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- PDB-5v3g: PRDM9-allele-C ZnF8-13 -

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Basic information

Entry
Database: PDB / ID: 5v3g
TitlePRDM9-allele-C ZnF8-13
Components
  • DNA (5'-D(*AP*GP*GP*GP*CP*AP*AP*CP*GP*CP*TP*CP*AP*CP*TP*GP*GP*GP*GP*TP*C)-3')
  • DNA (5'-D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*TP*GP*CP*CP*C)-3')
  • PR domain zinc finger protein 9
Keywordstransferase/dna / C2H2 type Zinc fingers / DNA binding / transferase-dna complex
Function / homology
Function and homology information


histone-lysine N-methyltransferase / methyltransferase activity / methylation
Similarity search - Function
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) / PR domain zinc finger protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.416 Å
AuthorsPatel, A. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 049245 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence.
Authors: Patel, A. / Zhang, X. / Blumenthal, R.M. / Cheng, X.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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
E: DNA (5'-D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*TP*GP*CP*CP*C)-3')
F: DNA (5'-D(*AP*GP*GP*GP*CP*AP*AP*CP*GP*CP*TP*CP*AP*CP*TP*GP*GP*GP*GP*TP*C)-3')
D: PR domain zinc finger protein 9
B: DNA (5'-D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*TP*GP*CP*CP*C)-3')
C: DNA (5'-D(*AP*GP*GP*GP*CP*AP*AP*CP*GP*CP*TP*CP*AP*CP*TP*GP*GP*GP*GP*TP*C)-3')
A: PR domain zinc finger protein 9
G: PR domain zinc finger protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,72120
Polymers86,8717
Non-polymers85013
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, fluorescence polarization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15520 Å2
ΔGint-106 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.151, 123.778, 70.200
Angle α, β, γ (deg.)90.00, 116.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6400.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*AP*GP*GP*GP*CP*AP*AP*CP*GP*CP*TP*CP*AP*CP*TP*GP*GP*GP*GP*TP*C)-3')


Mass: 6489.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein PR domain zinc finger protein 9


Mass: 20364.125 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: meiotic cells / Gene: PRMD9 / Variant: allale-C / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D9IWL3, histone-lysine N-methyltransferase
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.84 Å3/Da / Density % sol: 56.7 % / Description: Thick plate
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M Bis-Tris Propane (pH-7.3) and 23% W/V PEG3350

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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: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.416→35.2 Å / Num. obs: 35662 / % possible obs: 96.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Χ2: 0.997 / Net I/σ(I): 22.68
Reflection shellResolution: 2.42→2.52 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2949 / CC1/2: 0.541 / Rpim(I) all: 0.442 / Χ2: 1.004 / % possible all: 72.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.416→35.183 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 1775 5 %
Rwork0.1731 --
obs0.1758 35530 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.416→35.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 1710 13 116 4712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0224863
X-RAY DIFFRACTIONf_angle_d2.2676905
X-RAY DIFFRACTIONf_dihedral_angle_d20.0062571
X-RAY DIFFRACTIONf_chiral_restr0.1724
X-RAY DIFFRACTIONf_plane_restr0.014609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4163-2.48160.42900.3131687X-RAY DIFFRACTION63
2.4816-2.55460.37621310.29052356X-RAY DIFFRACTION88
2.5546-2.6370.32091410.27012675X-RAY DIFFRACTION98
2.637-2.73120.3081390.25022688X-RAY DIFFRACTION100
2.7312-2.84050.30421370.22822711X-RAY DIFFRACTION100
2.8405-2.96970.28771420.23862687X-RAY DIFFRACTION100
2.9697-3.12620.34871410.24022688X-RAY DIFFRACTION100
3.1262-3.32190.28721400.1972699X-RAY DIFFRACTION99
3.3219-3.57820.22561410.16662641X-RAY DIFFRACTION98
3.5782-3.93790.20171430.16052739X-RAY DIFFRACTION100
3.9379-4.50670.17441430.13532696X-RAY DIFFRACTION100
4.5067-5.67410.20271450.14472740X-RAY DIFFRACTION100
5.6741-35.18650.16731420.14322748X-RAY DIFFRACTION100
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)
16.3804-5.78455.56146.2068-4.01147.8253-0.72070.0256-0.41910.43470.49140.2145-0.0365-0.43020.18890.839-0.18230.23670.6132-0.09480.5418-49.5782-18.1365110.2412
23.2068-4.3655-2.85467.50811.07127.23070.5681-0.4340.55440.0302-0.1921-0.12930.26150.7779-0.39950.5494-0.03910.16940.6955-0.06950.5764-40.1707-23.41495.904
34.52530.5883-4.2623.90410.57294.14670.40330.29140.1894-0.88820.3294-0.3045-0.2053-0.0102-0.71260.74060.02090.13760.62140.00480.4452-31.9376-20.73171.2526
46.48414.4701-5.57676.4128-5.66777.3126-0.19920.82730.6553-1.06410.7092-0.19750.2372-0.729-0.49690.6982-0.04730.15590.69-0.05070.4652-29.8068-22.143465.5467
55.59413.0773-6.42173.4845-4.98868.30340.2055-0.14340.24880.35620.0114-0.064-0.56060.1714-0.25650.5883-0.05930.15150.4223-0.10830.4347-43.6175-20.363998.5897
69.72276.03550.81047.419-2.47282.65010.26550.33630.42860.1473-0.08090.598-0.21510.0914-0.06140.50040.07030.12680.34120.03680.3202-57.7208-26.5405100.5868
72.29860.22520.27274.5169-0.53411.8147-0.1173-0.14710.38380.60220.3139-0.0625-0.13920.0357-0.16820.5704-0.1010.12790.4187-0.08880.497-39.0986-9.242697.6695
89.1001-0.8767-2.63782.66594.77878.75570.44630.6522-0.00460.67820.4104-0.5360.71220.1154-0.99480.4395-0.0663-0.05580.5087-0.09740.5209-28.8936-21.49492.3191
93.945-2.376-1.03426.13091.12832.4896-0.15760.2806-0.07780.238-0.03190.34280.0735-0.28790.18680.3687-0.0341-0.0160.4733-0.00020.4279-36.2505-32.114380.2849
104.7984-0.3006-0.28013.4271-3.57673.9189-0.0790.0532-0.0776-0.29680.3640.0338-0.1477-0.9259-0.30860.7285-0.005-0.04830.82250.08050.6371-42.5221-20.652864.3125
115.1184-6.89872.41069.9586-1.44225.7292-0.26010.22410.38940.21460.1303-0.8899-0.56680.04570.16951.1341-0.26590.2080.7245-0.10920.6591-23.6782-9.773161.5898
125.4208-4.01392.71367.3966-2.32848.62270.0443-0.47620.05130.5805-0.15590.2182-0.3611-0.14220.02790.4962-0.2145-0.04540.63720.00270.3649-78.061112.14107.6444
135.56051.32762.58713.0098-0.71056.6854-0.3271.0626-0.0523-0.74410.44690.358-0.50190.0162-0.15760.5806-0.0327-0.10080.6035-0.07860.3665-92.070112.819476.0877
146.5825-2.0161-4.42583.2945-0.39328.0956-0.3245-0.01380.0322-0.7511.0369-0.5921-0.53911.1977-0.66910.9814-0.3459-0.14671.2428-0.04540.5114-96.745311.314161.9955
151.5658-0.65570.01892.8966-0.78935.2895-0.10590.2464-0.2680.1808-0.0047-0.1258-0.55190.14650.1250.454-0.0325-0.09020.5033-0.06240.4073-87.633711.805286.2325
163.7567-1.20750.85127.776-0.62632.11940.2591-0.5216-0.29460.5231-0.18330.62780.7537-1.727-0.17890.3979-0.2333-0.05750.71970.07240.3898-76.244116.0345110.647
177.82455.041.96094.12831.60522.37010.0818-0.0654-0.7236-0.0266-0.0436-0.5414-0.14390.1111-0.02860.37540.0265-0.01530.40310.04150.3652-71.0258.7924104.0675
181.582-0.1708-0.95743.9226-5.30327.78590.2606-0.10340.04720.719-0.10950.1918-0.42110.0474-0.04520.4209-0.0610.02430.3326-0.09730.4601-93.239614.232294.881
193.1641.98520.21855.60753.39086.5882-0.17640.6668-0.3826-0.72780.4803-0.30670.34520.1792-0.28260.60430.03550.01330.41120.00480.4454-89.406710.491270.3021
206.6994-5.90222.12258.13442.80148.2115-0.5365-0.0191-0.5043-1.44131.33060.83840.72640.0662-0.37261.1116-0.1734-0.08620.74610.10381.2321-61.3248-7.2352102.0414
219.5598-0.81452.10233.59953.52259.42110.2195-0.2130.5452-0.50690.4735-0.01670.042-0.0177-0.37131.21870.05470.12951.14370.23221.0634-64.4276-2.5435108.7092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'E' and (resid 6 through 10 )
3X-RAY DIFFRACTION3chain 'E' and (resid 11 through 21 )
4X-RAY DIFFRACTION4chain 'F' and (resid -19 through -10 )
5X-RAY DIFFRACTION5chain 'F' and (resid -9 through 1 )
6X-RAY DIFFRACTION6chain 'D' and (resid 715 through 742 )
7X-RAY DIFFRACTION7chain 'D' and (resid 743 through 786 )
8X-RAY DIFFRACTION8chain 'D' and (resid 787 through 798 )
9X-RAY DIFFRACTION9chain 'D' and (resid 799 through 826 )
10X-RAY DIFFRACTION10chain 'D' and (resid 827 through 853 )
11X-RAY DIFFRACTION11chain 'D' and (resid 854 through 881 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 10 )
13X-RAY DIFFRACTION13chain 'B' and (resid 11 through 21 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 5 )
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 15 )
16X-RAY DIFFRACTION16chain 'C' and (resid 16 through 21 )
17X-RAY DIFFRACTION17chain 'A' and (resid 715 through 770 )
18X-RAY DIFFRACTION18chain 'A' and (resid 771 through 814 )
19X-RAY DIFFRACTION19chain 'A' and (resid 815 through 882 )
20X-RAY DIFFRACTION20chain 'G' and (resid 716 through 730 )
21X-RAY DIFFRACTION21chain 'G' and (resid 731 through 741 )

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