[English] 日本語
Yorodumi
- PDB-7f4e: Crystal structure of Hst2 in complex with H3K9bz peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f4e
TitleCrystal structure of Hst2 in complex with H3K9bz peptide
Components
  • Histone H3
  • NAD-dependent protein deacetylase HST2
KeywordsNUCLEAR PROTEIN / histone modification / histone benzoylation / protein-protein interaction / NAD-dependent histone deacetylase
Function / homology
Function and homology information


negative regulation of mitotic recombination / sexual sporulation resulting in formation of a cellular spore / NAD-dependent histone H4K16 deacetylase activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / replication fork protection complex / positive regulation of transcription by RNA polymerase I ...negative regulation of mitotic recombination / sexual sporulation resulting in formation of a cellular spore / NAD-dependent histone H4K16 deacetylase activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / NAD+ binding / CENP-A containing nucleosome / structural constituent of chromatin / nucleosome / chromatin organization / transferase activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
NAD-dependent protein deacetylase HST2 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWang, D. / Yan, F. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37010303 China
National Natural Science Foundation of China (NSFC)31970576 China
CitationJournal: Nat Commun / Year: 2022
Title: Global profiling of regulatory elements in the histone benzoylation pathway.
Authors: Wang, D. / Yan, F. / Wu, P. / Ge, K. / Li, M. / Li, T. / Gao, Y. / Peng, C. / Chen, Y.
History
DepositionJun 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-dependent protein deacetylase HST2
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7283
Polymers33,6632
Non-polymers651
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-3 kcal/mol
Surface area13370 Å2
Unit cell
Length a, b, c (Å)42.150, 68.402, 94.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NAD-dependent protein deacetylase HST2 / Homologous to SIR2 protein 2 / Regulatory protein SIR2 homolog 2


Mass: 32523.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HST2, YPL015C, LPA2C / Production host: Escherichia coli (E. coli)
References: UniProt: P53686, protein acetyllysine N-acetyltransferase
#2: Protein/peptide Histone H3 /


Mass: 1139.263 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P61830
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% (w/v) PEG 1500, 0.1M MMT/Sodium hydroxide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 26704 / % possible obs: 98.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Χ2: 0.959 / Net I/σ(I): 6.7 / Num. measured all: 167194
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.814.50.80212030.6360.3990.9010.98189.9
1.81-1.845.30.74712600.7190.3480.8280.9995.3
1.84-1.885.80.69213000.7810.3110.760.98698.9
1.88-1.926.20.55613550.8860.2420.6080.97799.6
1.92-1.966.50.4712920.9230.1990.5120.99299.7
1.96-26.50.39213390.9370.1670.4260.98499.7
2-2.0560.29813090.9590.1310.3261.00199.5
2.05-2.116.50.2513440.9710.1060.2721.02699.9
2.11-2.176.80.23113230.9780.0960.251.01499.9
2.17-2.246.80.17213230.9860.0710.1870.9999.9
2.24-2.326.60.14213370.990.0590.1540.96899.7
2.32-2.426.50.12313370.9920.0520.1340.94599.8
2.42-2.5360.10213430.9920.0450.1110.94899.8
2.53-2.666.80.08413380.9960.0350.0910.93399.7
2.66-2.836.70.07113570.9970.0290.0770.94199.9
2.83-3.046.60.05913490.9970.0250.0640.88799.7
3.04-3.356.10.04813600.9970.0210.0520.89199.3
3.35-3.836.80.04113730.9980.0170.0440.8999.6
3.83-4.836.20.03713790.9980.0160.040.88499.3
4.83-506.10.04214830.9970.0190.0460.98598.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1A

1q1a


Resolution: 1.78→28.61 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1215 4.82 %
Rwork0.1838 23978 -
obs0.1853 25193 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.45 Å2 / Biso mean: 32.0897 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: final / Resolution: 1.78→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 1 234 2528
Biso mean--30.83 36.49 -
Num. residues----287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.850.2799940.24161739183362
1.85-1.940.29831260.23532347247385
1.94-2.040.28391380.21012721285997
2.04-2.170.23151490.186427972946100
2.17-2.330.22141430.187528232966100
2.33-2.570.23941390.190328272966100
2.57-2.940.2471300.185428652995100
2.94-3.70.18531470.17622864301199
3.7-28.610.17621490.16492995314499
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)
11.27310.71490.42981.9760.48612.86680.05320.46350.0484-0.4287-0.03480.10320.0488-0.1167-0.06210.16380.0238-0.03070.2293-0.0330.1128-13.95231.7726-38.406
21.8705-1.5678-3.1354.11441.50135.509-0.5555-0.3888-0.96760.7253-0.09410.13721.31120.91740.28690.4320.22350.08470.6455-0.05150.77576.6664-6.2014-16.175
33.218-2.5956-1.81752.28670.48877.5817-0.3165-0.7194-0.7066-0.01330.21230.17690.70560.1861-0.04110.28060.01250.03410.24870.04380.17511.82340.2897-6.2763
41.1646-0.35692.06660.6072-0.88473.941-0.4220.26270.25620.2937-0.16490.14010.15250.9283-0.49260.23730.01310.09330.3177-0.03120.22638.49424.7315-20.4245
50.97240.24190.3721.91830.46761.73720.0281-0.02440.06940.21540.1307-0.1587-0.19370.22580.05430.1135-0.0260.01630.1302-0.0350.14730.042211.4478-19.0948
62.14650.4168-0.0992.56610.23322.17570.00620.1734-0.0119-0.0689-0.00380.21870.071-0.1466-0.02120.07490.0034-0.00970.1074-0.02490.1361-15.27182.1966-31.8908
75.0669-0.94342.75570.2497-0.25872.5350.2972-0.8923-0.30890.5138-0.1610.3617-0.481-0.8942-0.21250.7182-0.12960.05950.4180.0450.2789-12.77132.0655-11.1839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 39 )A8 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 62 )A40 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 76 )A63 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 94 )A77 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 189 )A95 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 293 )A190 - 293
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 14 )C6 - 14

+
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