[English] 日本語
Yorodumi
- PDB-5ums: Crystal structure of middle double PH domain of human FACT comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ums
TitleCrystal structure of middle double PH domain of human FACT complex subunit SSRP1
ComponentsFACT complex subunit SSRP1FACT (biology)
KeywordsTRANSCRIPTION / Histone chaperone / Double PH domain / FACT
Function / homology
Function and homology information


FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat ...FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / histone binding / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
PH-domain like - #150 / : / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH 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) ...PH-domain like - #150 / : / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH 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 / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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 SSRP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.569 Å
AuthorsSu, D. / Hu, Q. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116829 United States
CitationJournal: To Be Published
Title: Crystal structure of middle double PH domain of human FACT complex subunit SSRP1
Authors: Hu, Q. / Su, D. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
History
DepositionJan 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FACT complex subunit SSRP1


Theoretical massNumber of molelcules
Total (without water)30,4601
Polymers30,4601
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.810, 82.290, 48.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-695-

HOH

-
Components

#1: Protein FACT complex subunit SSRP1 / FACT (biology) / Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin ...Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin transcription complex 80 kDa subunit / FACTp80 / Facilitates chromatin transcription complex subunit SSRP1 / Recombination signal sequence recognition protein 1 / Structure-specific recognition protein 1 / hSSRP1 / T160


Mass: 30460.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSRP1, FACT80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08945
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, pH 6.5, 28% polyethylene glycol monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.569→28.16 Å / Num. obs: 35760 / % possible obs: 93.1 % / Redundancy: 2.3 % / Net I/σ(I): 29.6

-
Processing

Software
NameVersionClassification
PHENIXdev_972refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GCL

2gcl


Resolution: 1.569→28.157 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.42
RfactorNum. reflection% reflection
Rfree0.2274 602 1.69 %
Rwork0.198 --
obs0.1985 35727 98.04 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Bsol: 40.436 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0328 Å20 Å2-0 Å2
2---8.9476 Å20 Å2
3---3.9148 Å2
Refinement stepCycle: LAST / Resolution: 1.569→28.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 0 195 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042067
X-RAY DIFFRACTIONf_angle_d0.6232800
X-RAY DIFFRACTIONf_dihedral_angle_d13.864801
X-RAY DIFFRACTIONf_chiral_restr0.061305
X-RAY DIFFRACTIONf_plane_restr0.004361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5691-1.7270.27441570.26918691X-RAY DIFFRACTION99
1.727-1.97690.26191370.21138836X-RAY DIFFRACTION100
1.9769-2.49040.24261620.1868808X-RAY DIFFRACTION99
2.4904-28.16140.21191460.19458790X-RAY DIFFRACTION95

+
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