[English] 日本語
Yorodumi
- PDB-3q35: Structure of the Rtt109-AcCoA/Vps75 complex and implications for ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q35
TitleStructure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation
Components
  • Histone acetyltransferase
  • Vacuolar protein sorting-associated protein 75
KeywordsTRANSFERASE/CHAPERONE / Rtt109:Vps75=2:2 stoichiometry complex / Acetyl Coenzyme A (ACoA) bound / autoacetylation at Rtt109 Lys290 / nuclear / TRANSFERASE-CHAPERONE complex
Function / homology
Function and homology information


histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / histone H3K14 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / transposable element silencing / histone H3 acetyltransferase activity / replication-born double-strand break repair via sister chromatid exchange ...histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / histone H3K14 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / transposable element silencing / histone H3 acetyltransferase activity / replication-born double-strand break repair via sister chromatid exchange / acetyltransferase activator activity / histone H3K27 acetyltransferase activity / protein-lysine-acetyltransferase activity / cellular response to stress / histone acetyltransferase / protein modification process / double-strand break repair via nonhomologous end joining / nucleosome assembly / protein transport / regulation of gene expression / histone binding / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein
Similarity search - Domain/homology
ACETYL COENZYME *A / Vacuolar protein sorting-associated protein 75 / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTang, Y. / Yuan, H. / Meeth, K. / Marmorstein, R.
Citation
Journal: Structure / Year: 2011
Title: Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation.
Authors: Tang, Y. / Holbert, M.A. / Delgoshaie, N. / Wurtele, H. / Guillemette, B. / Meeth, K. / Yuan, H. / Drogaris, P. / Lee, E.H. / Durette, C. / Thibault, P. / Verreault, A. / Cole, P.A. / Marmorstein, R.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP.
Authors: Tang, Y. / Holbert, M.A. / Wurtele, H. / Meeth, K. / Rocha, W. / Gharib, M. / Jiang, E. / Thibault, P. / Verreault, A. / Verrault, A. / Cole, P.A. / Marmorstein, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of Vps75 and implications for histone chaperone function.
Authors: Tang, Y. / Meeth, K. / Jiang, E. / Luo, C. / Marmorstein, R.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone acetyltransferase
B: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5134
Polymers77,6422
Non-polymers8722
Water19811
1
A: Histone acetyltransferase
B: Vacuolar protein sorting-associated protein 75
hetero molecules

A: Histone acetyltransferase
B: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,0268
Polymers155,2834
Non-polymers1,7434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12770 Å2
ΔGint-55 kcal/mol
Surface area56300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.0850, 119.0010, 80.2920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Histone acetyltransferase / Regulator of Ty1 transposition protein 109


Mass: 50348.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BamHI/XhoI insert
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KIM2, L1377, REM50, RTT109, YLL002W / Plasmid: 6His-TEV-pCDF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q07794, histone acetyltransferase
#2: Protein Vacuolar protein sorting-associated protein 75


Mass: 27292.619 Da / Num. of mol.: 1 / Fragment: unp residues 1-232
Source method: isolated from a genetically manipulated source
Details: BamHI/XhoI insert
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: N0890, VPS75, YNL246W / Plasmid: GST-TEV-pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: P53853
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10.0% (v/v) PEG8000; 8% (v/v) ethylene glycol; 100 mM Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.988 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 15348 / Num. obs: 15302 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.083 / Net I/σ(I): 16.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.427 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
AMoREphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3Q33

3q33


Resolution: 3.3→48.01 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 735 5.02 %
Rwork0.2071 --
obs0.2091 14631 99.37 %
all-15348 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.394 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-34.3659 Å2-0 Å2-0 Å2
2---16.2766 Å20 Å2
3----18.0893 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 55 11 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115147
X-RAY DIFFRACTIONf_angle_d1.3096956
X-RAY DIFFRACTIONf_dihedral_angle_d23.6343147
X-RAY DIFFRACTIONf_chiral_restr0.082754
X-RAY DIFFRACTIONf_plane_restr0.006878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.55490.30681590.26482627X-RAY DIFFRACTION97
3.5549-3.91250.27821510.23412746X-RAY DIFFRACTION100
3.9125-4.47830.26621480.20452780X-RAY DIFFRACTION100
4.4783-5.64080.20221360.18242796X-RAY DIFFRACTION100
5.6408-48.01540.23291410.19692947X-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)
12.89940.6941-2.26312.9023-2.88125.70880.0820.27570.33390.32260.01940.22-0.507-0.571500.55430.11120.02890.7729-0.05920.7171-20.349519.2253-0.2737
2-0.1667-0.2583-0.080.66530.09920.1246-0.45670.42850.49850.60940.4744-0.5945-2.2884-0.0147-01.88370.1193-0.12151.1268-0.03641.2291-19.681129.766433.4424
32.8244-0.0248-1.55722.9139-2.87955.7841-0.16890.2549-0.1312-0.5014-0.1639-0.03850.3752-0.3466-00.63240.0101-0.04960.7289-0.06060.7544-12.183214.5456-11.8322
42.10190.03410.25470.82961.57052.0249-0.0063-0.13710.00210.221-0.1336-1.3763-0.49550.6995-01.0241-0.1145-0.09560.92730.15551.22664.469420.2964-3.0528
52.69511.0564-2.76722.4702-1.06313.83540.150.12480.11290.4233-0.11030.51290.0626-0.4783-00.59840.03290.03580.8642-0.08070.8408-24.123611.26774.4478
61.8128-1.08680.71710.506-0.12531.5707-0.1954-0.3415-0.28820.47440.15530.02950.1222-0.04501.17270.03010.15090.84010.07570.8713-13.3569-1.652739.7258
73.18340.84991.5623.07912.02675.9945-0.01310.1238-0.1807-0.1581-0.10840.34370.3463-0.2293-00.928-0.02350.25880.7305-0.00380.8884-24.3354-4.973627.6755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:127)
2X-RAY DIFFRACTION2(chain A and resid 128:176)
3X-RAY DIFFRACTION3(chain A and resid 177:269)
4X-RAY DIFFRACTION4(chain A and resid 270:321)
5X-RAY DIFFRACTION5(chain A and resid 322:404)
6X-RAY DIFFRACTION6(chain B and resid 9:114)
7X-RAY DIFFRACTION7(chain B and resid 115:226)

+
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