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- PDB-8sr6: Crystal structure of legAS4 from Legionella pneumophila subsp. pn... -

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Basic information

Entry
Database: PDB / ID: 8sr6
TitleCrystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (3-17)peptide
Components
  • Eukaryotic huntingtin interacting protein B
  • Histone 3 peptide
KeywordsCELL INVASION / ankyrin repeats / histone methyltransferase activity
Function / homology
Function and homology information


histone H3K36 methyltransferase activity / nucleosomal DNA binding / euchromatin / structural constituent of chromatin / nucleosome / positive regulation of cell growth / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / nucleoplasm / nucleus
Similarity search - Function
LegAS4-like, SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeat profile. / Histone H3 signature 1. / Ankyrin repeat region circular profile. ...LegAS4-like, SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeat profile. / Histone H3 signature 1. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Ankyrin repeat-containing domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / Eukaryotic huntingtin interacting protein B / Histone H3.3C
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsXu, C. / Chung, I.Y.W. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Histone methyltransferase activity of the secreted Legionella pneumophila SET-domain effector RomA/LegAS4 depends on its ankyrin domain
Authors: Xu, C. / Chung, I.Y.W. / Cygler, M.
History
DepositionMay 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic huntingtin interacting protein B
B: Histone 3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,75216
Polymers53,5092
Non-polymers1,24214
Water2,288127
1
A: Eukaryotic huntingtin interacting protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,16015
Polymers51,9171
Non-polymers1,24214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone 3 peptide


Theoretical massNumber of molelcules
Total (without water)1,5921
Polymers1,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.320, 69.320, 196.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Eukaryotic huntingtin interacting protein B


Mass: 51917.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Gene: legAS4, lpg1718 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZUS4
#2: Protein/peptide Histone 3 peptide / Histone H3.3C / Histone H3.5


Mass: 1591.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2

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Non-polymers , 6 types, 141 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris 6.5 and 38% PPG P400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1806 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 2.22→44.21 Å / Num. obs: 27729 / % possible obs: 99.5 % / Redundancy: 8.4 % / CC1/2: 0.997 / Net I/σ(I): 14.41
Reflection shellResolution: 2.22→2.34 Å / Num. unique obs: 3836 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→44.21 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 1387 5 %
Rwork0.185 --
obs0.1873 27727 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 54 127 3945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.596
X-RAY DIFFRACTIONf_dihedral_angle_d15.2431446
X-RAY DIFFRACTIONf_chiral_restr0.044575
X-RAY DIFFRACTIONf_plane_restr0.004686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.30.34121310.28662486X-RAY DIFFRACTION96
2.3-2.390.32231370.25352603X-RAY DIFFRACTION100
2.39-2.50.31641370.22882610X-RAY DIFFRACTION100
2.5-2.630.28831370.22582588X-RAY DIFFRACTION100
2.63-2.80.25851360.22052598X-RAY DIFFRACTION100
2.8-3.010.34991410.2432669X-RAY DIFFRACTION100
3.01-3.320.23171370.22012599X-RAY DIFFRACTION100
3.32-3.80.25711390.20352655X-RAY DIFFRACTION100
3.8-4.780.20131410.14312681X-RAY DIFFRACTION100
4.78-44.210.17681510.1582851X-RAY DIFFRACTION100
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)
14.48972.89082.16815.7562-2.06196.0822-0.26760.3298-0.1144-0.80030.2999-0.1522-0.11870.19960.01930.688-0.0020.120.3146-0.03390.38796.14-8.185-33.879
22.4112-2.46070.24324.71820.05382.3034-0.0134-0.2791-0.1307-0.04810.2025-0.132-0.1011-0.0168-0.20550.3689-0.01580.04870.3484-0.0370.42579.878-13.143-18.241
31.8334-0.3281-0.19942.40280.86552.56260.02-0.15760.0612-0.12530.1054-0.42590.1280.3482-0.11520.42610.06850.02360.5875-0.09660.65134.872-27.576-13.201
44.4231-1.3129-1.98463.33891.19544.8050.2291-0.29980.26540.22140.1592-0.17870.10120.1499-0.40110.4123-0.0024-0.04350.5975-0.0830.512319.915-14.34713.914
56.1309-3.49486.66812.0603-3.8697.31640.5727-1.2930.64021.50210.0601-0.36490.4166-0.4791-0.70920.9867-0.2246-0.01870.9298-0.06420.67299.112-11.886-4.261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 82:116 )A82 - 116
2X-RAY DIFFRACTION2( CHAIN A AND RESID 117:255 )A117 - 255
3X-RAY DIFFRACTION3( CHAIN A AND RESID 256:411 )A256 - 411
4X-RAY DIFFRACTION4( CHAIN A AND RESID 412:532 )A412 - 532
5X-RAY DIFFRACTION5( CHAIN B AND RESID 3:17 )B3 - 17

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