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- PDB-5eh2: Human PRDM9 allele-A ZnF Domain with Associated Recombination Hot... -

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Basic information

Entry
Database: PDB / ID: 5eh2
TitleHuman PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence III
Components
  • DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)-3')
  • DNA (5'-D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)-3')
  • Histone-lysine N-methyltransferase PRDM9
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / recombination / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


recombination hotspot binding / positive regulation of reciprocal meiotic recombination / male gamete generation / meiotic gene conversion / [histone H3]-lysine9 N-trimethyltransferase / positive regulation of fertilization / histone H4K20me methyltransferase activity / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H3K9 trimethyltransferase activity ...recombination hotspot binding / positive regulation of reciprocal meiotic recombination / male gamete generation / meiotic gene conversion / [histone H3]-lysine9 N-trimethyltransferase / positive regulation of fertilization / histone H4K20me methyltransferase activity / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H3K9 trimethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / female gamete generation / [histone H3]-lysine4 N-trimethyltransferase / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / PKMTs methylate histone lysines / Meiotic recombination / chromosome / regulation of gene expression / methylation / transcription cis-regulatory region binding / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
PRDM7/PRDM9, PR/SET domain / : / C2H2-type zinc finger / Ancestral KRAB domain / SSXRD motif / SSXRD motif / KRAB-related domain profile. / PR domain zinc finger protein 2, PR domain / KRAB box / krueppel associated box ...PRDM7/PRDM9, PR/SET domain / : / C2H2-type zinc finger / Ancestral KRAB domain / SSXRD motif / SSXRD motif / KRAB-related domain profile. / PR domain zinc finger protein 2, PR domain / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / SET domain superfamily / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase PRDM9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPatel, A. / Horton, J.R. / Wilson, G.G. / Zhang, X. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-22 United States
CitationJournal: Genes Dev. / Year: 2016
Title: Structural basis for human PRDM9 action at recombination hot spots.
Authors: Patel, A. / Horton, J.R. / Wilson, G.G. / Zhang, X. / Cheng, X.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)-3')
D: DNA (5'-D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)-3')
A: DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)-3')
B: DNA (5'-D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)-3')
E: Histone-lysine N-methyltransferase PRDM9
F: Histone-lysine N-methyltransferase PRDM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,26714
Polymers59,7436
Non-polymers5238
Water2,198122
1
C: DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)-3')
D: DNA (5'-D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)-3')
F: Histone-lysine N-methyltransferase PRDM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1337
Polymers29,8723
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-47 kcal/mol
Surface area12780 Å2
MethodPISA
2
A: DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)-3')
B: DNA (5'-D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)-3')
E: Histone-lysine N-methyltransferase PRDM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1337
Polymers29,8723
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-43 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.208, 57.756, 76.206
Angle α, β, γ (deg.)90.15, 75.30, 83.30
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)-3')


Mass: 6489.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)-3')


Mass: 6400.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Histone-lysine N-methyltransferase PRDM9 / PR domain zinc finger protein 9 / PR domain-containing protein 9


Mass: 16982.342 Da / Num. of mol.: 2 / Fragment: ZnF8-12 (UNP residues 717-858)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM9, PFM6 / Variant: Alelle-A / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon-plus RIL
References: UniProt: Q9NQV7, histone-lysine N-methyltransferase
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.058 M Bistris Propane, 0.042 M Citric acid, 20% PEG3350
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→32.75 Å / Num. obs: 41966 / % possible obs: 90.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.63
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.2 / % possible all: 76.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Zn SAD determined structure

Resolution: 2.05→32.747 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 1983 4.74 %
Rwork0.2008 --
obs0.2022 41843 89.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→32.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 1710 8 122 3632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093777
X-RAY DIFFRACTIONf_angle_d1.1615434
X-RAY DIFFRACTIONf_dihedral_angle_d24.6421555
X-RAY DIFFRACTIONf_chiral_restr0.054570
X-RAY DIFFRACTIONf_plane_restr0.007416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0461-2.09730.3719990.32132113X-RAY DIFFRACTION67
2.0973-2.1540.27581320.29572607X-RAY DIFFRACTION81
2.154-2.21730.30761400.28332691X-RAY DIFFRACTION85
2.2173-2.28890.34611370.29292810X-RAY DIFFRACTION88
2.2889-2.37070.32111400.23392929X-RAY DIFFRACTION92
2.3707-2.46550.26961550.22322993X-RAY DIFFRACTION94
2.4655-2.57770.27081560.22573030X-RAY DIFFRACTION96
2.5777-2.71360.27211560.23133070X-RAY DIFFRACTION97
2.7136-2.88350.24481500.23573105X-RAY DIFFRACTION97
2.8835-3.10590.29191560.24513050X-RAY DIFFRACTION97
3.1059-3.41820.25771430.2153057X-RAY DIFFRACTION95
3.4182-3.91210.21621420.18892998X-RAY DIFFRACTION94
3.9121-4.92620.1781510.16662972X-RAY DIFFRACTION93
4.9262-32.7510.19571260.1582435X-RAY DIFFRACTION77

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