[English] 日本語
Yorodumi
- PDB-3tw1: Structure of Rtt106-AHN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tw1
TitleStructure of Rtt106-AHN
ComponentsHistone chaperone RTT106
KeywordsCHAPERONE / tandem pleckstrin-homology domains / chromosomal protein / nucleus / phosphoprotein / transcription / transcription regulation
Function / homology
Function and homology information


transposition / DNA replication-dependent chromatin assembly / nucleosome binding / transcription elongation by RNA polymerase II / heterochromatin formation / chromatin organization / chromosome / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II ...transposition / DNA replication-dependent chromatin assembly / nucleosome binding / transcription elongation by RNA polymerase II / heterochromatin formation / chromatin organization / chromosome / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
PH-domain like - #120 / Rtt106, pleckstrin homology domain / Histone chaperone Rtt106, N-terminal domain / Histone chaperone Rtt106, N-terminal domain superfamily / Histone chaperone Rtt106 N-terminal domain / Pleckstrin homology domain / : / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like ...PH-domain like - #120 / Rtt106, pleckstrin homology domain / Histone chaperone Rtt106, N-terminal domain / Histone chaperone Rtt106, N-terminal domain superfamily / Histone chaperone Rtt106 N-terminal domain / Pleckstrin homology domain / : / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
N-[2-(1H-IMIDAZOL-4-YL)ETHYL]ACETAMIDE / Histone chaperone RTT106
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.772 Å
AuthorsSu, D. / Thompson, J.R. / Mer, G.
CitationJournal: Nature / Year: 2012
Title: Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106.
Authors: Su, D. / Hu, Q. / Li, Q. / Thompson, J.R. / Cui, G. / Fazly, A. / Davies, B.A. / Botuyan, M.V. / Zhang, Z. / Mer, G.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Jul 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 1.4Sep 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 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone chaperone RTT106
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8555
Polymers27,3651
Non-polymers4914
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.517, 91.845, 34.824
Angle α, β, γ (deg.)90.00, 105.12, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Histone chaperone RTT106 / Regulator of Ty1 transposition protein 106


Mass: 27364.682 Da / Num. of mol.: 1 / Fragment: UNP residues 68-301 / Mutation: F251L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: N1346, RTT106, YNL206C / Plasmid: PTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40161
#2: Chemical ChemComp-AHN / N-[2-(1H-IMIDAZOL-4-YL)ETHYL]ACETAMIDE / N-ACETYLHISTAMINE


Mass: 153.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11N3O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMUTATION N171K IS A NATURAL VARIANT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4% v/v tacsimate, 12% PEG3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 24330 / Num. obs: 22670 / % possible obs: 93 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.6
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.2 / % possible all: 83.7

-
Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
PHASERphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FSS

3fss


Resolution: 1.772→32.173 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU ML: 0.51 / σ(F): 1.35 / Phase error: 19.59 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2102 1173 5.17 %
Rwork0.1748 --
obs0.1767 22668 93.18 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.002 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0928 Å20 Å20.4345 Å2
2--2.6839 Å20 Å2
3----2.5911 Å2
Refinement stepCycle: LAST / Resolution: 1.772→32.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 34 189 2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161977
X-RAY DIFFRACTIONf_angle_d1.5492684
X-RAY DIFFRACTIONf_dihedral_angle_d12.938766
X-RAY DIFFRACTIONf_chiral_restr0.107307
X-RAY DIFFRACTIONf_plane_restr0.007340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.772-1.85260.36541260.34062595X-RAY DIFFRACTION90
1.8526-1.95030.36481450.25552678X-RAY DIFFRACTION93
1.9503-2.07240.2171380.18282725X-RAY DIFFRACTION94
2.0724-2.23240.21041640.15922718X-RAY DIFFRACTION95
2.2324-2.4570.22171470.14772757X-RAY DIFFRACTION95
2.457-2.81230.17971360.15572769X-RAY DIFFRACTION96
2.8123-3.54250.1941550.15032662X-RAY DIFFRACTION93
3.5425-32.17780.20681620.18832591X-RAY DIFFRACTION89
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)
15.0583-3.6029-1.27034.55371.90066.3794-0.097-0.0292-0.41770.3536-0.05050.21990.47330.08520.10480.2175-0.04380.01160.26240.04770.390911.36474.948713.9739
22.0315-1.10450.38171.9585-0.28392.5424-0.0698-0.0913-0.3139-0.0680.12780.29120.0403-0.2101-0.00750.1875-0.01690.01650.20780.0270.254616.931180.814811.2667
31.8409-1.83710.81118.1726-0.73061.2225-0.09440.11840.08430.0630.0656-0.2088-0.11510.04320.08370.2462-0.03640.00910.24230.0080.242417.612295.88124.9328
42.8151.0782-0.52237.0402-1.07062.2193-0.0480.11050.1695-0.34570.07960.34590.0296-0.1931-0.00060.2381-0.0038-0.03230.23730.01330.212612.9094104.1114-1.1372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 70:108)
2X-RAY DIFFRACTION2chain 'A' and (resseq 109:196)
3X-RAY DIFFRACTION3chain 'A' and (resseq 197:235)
4X-RAY DIFFRACTION4chain 'A' and (resseq 236:301)

+
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