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- PDB-5ei9: Human PRDM9 allele-A ZnF Domain with Associated Recombination Hot... -

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Basic information

Entry
Database: PDB / ID: 5ei9
TitleHuman PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence I
Components
  • DNA (5'-D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)-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 / positive regulation of fertilization / male gamete generation / meiotic gene conversion / [histone H3]-lysine9 N-trimethyltransferase / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity ...recombination hotspot binding / positive regulation of reciprocal meiotic recombination / positive regulation of fertilization / male gamete generation / meiotic gene conversion / [histone H3]-lysine9 N-trimethyltransferase / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H3K9 trimethyltransferase activity / female gamete generation / [histone H3]-lysine36 N-trimethyltransferase / [histone H3]-lysine4 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: 1.921 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 29, 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
A: DNA (5'-D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)-3')
F: Histone-lysine N-methyltransferase PRDM9
E: Histone-lysine N-methyltransferase PRDM9
C: DNA (5'-D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)-3')
B: DNA (5'-D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)-3')
D: DNA (5'-D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,26714
Polymers59,7436
Non-polymers5238
Water3,027168
1
A: DNA (5'-D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)-3')
E: Histone-lysine N-methyltransferase PRDM9
B: DNA (5'-D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1337
Polymers29,8723
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-44 kcal/mol
Surface area12590 Å2
MethodPISA
2
F: Histone-lysine N-methyltransferase PRDM9
C: DNA (5'-D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)-3')
D: DNA (5'-D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1337
Polymers29,8723
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-49 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.329, 55.740, 76.038
Angle α, β, γ (deg.)89.85, 75.50, 86.58
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 6489.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: 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 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon-plus RIL
References: UniProt: Q9NQV7, histone-lysine N-methyltransferase
#3: DNA chain DNA (5'-D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)-3')


Mass: 6400.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 168 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.058 M Bistris Propane, 0.042 M Citric acid, 25% 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: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→32.98 Å / Num. obs: 52634 / % possible obs: 99.9 % / Redundancy: 24.9 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.39
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.6 / % possible all: 99.6

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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: 1.921→32.98 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 3954 3.79 %
Rwork0.2144 --
obs0.2153 104452 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.921→32.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 1709 8 168 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093781
X-RAY DIFFRACTIONf_angle_d1.1175439
X-RAY DIFFRACTIONf_dihedral_angle_d25.9991553
X-RAY DIFFRACTIONf_chiral_restr0.047570
X-RAY DIFFRACTIONf_plane_restr0.007417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.921-1.94440.3911820.33681809X-RAY DIFFRACTION51
1.9444-1.9690.38421320.3593422X-RAY DIFFRACTION94
1.969-1.99490.32381450.32833654X-RAY DIFFRACTION97
1.9949-2.02220.40721260.31243601X-RAY DIFFRACTION98
2.0222-2.05110.31911430.29653610X-RAY DIFFRACTION98
2.0511-2.08170.3131790.29123550X-RAY DIFFRACTION99
2.0817-2.11420.27811450.27413748X-RAY DIFFRACTION99
2.1142-2.14890.26731490.27043652X-RAY DIFFRACTION100
2.1489-2.1860.3221360.25293629X-RAY DIFFRACTION100
2.186-2.22570.28481410.26393784X-RAY DIFFRACTION100
2.2257-2.26850.27541660.23513512X-RAY DIFFRACTION100
2.2685-2.31480.23541320.2263778X-RAY DIFFRACTION100
2.3148-2.36510.25521540.22943676X-RAY DIFFRACTION100
2.3651-2.42010.32971460.23433687X-RAY DIFFRACTION100
2.4201-2.48060.24941520.23053666X-RAY DIFFRACTION100
2.4806-2.54770.31121340.23583716X-RAY DIFFRACTION100
2.5477-2.62260.23981420.2373738X-RAY DIFFRACTION100
2.6226-2.70720.27661560.24463565X-RAY DIFFRACTION100
2.7072-2.80390.27181400.24143674X-RAY DIFFRACTION100
2.8039-2.91610.23511400.24163742X-RAY DIFFRACTION100
2.9161-3.04870.24981400.24773680X-RAY DIFFRACTION100
3.0487-3.20930.29761460.2533620X-RAY DIFFRACTION99
3.2093-3.41020.23251340.21813633X-RAY DIFFRACTION98
3.4102-3.67320.23121360.20813683X-RAY DIFFRACTION99
3.6732-4.04230.19541420.18993688X-RAY DIFFRACTION100
4.0423-4.62580.2371360.17983670X-RAY DIFFRACTION100
4.6258-5.82290.21931380.1753682X-RAY DIFFRACTION100
5.8229-32.98980.15321420.16583629X-RAY DIFFRACTION98

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