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- PDB-3tu4: Crystal structure of the Sir3 BAH domain in complex with a nucleo... -

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Basic information

Entry
Database: PDB / ID: 3tu4
TitleCrystal structure of the Sir3 BAH domain in complex with a nucleosome core particle.
Components
  • (DNA (146-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Regulatory protein SIR3
KeywordsSignaling Protein/Structural Protein/DNA / histones / nucleosome / gene silencing / Signaling Protein-Structural Protein-DNA complex
Function / homology
Function and homology information


establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / mitotic DNA replication checkpoint signaling / chromatin silencing complex / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation ...establishment of protein-containing complex localization to telomere / nuclear-transcribed mRNA catabolic process, non-stop decay / telomere tethering at nuclear periphery / mitotic DNA replication checkpoint signaling / chromatin silencing complex / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / heterochromatin / nucleosome binding / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / single-stranded DNA binding / double-stranded DNA binding / nucleic acid binding / chromosome, telomeric region / protein heterodimerization activity / chromatin binding / nucleolus / mitochondrion / DNA binding / nucleoplasm / 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 / 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 / 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 1.1 / Regulatory protein SIR3 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsArmache, K.-J. / Garlick, J.D. / Canzio, D. / Narlikar, G.J. / Kingston, R.E.
CitationJournal: Science / Year: 2011
Title: Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution.
Authors: Armache, K.J. / Garlick, J.D. / Canzio, D. / Narlikar, G.J. / Kingston, R.E.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references / Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (146-MER)
J: DNA (146-MER)
K: Regulatory protein SIR3
L: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)253,41512
Polymers253,41512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)198,88710
Polymers198,88710
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57080 Å2
ΔGint-396 kcal/mol
Surface area73430 Å2
MethodPISA
3
K: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)27,2641
Polymers27,2641
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
L: Regulatory protein SIR3


Theoretical massNumber of molelcules
Total (without water)27,2641
Polymers27,2641
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.880, 102.880, 555.750
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 H3.2


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein Regulatory protein SIR3 / Silent information regulator 3


Mass: 27263.922 Da / Num. of mol.: 2 / Fragment: BAH domain / Mutation: D205N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P06701

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (146-MER)


Mass: 45137.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic construct
#6: DNA chain DNA (146-MER)


Mass: 45609.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic construct

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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: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2011
RadiationMonochromator: Si(111), side bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 66268 / Num. obs: 66104 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASER(CCP4-6.1.1)phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.548 Å / SU ML: 0.83 / σ(F): 0 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1767 2.74 %
Rwork0.1919 --
obs0.1932 64428 97.45 %
all-64428 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.927 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5167 Å20 Å2-0 Å2
2--2.5167 Å20 Å2
3----5.0334 Å2
Refinement stepCycle: LAST / Resolution: 3→44.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9674 5986 0 0 15660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316548
X-RAY DIFFRACTIONf_angle_d0.83523609
X-RAY DIFFRACTIONf_dihedral_angle_d23.036678
X-RAY DIFFRACTIONf_chiral_restr0.0532659
X-RAY DIFFRACTIONf_plane_restr0.0031990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08110.35291290.33224512X-RAY DIFFRACTION92
3.0811-3.17170.38211290.2884634X-RAY DIFFRACTION94
3.1717-3.27410.36611340.2784769X-RAY DIFFRACTION96
3.2741-3.39110.32981410.24344791X-RAY DIFFRACTION97
3.3911-3.52680.28421380.21994850X-RAY DIFFRACTION98
3.5268-3.68720.35221330.26644723X-RAY DIFFRACTION95
3.6872-3.88150.24891400.20834837X-RAY DIFFRACTION99
3.8815-4.12450.19911370.16174924X-RAY DIFFRACTION99
4.1245-4.44270.15521390.14314912X-RAY DIFFRACTION100
4.4427-4.88930.19071430.14094947X-RAY DIFFRACTION100
4.8893-5.59570.19971310.16284910X-RAY DIFFRACTION100
5.5957-7.04540.25571400.19844954X-RAY DIFFRACTION100
7.0454-44.55320.21551330.17184898X-RAY DIFFRACTION98
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)
12.84881.0996-0.0633.33930.74413.6250.33690.1077-0.21980.0777-0.15060.51140.4739-0.1924-0.02650.41360.1143-0.19360.3904-0.17770.166326.066-28.4073-9.2381
23.3796-1.12350.02783.33880.39113.68980.3821-0.15370.256-0.0589-0.19530.4314-0.4559-0.124-0.09340.4523-0.12140.21090.4221-0.18040.197926.155628.391659.9944
36.19570.1399-0.78591.506-0.31951.829-0.029-0.0766-0.24510.0676-0.09750.47260.6029-0.47440.11260.5244-0.20890.02450.4485-0.13810.469610.3037-17.790424.6998
44.9524-1.0392-1.35022.35970.27072.64660.1222-0.0198-0.2588-0.1355-0.19230.4250.3868-0.35030.10750.4217-0.1006-0.02730.3394-0.07950.326219.5321-19.145818.1026
56.2285-2.08610.11892.88630.18222.81740.00870.20050.2146-0.4401-0.0067-0.066-0.4061-0.1355-0.00510.4241-0.0515-0.03110.3089-0.09720.112730.13879.99468.2596
62.4102-1.92250.08795.1504-0.13243.48490.09760.28270.0962-0.6649-0.0289-0.2219-0.15040.25-0.06290.4016-0.14390.01660.3646-0.10220.27137.40594.89348.9214
75.24970.22960.36811.7282-0.06421.7841-0.03920.00730.3343-0.026-0.0820.4977-0.5379-0.50050.10610.4820.2150.00840.4217-0.12310.444911.007317.338126.3387
84.20770.60841.22022.45120.26722.6040.1508-0.04470.24820.0387-0.14920.4555-0.4745-0.33640.07340.41160.07870.03210.3337-0.09250.322619.642719.093532.5143
93.92971.35630.05982.39440.07742.39250.088-0.1764-0.13310.3918-0.04580.06040.4092-0.024-0.0160.31910.06410.02930.2555-0.10980.046830.4618-9.929142.3848
102.99242.08880.05254.6946-0.73243.58580.0048-0.2616-0.12340.45670.0341-0.27090.28880.2112-0.05860.40640.1306-0.0320.4326-0.13390.267537.4092-5.077941.6837
111.4855-0.0057-0.03131.33530.11661.6313-0.0225-0.004-0.0266-0.01220.04860.06210.0006-0.1179-0.01410.5370.0092-0.01920.6002-0.12890.545223.44660.167825.2157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'K'
2X-RAY DIFFRACTION2chain 'L'
3X-RAY DIFFRACTION3chain 'A'
4X-RAY DIFFRACTION4chain 'B'
5X-RAY DIFFRACTION5chain 'C'
6X-RAY DIFFRACTION6chain 'D'
7X-RAY DIFFRACTION7chain 'E'
8X-RAY DIFFRACTION8chain 'F'
9X-RAY DIFFRACTION9chain 'G'
10X-RAY DIFFRACTION10chain 'H'
11X-RAY DIFFRACTION11(chain 'I') or (chain 'J')

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