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- PDB-6mr4: Crystal structure of the Sth1 bromodomain from S.cerevisiae -

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Basic information

Entry
Database: PDB / ID: 6mr4
TitleCrystal structure of the Sth1 bromodomain from S.cerevisiae
ComponentsNuclear protein STH1/NPS1
KeywordsGENE REGULATION / Bromodomain / gene expression / chromatin structure / acetylated-lysine histone binding
Function / homology
Function and homology information


chromatin remodeling at centromere / DNA translocase activity / RSC-type complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / histone reader activity / meiotic cell cycle ...chromatin remodeling at centromere / DNA translocase activity / RSC-type complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / histone reader activity / meiotic cell cycle / chromosome segregation / helicase activity / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / base-excision repair / double-strand break repair / DNA helicase / chromatin remodeling / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain ...Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Nuclear protein STH1/NPS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsSeo, H.S. / Hashimoto, H. / Krolak, A. / Debler, E.W. / Blus, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Structure / Year: 2019
Title: Substrate Affinity and Specificity of the ScSth1p Bromodomain Are Fine-Tuned for Versatile Histone Recognition.
Authors: Blus, B.J. / Hashimoto, H. / Seo, H.S. / Krolak, A. / Debler, E.W.
History
DepositionOct 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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: Nuclear protein STH1/NPS1
B: Nuclear protein STH1/NPS1
C: Nuclear protein STH1/NPS1
D: Nuclear protein STH1/NPS1
E: Nuclear protein STH1/NPS1
F: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)80,1186
Polymers80,1186
Non-polymers00
Water48627
1
A: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)13,3531
Polymers13,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)13,3531
Polymers13,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)13,3531
Polymers13,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)13,3531
Polymers13,3531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)13,3531
Polymers13,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)13,3531
Polymers13,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Nuclear protein STH1/NPS1
F: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)26,7062
Polymers26,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-6 kcal/mol
Surface area12080 Å2
MethodPISA
8
B: Nuclear protein STH1/NPS1

B: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)26,7062
Polymers26,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1830 Å2
ΔGint-9 kcal/mol
Surface area11930 Å2
MethodPISA
9
C: Nuclear protein STH1/NPS1

E: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)26,7062
Polymers26,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area1900 Å2
ΔGint-8 kcal/mol
Surface area12060 Å2
MethodPISA
10
D: Nuclear protein STH1/NPS1

D: Nuclear protein STH1/NPS1


Theoretical massNumber of molelcules
Total (without water)26,7062
Polymers26,7062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1970 Å2
ΔGint-7 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.753, 74.619, 72.541
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog


Mass: 13352.991 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: STH1, NPS1, YIL126W / Production host: Escherichia coli (E. coli) / References: UniProt: P32597, DNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2015
RadiationMonochromator: Cryo cooled double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.71→72.45 Å / Num. obs: 20385 / % possible obs: 98.6 % / Redundancy: 3.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.8
Reflection shellResolution: 2.71→2.84 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2722 / CC1/2: 0.6 / % possible all: 99.5

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Processing

Software
NameClassification
HKL-2000data collection
XDSdata scaling
XDSdata reduction
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TLP

3tlp


Resolution: 2.71→72.449 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / Phase error: 30.61
RfactorNum. reflection% reflection
Rfree0.2699 1044 5.12 %
Rwork0.2377 --
obs0.2394 20371 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.71→72.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5476 0 0 27 5503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065607
X-RAY DIFFRACTIONf_angle_d0.617565
X-RAY DIFFRACTIONf_dihedral_angle_d12.4642145
X-RAY DIFFRACTIONf_chiral_restr0.039790
X-RAY DIFFRACTIONf_plane_restr0.004983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7102-2.85310.33481450.33512780X-RAY DIFFRACTION99
2.8531-3.03180.34751400.31592764X-RAY DIFFRACTION99
3.0318-3.26590.33041400.29192781X-RAY DIFFRACTION99
3.2659-3.59460.30711600.26182748X-RAY DIFFRACTION99
3.5946-4.11470.25171400.21852766X-RAY DIFFRACTION98
4.1147-5.18380.24321590.20752740X-RAY DIFFRACTION98
5.1838-72.47520.22941600.19482748X-RAY DIFFRACTION96
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)
15.3508-0.4008-1.90516.03011.66876.4777-0.30750.0569-0.642-0.64240.45440.34061.3682-0.4474-0.07320.6108-0.20480.06970.56090.02720.403-43.55658.088525.0627
24.82171.7897-1.6527.68052.98032.9366-0.3256-0.6652-0.1716-0.12090.2765-0.3489-0.53480.63030.04370.5717-0.0872-0.03870.58730.14560.3106-35.430127.484324.1889
33.92033.1753-0.55626.9974-5.48595.8890.2373-0.73860.46130.2958-0.24170.2804-0.11770.07110.04340.554-0.09220.08760.4595-0.00680.3269-42.4921.423833.8414
44.45191.2141-1.05876.89151.34837.92620.0150.2314-0.0695-0.27480.43720.5250.0151-1.293-0.47050.5577-0.074-0.09840.56260.140.4659-49.83918.153224.1163
55.44-0.61431.52565.88781.15466.26990.03150.1458-0.148-0.139-0.0616-0.24770.20660.0549-0.00820.271-0.03330.1680.25840.00820.411-1.918227.328825.6815
63.61523.1148-0.69064.57131.01549.3547-0.07970.4818-0.6-0.39690.296-0.83571.121.1962-0.23790.41820.10270.02040.4746-0.08130.7988.117122.924.2239
75.71620.71490.044.0216-1.72474.6652-0.29580.13040.3366-0.12790.1685-0.19350.0461-0.18940.12730.6916-0.11590.0980.3123-0.08680.2589-19.953750.835910.3685
83.4588-0.76630.1122.9977-0.01233.955-0.54231.1207-0.1961-1.16750.5072-0.3692-0.09050.27990.04560.9061-0.23130.11980.6454-0.07890.466-18.680947.26060.802
96.79221.9458-3.82071.2339-3.23217.7077-0.4191-0.61961.4751-1.0596-0.35670.1093-1.87760.84240.37781.2561-0.1143-0.28130.43830.25141.05784.04051.404625.4035
103.09840.32931.10197.7671-1.14656.9111-0.55230.2043-0.00850.46510.20970.1298-0.74510.11570.26720.5823-0.0775-0.1490.46620.03880.7805-0.6242-15.039431.3264
112.9945-0.3342-1.36693.0264-0.81634.49330.08280.21210.2411-0.4117-0.276-1.2356-1.04250.67520.22060.8971-0.1649-0.15910.52540.13140.95134.8736-10.560920.4503
125.65771.963-3.61987.8148-0.95845.611-0.62870.66210.4248-0.29750.4961-0.3485-0.772-0.7436-0.06130.7918-0.0632-0.28390.37250.09820.813-7.8068-7.286422.4996
1310.84211.6026.21374.4068-0.05289.5423-1.2701-0.23583.1985-0.2188-0.05390.4462-1.2763-0.12681.03140.88130.0382-0.06480.4798-0.00010.6474-36.248725.2112-11.5134
143.88681.09691.17943.878-2.16953.7896-0.21170.3924-0.2351-0.15360.2807-0.5625-0.4926-0.0153-0.05960.56880.04520.05370.4078-0.1210.2519-31.83335.5404-11.5866
158.51361.09142.069.03171.06247.49150.23160.34130.57220.39560.6145-1.3278-0.02261.0541-0.72120.4449-0.02930.11320.4865-0.09190.5994-24.308716.8902-12.9801
165.850.7278-1.09680.1502-0.36751.4218-0.4141.20771.1993-1.31580.75940.0669-1.29360.4601-0.18851.0001-0.23990.09110.56470.02310.501-33.264621.5558-21.2947
176.0142-5.1928-5.36248.47684.28696.5517-0.2243-0.48-0.9270.5695-0.35510.68151.2986-0.32010.57880.6881-0.1755-0.05530.44140.11830.5388-29.66394.963821.0589
186.1074-4.4884-0.676510.1177-1.76973.58630.14780.4421-0.1580.0824-0.2866-0.201-0.40370.08280.1430.4792-0.11610.04320.3215-0.0510.1982-30.058722.634611.3004
193.63190.5570.94786.19251.19392.48180.03350.5716-0.497-0.52540.0016-0.25640.08850.0913-0.00390.4723-0.03940.12230.4147-0.0340.3442-23.061211.06059.691
206.2361-2.4053-3.41346.63645.40879.2799-0.1836-0.58810.12050.84890.6629-1.12440.29871.0756-0.43450.3521-0.0039-0.06440.48430.03080.3929-20.848610.802922.6379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1250 through 1275 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1276 through 1293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1294 through 1309 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1310 through 1358 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1251 through 1337 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1338 through 1356 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1250 through 1314 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1315 through 1358 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1251 through 1264 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1265 through 1299 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1300 through 1332 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1333 through 1358 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1251 through 1275 )
14X-RAY DIFFRACTION14chain 'E' and (resid 1276 through 1299 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1300 through 1332 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1333 through 1358 )
17X-RAY DIFFRACTION17chain 'F' and (resid 1251 through 1275 )
18X-RAY DIFFRACTION18chain 'F' and (resid 1276 through 1299 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1300 through 1332 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1333 through 1358 )

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