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- PDB-8pef: Crystal structure of SLF1 Ankyrin repeat domain in complex with H... -

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Basic information

Entry
Database: PDB / ID: 8pef
TitleCrystal structure of SLF1 Ankyrin repeat domain in complex with H4 tail (K20me0)
Components
  • Histone H4
  • SMC5-SMC6 complex localization factor protein 1
KeywordsNUCLEAR PROTEIN / DNA repair / SMC5/6 / nucleosome / Histone 4 / SLF1 / Ankyrin repeat / RAD18 / K20me0 / Interstrand crosslinks
Function / homology
Function and homology information


positive regulation of maintenance of mitotic sister chromatid cohesion / Smc5-Smc6 complex / nuclear inclusion body / protein localization to site of double-strand break / chromatin looping / regulation of telomere maintenance / positive regulation of double-strand break repair / protein sumoylation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin ...positive regulation of maintenance of mitotic sister chromatid cohesion / Smc5-Smc6 complex / nuclear inclusion body / protein localization to site of double-strand break / chromatin looping / regulation of telomere maintenance / positive regulation of double-strand break repair / protein sumoylation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / positive regulation of protein-containing complex assembly / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / site of double-strand break / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / centrosome / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
: / SMC5-SMC6 complex localization factor protein 1 / TopBP1/SLF1, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / breast cancer carboxy-terminal domain / BRCT domain / BRCT domain superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site ...: / SMC5-SMC6 complex localization factor protein 1 / TopBP1/SLF1, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / breast cancer carboxy-terminal domain / BRCT domain / BRCT domain superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Histone-fold
Similarity search - Domain/homology
Histone H4 / SMC5-SMC6 complex localization factor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsNasir, N. / Ryder, E.L. / Wu, Q.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural mechanisms of SLF1 interactions with Histone H4 and RAD18 at the stalled replication fork.
Authors: Ryder, E.L. / Nasir, N. / Durgan, A.E.O. / Jenkyn-Bedford, M. / Tye, S. / Zhang, X. / Wu, Q.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SMC5-SMC6 complex localization factor protein 1
B: Histone H4


Theoretical massNumber of molelcules
Total (without water)16,7812
Polymers16,7812
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-1 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.680, 50.940, 139.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1020-

HOH

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Components

#1: Protein SMC5-SMC6 complex localization factor protein 1 / Ankyrin repeat domain-containing protein 32 / BRCT domain-containing protein 1 / Smc5/6 localization factor 1


Mass: 14912.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLF1, ANKRD32, BRCTD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQI6
#2: Protein/peptide Histone H4


Mass: 1869.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-Terminus: Biotin C-Terminus: Amidation / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Sodium malonate dibasic monohydrate 0.1M Hepes pH 7 30% (w/v) Poly(acrylic acid sodium salt) 2100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.28→29.6 Å / Num. obs: 35141 / % possible obs: 99.97 % / Redundancy: 11.4 % / Biso Wilson estimate: 17.09 Å2 / CC1/2: 0.99 / CC star: 0.998 / Net I/σ(I): 10.02
Reflection shellResolution: 1.28→1.326 Å / Num. unique obs: 3459 / CC1/2: 0.331 / CC star: 0.705

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→29.6 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 1763 5.02 %
Rwork0.194 33374 -
obs0.1955 35137 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.37 Å2
Refinement stepCycle: LAST / Resolution: 1.28→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 0 118 1231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461129
X-RAY DIFFRACTIONf_angle_d0.771533
X-RAY DIFFRACTIONf_chiral_restr0.0754185
X-RAY DIFFRACTIONf_plane_restr0.007199
X-RAY DIFFRACTIONf_dihedral_angle_d4.7839152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.4191310.39352539X-RAY DIFFRACTION100
1.31-1.350.36861460.37182504X-RAY DIFFRACTION100
1.35-1.40.33581300.31382533X-RAY DIFFRACTION100
1.4-1.450.27931420.27562565X-RAY DIFFRACTION100
1.45-1.50.26461340.2442538X-RAY DIFFRACTION100
1.5-1.570.28451440.21442524X-RAY DIFFRACTION100
1.57-1.660.23381370.19712532X-RAY DIFFRACTION100
1.66-1.760.24051410.18552562X-RAY DIFFRACTION99.93
1.76-1.90.18891250.18032557X-RAY DIFFRACTION99.93
1.9-2.090.20421420.16592568X-RAY DIFFRACTION100
2.09-2.390.20471420.17812576X-RAY DIFFRACTION99.96
2.39-3.010.23971270.1972611X-RAY DIFFRACTION100
3.01-29.60.19581220.17442765X-RAY DIFFRACTION99.97

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