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- PDB-4kud: Crystal structure of N-terminal acetylated Sir3 BAH domain D205N ... -

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Basic information

Entry
Database: PDB / ID: 4kud
TitleCrystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle
Components
  • Histone H2A.2
  • Histone H2B.1
  • Histone H3
  • Histone H4
  • Regulatory protein SIR3
  • nucloesome DNA
KeywordsSTRUCTURAL PROTEIN/TRANSCRIPTION/DNA / PROTEPROTEIN-DNA COMPLEX / nucleosome / BAH domain / silencing / nucleus / STRUCTURAL PROTEIN-TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / establishment of protein-containing complex localization to telomere / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / nuclear-transcribed mRNA catabolic process, non-stop decay / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / telomere tethering at nuclear periphery ...sexual sporulation resulting in formation of a cellular spore / establishment of protein-containing complex localization to telomere / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / nuclear-transcribed mRNA catabolic process, non-stop decay / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / telomere tethering at nuclear periphery / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA replication checkpoint signaling / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / chromatin silencing complex / DNA damage tolerance / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / DNA replication origin binding / intracellular copper ion homeostasis / DNA replication initiation / Ub-specific processing proteases / subtelomeric heterochromatin formation / heterochromatin / nucleosome binding / CENP-A containing nucleosome / aerobic respiration / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / single-stranded DNA binding / chromatin organization / double-stranded DNA binding / nucleic acid binding / chromosome, telomeric region / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / identical protein binding / nucleus
Similarity search - Function
: / Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily ...: / Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / SH3 type barrels. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Roll / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B.1 / Histone H4 / Histone H2A.2 / Regulatory protein SIR3 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.203 Å
AuthorsYang, D. / Fang, Q. / Wang, M. / Ren, R. / Wang, H. / He, M. / Sun, Y. / Yang, N. / Xu, R.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: N alpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain.
Authors: Yang, D. / Fang, Q. / Wang, M. / Ren, R. / Wang, H. / He, M. / Sun, Y. / Yang, N. / Xu, R.M.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A.2
D: Histone H2B.1
E: Histone H3
F: Histone H4
G: Histone H2A.2
H: Histone H2B.1
I: nucloesome DNA
J: nucloesome DNA
K: Regulatory protein SIR3
L: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)253,78412
Polymers253,78412
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.330, 108.330, 498.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 5 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3


Mass: 15391.007 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61830
#2: Protein Histone H4


Mass: 11395.390 Da / Num. of mol.: 2 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02309
#3: Protein Histone H2A.2


Mass: 13997.177 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HTA2, H2A2, YBL003C, YBL0103 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04912
#4: Protein Histone H2B.1 / Suppressor of Ty protein 12


Mass: 14280.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02293
#6: Protein Regulatory protein SIR3 / Silent information regulator 3


Mass: 26773.307 Da / Num. of mol.: 2 / Fragment: BAH domain, UNP residues 2-219 / Mutation: D205N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10 / Cell (production host): sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06701

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DNA chain / Non-polymers , 2 types, 68 molecules IJ

#5: DNA chain nucloesome DNA


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 16% PEG 400, 0.1M KCl, 0.01M CaCl2, 0.05M sodium citrate(pH4.8), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 53876 / Num. obs: 54233 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 81.9 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.5
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5345 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ID3, 2FVU

1id3

2fvu


Resolution: 3.203→45.386 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8268 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 2757 5.12 %RANDOM
Rwork0.1977 ---
obs0.1997 53825 99.46 %-
all-54822 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.968 Å2 / ksol: 0.276 e/Å3
Displacement parametersBiso max: 219.78 Å2 / Biso mean: 94.6105 Å2 / Biso min: 39.49 Å2
Baniso -1Baniso -2Baniso -3
1-7.155 Å20 Å2-0 Å2
2--7.155 Å20 Å2
3----14.31 Å2
Refinement stepCycle: LAST / Resolution: 3.203→45.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9686 5980 0 66 15732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616557
X-RAY DIFFRACTIONf_angle_d0.9823610
X-RAY DIFFRACTIONf_dihedral_angle_d24.5726704
X-RAY DIFFRACTIONf_chiral_restr0.0552653
X-RAY DIFFRACTIONf_plane_restr0.0031988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2028-3.25810.32381450.306253899
3.2581-3.31730.29931340.2932251899
3.3173-3.38110.3371530.2698255899
3.3811-3.45010.29571540.2653251599
3.4501-3.5250.30721350.2494256899
3.525-3.6070.27611410.2383257199
3.607-3.69720.2571440.2162249399
3.6972-3.79710.27491580.2162531100
3.7971-3.90880.24131300.21272599100
3.9088-4.03490.26951340.20242540100
4.0349-4.1790.2521350.20112578100
4.179-4.34620.24651260.18072573100
4.3462-4.54380.19451200.17562581100
4.5438-4.78310.21420.16622517100
4.7831-5.08240.21041280.1732576100
5.0824-5.47420.24091350.18492565100
5.4742-6.0240.26121330.21032604100
6.024-6.89310.24561330.21672548100
6.8931-8.67460.20431360.156256899
8.6746-45.390.16491410.1574252798

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