Aitkenhead, H. / Gravard, A.E. / Gileadi, O. / Svejstrup, J.Q.
History
DepositionJul 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
A: Transcription intermediary factor 1-beta
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
F: Transcription intermediary factor 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,12512
Polymers142,6024
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13830 Å2
ΔGint-121 kcal/mol
Surface area43210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)299.914, 299.914, 299.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 / ATP-dependent helicase 1 / hHEL1


Mass: 28799.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCAD1, KIAA1122 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4L7, DNA helicase
#2: Protein Transcription intermediary factor 1-beta / TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-associated protein 1 / KAP-1 / KRAB-interacting ...TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-associated protein 1 / KAP-1 / KRAB-interacting protein 1 / KRIP-1 / Nuclear corepressor KAP-1 / RING finger protein 96 / RING-type E3 ubiquitin transferase TIF1-beta / Tripartite motif-containing protein 28


Mass: 42501.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM28, KAP1, RNF96, TIF1B / Production host: Escherichia coli (E. coli)
References: UniProt: Q13263, RING-type E3 ubiquitin transferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.2 M Sodium Malonate, 0.5 % Jeffamine ED-2003 and 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 5.5→80.1 Å / Num. obs: 14734 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 280 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.04 / Net I/σ(I): 11.5
Reflection shellResolution: 5.5→6.15 Å / Redundancy: 19.5 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3240 / CC1/2: 0.16 / Rpim(I) all: 0.29 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 5.505→74.978 Å / SU ML: 1.53 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 45.15
RfactorNum. reflection% reflection
Rfree0.3026 713 4.85 %
Rwork0.2794 --
obs0.2805 14699 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.505→74.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 8 0 5063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055143
X-RAY DIFFRACTIONf_angle_d0.8326942
X-RAY DIFFRACTIONf_dihedral_angle_d20.2413168
X-RAY DIFFRACTIONf_chiral_restr0.04802
X-RAY DIFFRACTIONf_plane_restr0.005897
LS refinement shellHighest resolution: 5.505 Å

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