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- PDB-6qu1: Crystal structure of the KAP1 RBCC domain in complex with the SMA... -

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Basic information

Entry
Database: PDB / ID: 6qu1
TitleCrystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain at 3.7 angstrom resolution.
Components
  • SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
  • Transcription intermediary factor 1-beta,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 / negative regulation of DNA demethylation / Krueppel-associated box domain binding / chromosome separation / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / regulation of DNA recombination ...: / : / convergent extension involved in axis elongation / negative regulation of DNA demethylation / Krueppel-associated box domain binding / chromosome separation / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / regulation of DNA recombination / epigenetic programming of gene expression / DNA double-strand break processing / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / genomic imprinting / chromo shadow domain binding / Generic Transcription Pathway / ATP-dependent chromatin remodeler activity / SUMO transferase activity / nuclear replication fork / protein sumoylation / epithelial to mesenchymal transition / ATP-dependent activity, acting on DNA / heterochromatin / embryo implantation / positive regulation of DNA repair / SUMOylation of transcription cofactors / ubiquitin binding / helicase activity / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / HCMV Early Events / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / site of double-strand break / chromatin organization / DNA helicase / transcription coactivator activity / protein kinase activity / chromatin remodeling / DNA repair / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / 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 / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / helicase superfamily c-terminal domain / bromo domain / Bromodomain / Bromodomain-like superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Gavard, A. / Lim, M. / Williams, H.L. / Svejstrup, J.Q. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
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
DepositionFeb 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Transcription intermediary factor 1-beta,Transcription intermediary factor 1-beta
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5906
Polymers41,3282
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-2 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.496, 64.496, 287.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transcription intermediary factor 1-beta,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: 35985.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein is a construct with an internal deletion of residues 141-202,The protein is a construct with an internal deletion of residues 141-202,The protein is a construct with an internal ...Details: The protein is a construct with an internal deletion of residues 141-202,The protein is a construct with an internal deletion of residues 141-202,The protein is a construct with an internal deletion of residues 141-202,The protein is a construct with an internal deletion of residues 141-202,The protein is a construct with an internal deletion of residues 141-202,The protein is a construct with an internal deletion of residues 141-202
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
#2: Protein/peptide SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 / ATP-dependent helicase 1 / hHEL1


Mass: 5343.150 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25 % PEG 3350, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.7→29.431 Å / Num. obs: 7157 / % possible obs: 99.7 % / Redundancy: 9.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.106 / Net I/σ(I): 7.3
Reflection shellResolution: 3.7→4.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 2.081 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1948 / CC1/2: 0.816 / Rpim(I) all: 0.805 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H3A

6h3a


Resolution: 3.7→29.431 Å / Cross valid method: FREE R-VALUE / σ(F): 0.23
RfactorNum. reflection% reflection
Rfree0.3464 565 7.5 %
Rwork0.2997 --
obs0.3036 7061 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.7→29.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 4 0 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032477
X-RAY DIFFRACTIONf_angle_d0.6783344
X-RAY DIFFRACTIONf_dihedral_angle_d21.2881531
X-RAY DIFFRACTIONf_chiral_restr0.039389
X-RAY DIFFRACTIONf_plane_restr0.005430
LS refinement shellResolution: 3.7→3.895 Å
RfactorNum. reflection% reflection
Rfree0.3752 --
Rwork0.386 --
all-1687 -
obs--96 %

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