[English] 日本語
Yorodumi
- PDB-4khb: Structure of the Spt16D Pob3N heterodimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4khb
TitleStructure of the Spt16D Pob3N heterodimer
Components
  • Uncharacterized protein POB3N
  • Uncharacterized protein SPT16D
KeywordsTRANSCRIPTION/REPLICATION / PH like domains / TRANSCRIPTION-REPLICATION complex
Function / homology
Function and homology information


chromatin organization => GO:0006325 / FACT complex / replication fork protection complex / nucleosome binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA-templated DNA replication / histone binding / DNA replication / DNA repair / DNA binding / metal ion binding
Similarity search - Function
FACT complex subunit Spt16p/Cdc68p / Structure-specific recognition protein (SSRP1) / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) ...FACT complex subunit Spt16p/Cdc68p / Structure-specific recognition protein (SSRP1) / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FACT complex subunit / FACT complex subunit POB3
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsStuwe, T. / Zhang, E. / Ladurner, A.G.
CitationJournal: Nature / Year: 2013
Title: Structural basis of histone H2A-H2B recognition by the essential chaperone FACT.
Authors: Hondele, M. / Stuwe, T. / Hassler, M. / Halbach, F. / Bowman, A. / Zhang, E.T. / Nijmeijer, B. / Kotthoff, C. / Rybin, V. / Amlacher, S. / Hurt, E. / Ladurner, A.G.
History
DepositionApr 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein SPT16D
D: Uncharacterized protein POB3N
F: Uncharacterized protein POB3N
H: Uncharacterized protein POB3N
G: Uncharacterized protein SPT16D
E: Uncharacterized protein SPT16D
C: Uncharacterized protein SPT16D
B: Uncharacterized protein POB3N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,08017
Polymers146,2168
Non-polymers8659
Water4,774265
1
A: Uncharacterized protein SPT16D
B: Uncharacterized protein POB3N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8425
Polymers36,5542
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-32 kcal/mol
Surface area14940 Å2
MethodPISA
2
D: Uncharacterized protein POB3N
C: Uncharacterized protein SPT16D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8425
Polymers36,5542
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-34 kcal/mol
Surface area13890 Å2
MethodPISA
3
F: Uncharacterized protein POB3N
E: Uncharacterized protein SPT16D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7464
Polymers36,5542
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-67 kcal/mol
Surface area14220 Å2
MethodPISA
4
H: Uncharacterized protein POB3N
G: Uncharacterized protein SPT16D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6503
Polymers36,5542
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-62 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.391, 128.082, 132.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsheterodimer

-
Components

#1: Protein
Uncharacterized protein SPT16D


Mass: 14720.704 Da / Num. of mol.: 4 / Fragment: UNP residues 522-647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0052370, Spt16 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SDN1
#2: Protein
Uncharacterized protein POB3N


Mass: 21833.240 Da / Num. of mol.: 4 / Fragment: UNP residues 1-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0070340, Pob3 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHK5
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 2.2M NH4SO4, 0.2M Na-K-tatrate, 0.2M Na3citrate pH 5.6, VAPOR DIFFUSION, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→47.8 Å / Num. obs: 57453 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Biso Wilson estimate: 43.14 Å2
Reflection shellResolution: 2.4→2.5 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.778 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8163 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 2873 5 %
Rwork0.202 --
obs0.2043 57449 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.15 Å2 / Biso mean: 24.4568 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8981 0 45 265 9291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049296
X-RAY DIFFRACTIONf_angle_d0.91212525
X-RAY DIFFRACTIONf_chiral_restr0.0611293
X-RAY DIFFRACTIONf_plane_restr0.0031638
X-RAY DIFFRACTIONf_dihedral_angle_d17.723444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.43940.30971160.271526232739
2.4394-2.48140.34971450.273325282673
2.4814-2.52650.35541320.268725612693
2.5265-2.57510.30121420.266525682710
2.5751-2.62770.3461420.265825442686
2.6277-2.68480.2981510.24825362687
2.6848-2.74730.30681430.255926042747
2.7473-2.8160.331320.248825522684
2.816-2.89210.28721370.233725512688
2.8921-2.97720.29031360.239326102746
2.9772-3.07330.24061450.219825662711
3.0733-3.18310.26941210.212425912712
3.1831-3.31050.26661280.212525942722
3.3105-3.46110.23111350.207725862721
3.4611-3.64350.22921490.199925932742
3.6435-3.87170.18951170.17626262743
3.8717-4.17050.19651360.168326102746
4.1705-4.58990.20481440.153826272771
4.5899-5.25340.19741340.159926502784
5.2534-6.61590.25031320.20926772809
6.6159-47.7870.23131560.196227792935

+
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