[English] 日本語
Yorodumi
- PDB-5bsa: Structure of histone H3/H4 in complex with Spt2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bsa
TitleStructure of histone H3/H4 in complex with Spt2
Components
  • Histone H3.2
  • Histone H4
  • Protein SPT2 homolog
KeywordsTRANSCRIPTION REGULATOR / chaperone / transcription
Function / homology
Function and homology information


histone chaperone activity / RNA polymerase I core binding / transcription by RNA polymerase I / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / histone binding / protein heterodimerization activity / regulation of DNA-templated transcription ...histone chaperone activity / RNA polymerase I core binding / transcription by RNA polymerase I / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / histone binding / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Chromatin SPT2 / : / SPT2 chromatin protein / SPT2 N-terminal domain / SPT2 chromatin protein / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 ...Chromatin SPT2 / : / SPT2 chromatin protein / SPT2 N-terminal domain / SPT2 chromatin protein / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H4 / Histone H3.2 / Protein SPT2 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.611 Å
AuthorsChen, S. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2015
Title: Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2.
Authors: Chen, S. / Rufiange, A. / Huang, H. / Rajashankar, K.R. / Nourani, A. / Patel, D.J.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.2
B: Histone H3.2
C: Histone H4
D: Histone H4
E: Protein SPT2 homolog
F: Protein SPT2 homolog


Theoretical massNumber of molelcules
Total (without water)77,1766
Polymers77,1766
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-97 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.351, 128.351, 116.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

-
Components

#1: Protein Histone H3.2


Mass: 12673.827 Da / Num. of mol.: 2 / Fragment: residues 27-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Protein SPT2 homolog / Protein KU002155 / SPT2 domain-containing protein 1


Mass: 14651.086 Da / Num. of mol.: 2 / Fragment: residues 571-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTY2D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68D10
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.02 M NaCl, 0.2 M HEPES 7.5, 1.6 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. obs: 5704 / % possible obs: 98.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.3
Reflection shellResolution: 4.6→4.68 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1.3 / % possible all: 88.6

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
SHELXDEphasing
PHASERphasing
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOI

1aoi


Resolution: 4.611→49.115 Å / SU ML: 0.89 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3289 375 4.68 %
Rwork0.2387 --
obs0.243 8005 77.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.611→49.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 0 0 2733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132763
X-RAY DIFFRACTIONf_angle_d1.9723721
X-RAY DIFFRACTIONf_dihedral_angle_d18.053967
X-RAY DIFFRACTIONf_chiral_restr0.073443
X-RAY DIFFRACTIONf_plane_restr0.007483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6108-5.27730.3873710.28311363X-RAY DIFFRACTION42
5.2773-6.64620.38411390.31253004X-RAY DIFFRACTION92
6.6462-49.1180.27421650.18583263X-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