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- PDB-4c1q: Crystal structure of the PRDM9 SET domain in complex with H3K4me2... -

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Basic information

Entry
Database: PDB / ID: 4c1q
TitleCrystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy.
Components
  • HISTONE H3.1
  • HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / HISTONE METHYLTRANSFERASE / SET DOMAIN H3K4ME3
Function / homology
Function and homology information


: / : / : / : / : / : / recombination hotspot binding / : / : / Generic Transcription Pathway ...: / : / : / : / : / : / recombination hotspot binding / : / : / Generic Transcription Pathway / : / : / : / positive regulation of reciprocal meiotic recombination / : / : / positive regulation of fertilization / [histone H3]-lysine9 N-trimethyltransferase / male gamete generation / meiotic gene conversion / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / positive regulation of meiosis I / [histone H4]-lysine20 N-methyltransferase / [histone H3]-lysine36 N-trimethyltransferase / female gamete generation / [histone H3]-lysine4 N-trimethyltransferase / PKMTs methylate histone lysines / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin / negative regulation of apoptotic process / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding
Similarity search - Function
Ancestral KRAB domain / SSXRD motif / SSXRD motif / KRAB-related domain profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Beta-clip-like / SET domain ...Ancestral KRAB domain / SSXRD motif / SSXRD motif / KRAB-related domain profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Beta-clip-like / SET domain / SET domain / SET domain profile. / SET domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Beta Complex / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H3.1 / Histone-lysine N-methyltransferase PRDM9
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMathioudakis, N. / Cusack, S. / Kadlec, J.
CitationJournal: Cell Rep. / Year: 2013
Title: Molecular Basis for the Regulation of the H3K4 Methyltransferase Activity of Prdm9.
Authors: Wu, H. / Mathioudakis, N. / Diagouraga, B. / Dong, A. / Dombrovski, L. / Baudat, F. / Cusack, S. / De Massy, B. / Kadlec, J.
History
DepositionAug 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Oct 9, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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 PRDM9
B: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
C: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6597
Polymers41,0523
Non-polymers6074
Water1,09961
1
A: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
C: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6024
Polymers21,1532
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-5.5 kcal/mol
Surface area9800 Å2
MethodPISA
2
B: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0573
Polymers19,8991
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.730, 78.180, 107.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPILEILEAA199 - 2806 - 87
21ASPASPILEILEBB199 - 2806 - 87
12TYRTYRTRPTRPAA291 - 29398 - 100
22TYRTYRTRPTRPBB291 - 29398 - 100
13ASPASPARGARGAA306 - 323113 - 130
23ASPASPARGARGBB306 - 323113 - 130
14ASPASPVALVALAA325 - 355132 - 162
24ASPASPVALVALBB325 - 355132 - 162

NCS oper: (Code: given
Matrix: (0.998392, 0.034147, -0.045252), (-0.045571, 0.00864, -0.998924), (-0.033719, 0.99938, 0.010182)
Vector: -12.65421, -18.5019, 20.3454)

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Components

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

#1: Protein HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9 / PRDM9 / HYBRID STERILITY PROTEIN 1 / MEIOSIS-INDUCED FACTOR CONTAINING A PR/SET DOMAIN AND ZINC- ...PRDM9 / HYBRID STERILITY PROTEIN 1 / MEIOSIS-INDUCED FACTOR CONTAINING A PR/SET DOMAIN AND ZINC-FINGER MO PR DOMAIN ZINC FINGER PROTEIN 9 / PR DOMAIN-CONTAINING PROTEIN 9


Mass: 19899.029 Da / Num. of mol.: 2 / Fragment: SET DOMAIN, RESIDUES 198-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: Q96EQ9, histone-lysine N-methyltransferase
#2: Protein/peptide HISTONE H3.1 / HISTONE H3 / HISTONE H3/A / HISTONE H3/B / HISTONE H3/C / HISTON HISTONE H3/F / HISTONE H3/H / ...HISTONE H3 / HISTONE H3/A / HISTONE H3/B / HISTONE H3/C / HISTON HISTONE H3/F / HISTONE H3/H / HISTONE H3/I / HISTONE H3/J / HISTONE H3/K / HISTONE H3/L


Mass: 1253.474 Da / Num. of mol.: 1 / Fragment: N-TERMINUS, RESIDUES 2-11 / Source method: obtained synthetically / Details: DOUBLE METHYLATION ON LYSINE 4 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431

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Non-polymers , 4 types, 65 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5 AND 25% W/V PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.939
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 21499 / % possible obs: 99.5 % / Observed criterion σ(I): 2.3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RAY

3ray


Resolution: 2.3→49.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.231 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25223 1098 5.1 %RANDOM
Rwork0.20806 ---
obs0.21031 20355 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.71 Å20 Å20 Å2
2---2.32 Å20 Å2
3----3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 34 61 2840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192856
X-RAY DIFFRACTIONr_bond_other_d0.0020.022514
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9553881
X-RAY DIFFRACTIONr_angle_other_deg0.77735799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52924.258155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54815429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9191519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213305
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02696
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2065 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Rms dev position: 4.89 Å / Weight position: 0.5

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 82 -
Rwork0.297 1464 -
obs--99.17 %

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