[English] 日本語
Yorodumi
- PDB-2bqz: Crystal structure of a ternary complex of the human histone methy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bqz
TitleCrystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8)
Components
  • HISTONE H4
  • SET8 PROTEIN
KeywordsTRANSFERASE / HISTONE H4 METHYLTRANSFERSAE / LYSINE METHYLTRANSFERASE / SET DOMAIN
Function / homology
Function and homology information


[histone H4]-lysine20 N-trimethyltransferase / histone H4K20 trimethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / transposable element silencing by heterochromatin formation / regulation of stem cell division / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome ...[histone H4]-lysine20 N-trimethyltransferase / histone H4K20 trimethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / transposable element silencing by heterochromatin formation / regulation of stem cell division / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome / peptidyl-lysine monomethylation / regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of gene expression, epigenetic / histone methyltransferase activity / negative regulation of double-strand break repair via homologous recombination / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / regulation of signal transduction by p53 class mediator / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / methylation / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
SMYD5, SET domain / Class V SAM-dependent methyltransferases / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily ...SMYD5, SET domain / Class V SAM-dependent methyltransferases / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / : / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Beta Complex / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H4 / Histone-lysine N-trimethyltransferase SMYD5 / N-lysine methyltransferase KMT5A / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsXiao, B. / Jing, C. / Kelly, G. / Walker, P.A. / Muskett, F.W. / Frenkiel, T.A. / Martin, S.R. / Sarma, K. / Reinberg, D. / Gamblin, S.J. / Wilson, J.R.
CitationJournal: Genes Dev. / Year: 2005
Title: Specificity and Mechanism of the Histone Methyltransferase Pr-Set7
Authors: Xiao, B. / Jing, C. / Kelly, G. / Walker, P.A. / Muskett, F.W. / Frenkiel, T.A. / Martin, S.R. / Sarma, K. / Reinberg, D. / Gamblin, S.J. / Wilson, J.R.
History
DepositionApr 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SET8 PROTEIN
B: HISTONE H4
E: SET8 PROTEIN
F: HISTONE H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2926
Polymers39,5234
Non-polymers7692
Water11,043613
1
A: SET8 PROTEIN
B: HISTONE H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1463
Polymers19,7612
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: SET8 PROTEIN
F: HISTONE H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1463
Polymers19,7612
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.179, 46.322, 51.998
Angle α, β, γ (deg.)64.74, 86.66, 90.61
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98322, -0.12262, 0.13505), (-0.04742, -0.54307, -0.83835), (0.17614, -0.83069, 0.52814)
Vector: 11.6667, 32.69479, 11.51827)
DetailsTHE DIMER IN THIS ENTRY IS FORMED BY THE COMPLEXOF CHAIN A WITH A PEPTIDE CHAIN B AND CHAIN E WITHPEPTIDE CHAIN F. CHAINS A AND E ARE MONOMERIC IN THEPHYSIOLOGICAL STATE.

-
Components

#1: Protein SET8 PROTEIN / HISTONE-LYSINE METHYLTRANSFERASE PR-SET7


Mass: 18386.801 Da / Num. of mol.: 2 / Fragment: SET-DOMAIN, RESIDUES 192-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q86W83, UniProt: Q9NQR1*PLUS, histone-lysine N-methyltransferase
#2: Protein/peptide HISTONE H4


Mass: 1374.595 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-25 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P62805, UniProt: Q6GMV2*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAINS A AND E CORRESPONDS MOST CLOSELY TO THE NCBI ENTRY NP_065115. THERE IS A ...THE SEQUENCE OF CHAINS A AND E CORRESPONDS MOST CLOSELY TO THE NCBI ENTRY NP_065115. THERE IS A SINGLE SEQUENCE DIFFERENCE BETWEEN NP_065115 AND UNIPROT ENTRY Q86W83, AT POSITION 316, WHICH IS GIVEN AS PRO IN THE NCBI ENTRY BUT ARG IN UNIPROT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 34.92 %
Crystal growpH: 7 / Details: pH 7.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→19.9 Å / Num. obs: 63273 / % possible obs: 89.1 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.934 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2663 5 %RANDOM
Rwork0.187 ---
obs0.188 50828 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.58 Å2-0.1 Å2
2---1.87 Å20.41 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 50 613 3437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212870
X-RAY DIFFRACTIONr_bond_other_d0.0010.022568
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9853840
X-RAY DIFFRACTIONr_angle_other_deg0.72235988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4323334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12515537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023136
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02592
X-RAY DIFFRACTIONr_nbd_refined0.3220.3639
X-RAY DIFFRACTIONr_nbd_other0.2290.32633
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1390.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5479
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.358
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3520.3114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.546
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8931.51694
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5822696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11231176
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2994.51144
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
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 202
Rwork0.255 3734
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)
11.54020.229-0.17451.7726-0.06871.5966-0.0472-0.0387-0.1173-0.01020.02940.01370.0422-0.06630.01770.3989-0.0297-0.0190.5214-0.02440.4322-2.8050.7051.979
21.58240.21920.8311.61090.79142.38880.0145-0.00780.04540.06660.0286-0.1147-0.13090.1389-0.04310.4327-0.08750.01160.5326-0.01410.411114.15526.97720.165
30.5180.37280.21670.80350.32490.81330.0287-0.0274-0.0673-0.0098-0.01560.0136-0.0115-0.0037-0.01320.1487-0.0264-0.00460.2792-0.00610.1573.98312.29410.37
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A192 - 352
2X-RAY DIFFRACTION1B17 - 26
3X-RAY DIFFRACTION2E192 - 352
4X-RAY DIFFRACTION2F17 - 26
5X-RAY DIFFRACTION3W1 - 613

+
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