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- PDB-4o30: Crystal structure of ATXR5 in complex with histone H3.1 and AdoHcy -

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Basic information

Entry
Database: PDB / ID: 4o30
TitleCrystal structure of ATXR5 in complex with histone H3.1 and AdoHcy
Components
  • Histone-lysine N-methyltransferase ATXR6, putative
  • histone H3.1
KeywordsTRANSFERASE / histone methylation / chromatin / epigenetics / trithorax / SET domain / lysine methyltransferases / PCNA / histone H3 / nucleus
Function / homology
Function and homology information


[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / histone acetyltransferase activity / chloroplast / transcription coregulator activity / methylation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
: / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger ...: / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Beta Complex / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / S-ADENOSYL-L-HOMOCYSTEINE / Probable Histone-lysine N-methyltransferase ATXR5
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBergamin, E. / Mongeon, V. / Couture, J.F.
CitationJournal: Science / Year: 2014
Title: Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication.
Authors: Jacob, Y. / Bergamin, E. / Donoghue, M.T. / Mongeon, V. / LeBlanc, C. / Voigt, P. / Underwood, C.J. / Brunzelle, J.S. / Michaels, S.D. / Reinberg, D. / Couture, J.F. / Martienssen, R.A.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase ATXR6, putative
B: Histone-lysine N-methyltransferase ATXR6, putative
C: histone H3.1
D: histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0028
Polymers57,0774
Non-polymers9254
Water5,441302
1
A: Histone-lysine N-methyltransferase ATXR6, putative
C: histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0014
Polymers28,5382
Non-polymers4632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-9 kcal/mol
Surface area11000 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase ATXR6, putative
D: histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0014
Polymers28,5382
Non-polymers4632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-6 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.170, 87.310, 74.510
Angle α, β, γ (deg.)90.00, 127.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Histone-lysine N-methyltransferase ATXR6, putative


Mass: 26650.254 Da / Num. of mol.: 2 / Fragment: SET domain, UNP residues 146-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Gene: RCOM_1460410 / Production host: Escherichia coli (E. coli)
References: UniProt: B9RU15, histone-lysine N-methyltransferase
#2: Protein/peptide histone H3.1


Mass: 1888.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide (Genescript), histone H3

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Non-polymers , 4 types, 306 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 50% polypropylene glycol 400, 100mM Na-HEPES pH 6.0 and 5% DMSO, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 10, 2013
RadiationMonochromator: VariMax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→27 Å / Num. obs: 29417 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 44.14 Å2 / Rsym value: 0.052 / Net I/σ(I): 12.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4 / Rsym value: 0.3 / % possible all: 96.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
BUSTER2.10.0refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27 Å / Cor.coef. Fo:Fc: 0.9336 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1494 5.08 %RANDOM
Rwork0.2019 ---
obs0.2042 29410 98.26 %-
all-30880 --
Displacement parametersBiso mean: 43.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.9832 Å20 Å211.4422 Å2
2--1.1674 Å20 Å2
3----3.1506 Å2
Refine analyzeLuzzati coordinate error obs: 0.273 Å
Refinement stepCycle: LAST / Resolution: 2.1→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 60 302 3900
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013657HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084934HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1310SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes563HARMONIC5
X-RAY DIFFRACTIONt_it3657HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion17.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion482SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4248SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2727 155 5.51 %
Rwork0.2091 2659 -
all0.2127 2814 -
obs--98.26 %
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)
11.33410.16350.08561.54330.13351.04950.0626-0.116-0.04860.08110.00650.00730.1192-0.0181-0.069-0.1116-0.01070.0113-0.09910.0086-0.0874-25.8299-17.54972.9103
21.75810.57210.88291.41350.13982.0990.04010.02320.03860.1112-0.15950.014-0.0488-0.03460.1194-0.0840.02470.0269-0.1235-0.0552-0.1145-51.8881-2.457630.0686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|158 - A|374 }A158 - 374
2X-RAY DIFFRACTION2{ B|159 - B|374 }B159 - 374

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