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- PDB-4au7: The structure of the Suv4-20h2 ternary complex with histone H4 -

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Basic information

Entry
Database: PDB / ID: 4au7
TitleThe structure of the Suv4-20h2 ternary complex with histone H4
Components
  • HISTONE H4 PEPTIDE
  • HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2
KeywordsTRANSFERASE / EPIGENETICS
Function / homology
Function and homology information


: / heterochromatin => GO:0000792 / condensed chromosome, centromeric region => GO:0000779 / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / Condensation of Prophase Chromosomes / G2/M DNA damage checkpoint / HDMs demethylate histones / Processing of DNA double-strand break ends ...: / heterochromatin => GO:0000792 / condensed chromosome, centromeric region => GO:0000779 / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / Condensation of Prophase Chromosomes / G2/M DNA damage checkpoint / HDMs demethylate histones / Processing of DNA double-strand break ends / [histone H4]-lysine20 N-methyltransferase / Nonhomologous End-Joining (NHEJ) / histone H4K20 methyltransferase activity / : / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / positive regulation of isotype switching / Estrogen-dependent gene expression / S-adenosyl-L-methionine binding / positive regulation of double-strand break repair via nonhomologous end joining / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / CENP-A containing nucleosome / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / protein heterodimerization activity / DNA repair / chromatin binding / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. ...Histone-lysine N-methyltransferase / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Beta Complex / Histone-fold / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H4 / Histone-lysine N-methyltransferase KMT5C
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSouthall, S.M. / Cronin, N.B. / Wilson, J.R.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: A Novel Route to Product Specificity in the Suv4-20 Family of Histone H4K20 Methyltransferases.
Authors: Southall, S.M. / Cronin, N.B. / Wilson, J.R.
History
DepositionMay 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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 SUV420H2
B: HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2
C: HISTONE H4 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,17223
Polymers57,5993
Non-polymers1,57420
Water2,648147
1
A: HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2
C: HISTONE H4 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,44813
Polymers29,4372
Non-polymers1,01211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-34.3 kcal/mol
Surface area13390 Å2
MethodPISA
2
B: HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,72410
Polymers28,1621
Non-polymers5629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.270, 65.170, 209.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2 / SUPPRESSOR OF VARIEGATION 4-20 HOMOLOG 2 / SU(VAR)4-20 HOMOLOG 2 / SUV4-20H2


Mass: 28162.127 Da / Num. of mol.: 2 / Fragment: SET DOMAIN, RESIDUES 1-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q6Q783, histone-lysine N-methyltransferase
#2: Protein/peptide HISTONE H4 PEPTIDE


Mass: 1274.519 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-26 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P62806

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Non-polymers , 4 types, 167 molecules

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


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFIRST RESIDUE FROM VECTOR

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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: 2.25 Å3/Da / Density % sol: 44.8 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 9% PEG 3350, 0.1 M HEPES PH 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0081
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2012 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0081 Å / Relative weight: 1
ReflectionResolution: 2.1→55.3 Å / Num. obs: 29593 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RQ4

3rq4


Resolution: 2.07→55.33 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.589 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE C-TERMINUS OF MOECULE B IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24039 1570 5 %RANDOM
Rwork0.19255 ---
obs0.19498 29593 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--1.39 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.07→55.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 93 147 3878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193841
X-RAY DIFFRACTIONr_bond_other_d0.0050.022712
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9745176
X-RAY DIFFRACTIONr_angle_other_deg1.37736526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30622.663184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33215622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81538
X-RAY DIFFRACTIONr_chiral_restr0.1040.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214254
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02842
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.071→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 100 -
Rwork0.264 1638 -
obs--79.72 %
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)
10.42540.2104-0.31961.2811-0.09572.34880.0074-0.00180.0490.1294-0.02590.01820.21080.16560.01860.03820.0182-0.00260.03010.00750.0417-15.1412-11.118241.8245
20.9732-0.79220.32221.0762-0.28691.3236-0.005-0.13440.12680.06440.0352-0.0446-0.22560.1208-0.03030.0494-0.04550.01920.0988-0.02190.081-4.9339-38.7248.1057
38.6221-4.7476-4.89526.22875.785511.00460.1780.1042-0.1782-0.53920.249-0.370.55470.163-0.4270.33010.01660.00770.1012-0.0120.1388-11.8427-20.154727.3436
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 240
2X-RAY DIFFRACTION2B4 - 215
3X-RAY DIFFRACTION3C17 - 25

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