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- PDB-6qtm: Crystal structure of the Sir4 H-BRCT domain in complex with Ty5 p... -

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Basic information

Entry
Database: PDB / ID: 6qtm
TitleCrystal structure of the Sir4 H-BRCT domain in complex with Ty5 pS1095 peptide
Components
  • Regulatory protein SIR4
  • Ribonuclease H
KeywordsNUCLEAR PROTEIN / Heterochromatin
Function / homology
Function and homology information


transposition / establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin formation / DNA integration ...transposition / establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin formation / DNA integration / double-strand break repair via nonhomologous end joining / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / double-stranded DNA binding / chromosome, telomeric region / molecular adaptor activity / DNA-directed DNA polymerase activity / RNA binding / nucleus / cytoplasm
Similarity search - Function
GAG-pre-integrase domain / Protein of unknown function DUF5314 / GAG-pre-integrase domain / Ty5 Gag N-terminal region / Sir4, SID domain / Sir4 SID domain / Reverse transcriptase, RNA-dependent DNA polymerase / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase core domain / Integrase, catalytic core ...GAG-pre-integrase domain / Protein of unknown function DUF5314 / GAG-pre-integrase domain / Ty5 Gag N-terminal region / Sir4, SID domain / Sir4 SID domain / Reverse transcriptase, RNA-dependent DNA polymerase / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Integrase catalytic domain-containing protein / Regulatory protein SIR4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces paradoxus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGut, H. / Deshpande, I. / Keusch, J.J. / Challa, K. / Iesmantavicius, V. / Gasser, S.M.
CitationJournal: Embo J. / Year: 2019
Title: The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin.
Authors: Deshpande, I. / Keusch, J.J. / Challa, K. / Iesmantavicius, V. / Gasser, S.M. / Gut, H.
History
DepositionFeb 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Aug 11, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein SIR4
B: Regulatory protein SIR4
C: Regulatory protein SIR4
D: Ribonuclease H
E: Ribonuclease H
F: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,23512
Polymers50,6596
Non-polymers5766
Water1267
1
A: Regulatory protein SIR4
F: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0784
Polymers16,8862
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-28 kcal/mol
Surface area7540 Å2
MethodPISA
2
B: Regulatory protein SIR4
E: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9823
Polymers16,8862
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-22 kcal/mol
Surface area7160 Å2
MethodPISA
3
C: Regulatory protein SIR4
D: Ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1745
Polymers16,8862
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-43 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.930, 58.930, 270.460
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 Regulatory protein SIR4 / Silent information regulator 4


Mass: 15059.491 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Fragment, residues 961-1085 / Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SIR4, ASD1, STE9, UTH2, YDR227W, YD9934.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: P11978
#2: Protein/peptide Ribonuclease H /


Mass: 1826.763 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Saccharomyces paradoxus (yeast) / References: UniProt: O42838, ribonuclease H
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0 M ammonium sulfate 0.2 M sodium potassium tartrate 0.1 M tri-sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 10009 / % possible obs: 97.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 81.97 Å2 / CC1/2: 0.995 / Rsym value: 0.181 / Net I/σ(I): 7.7
Reflection shellResolution: 3→3.08 Å / Mean I/σ(I) obs: 1.1 / CC1/2: 0.62 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.33 Å / Cor.coef. Fo:Fc: 0.8691 / Cor.coef. Fo:Fc free: 0.8367 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 751 7.5 %RANDOM
Rwork0.2013 ---
obs0.2055 10009 96.86 %-
Displacement parametersBiso mean: 91.88 Å2
Baniso -1Baniso -2Baniso -3
1--23.8518 Å20 Å20 Å2
2---23.8518 Å20 Å2
3---47.7036 Å2
Refine analyzeLuzzati coordinate error obs: 0.663 Å
Refinement stepCycle: 1 / Resolution: 3→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 30 7 2986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013056HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.164112HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1103SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes408HARMONIC5
X-RAY DIFFRACTIONt_it3056HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion21.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion395SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3428SEMIHARMONIC4
LS refinement shellResolution: 3→3.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.264 204 7.49 %
Rwork0.2485 2520 -
all0.2497 2724 -
obs--96.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.71950.2721-1.7533.0219-0.13667.17590.20220.19040.320.17750.0467-0.1301-0.8231-0.0325-0.24880.1639-0.038-0.00480.0682-0.03270.01727.244636.16861.1474
21.94610.5701-0.04423.26840.61957.5714-0.06830.3161-0.29120.07990.0770.03740.5578-0.0527-0.00870.0999-0.0246-0.01750.2973-0.10690.10921.772119.272-20.3347
31.2209-0.4044-0.26232.0190.53727.3288-0.1228-0.13550.3327-0.15120.130.0715-0.6178-0.6683-0.00720.15180.1225-0.10610.3748-0.03720.2213-3.044934.7587-43.3792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|970 - A|1084 }
2X-RAY DIFFRACTION2{ B|970 - B|1084 }
3X-RAY DIFFRACTION3{ C|* }

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