[English] 日本語
Yorodumi
- PDB-5egb: Human PRDM9 allele-A ZnF Domain with Associated Recombination Hot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5egb
TitleHuman PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II
Components
  • DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*G)-3')
  • Histone-lysine N-methyltransferase PRDM9
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / zinc finger protein / 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 / MOLECULAR REPLACEMENT / Resolution: 1.977 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 26, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)-3')
D: DNA (5'-D(*TP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*G)-3')
A: Histone-lysine N-methyltransferase PRDM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1337
Polymers29,8723
Non-polymers2624
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-48 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.575, 79.221, 68.415
Angle α, β, γ (deg.)90.00, 95.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)-3')


Mass: 6489.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*TP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*G)-3')


Mass: 6400.123 Da / Num. of mol.: 1 / 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.: 1 / 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: Allele-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.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.055M Bis-Tris propane, 0.045M Citric Acid, 30% PEG3350
PH range: 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→29.64 Å / Num. obs: 22386 / % possible obs: 86.1 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.3
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 1.9 / % possible all: 37.6

-
Processing

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

Resolution: 1.977→29.639 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1115 5.01 %Random
Rwork0.1925 ---
obs0.1939 22258 86.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.977→29.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 855 4 167 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091917
X-RAY DIFFRACTIONf_angle_d1.0922756
X-RAY DIFFRACTIONf_dihedral_angle_d24.427793
X-RAY DIFFRACTIONf_chiral_restr0.048287
X-RAY DIFFRACTIONf_plane_restr0.005213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9773-2.06720.3093700.27571333X-RAY DIFFRACTION44
2.0672-2.17620.25761040.23011965X-RAY DIFFRACTION64
2.1762-2.31250.27071450.22562742X-RAY DIFFRACTION90
2.3125-2.4910.22151570.22112997X-RAY DIFFRACTION98
2.491-2.74150.30851580.25152991X-RAY DIFFRACTION99
2.7415-3.13780.31871580.25642985X-RAY DIFFRACTION98
3.1378-3.95180.19491590.16953027X-RAY DIFFRACTION99
3.9518-29.64230.15581640.14223103X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more