[English] 日本語
Yorodumi
- PDB-3gxw: Structure of the SH2 domain of the Candida glabrata transcription... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gxw
TitleStructure of the SH2 domain of the Candida glabrata transcription elongation factor Spt6, crystal form A
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / SH2-fold / three stranded anti-parallel beta sheet / N-terminal alpha helix / C-terminal alpha helix / Nucleus / SH2 domain / Transcription regulation
Function / homology
Function and homology information


transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / cellular response to stress / nucleosome binding / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / euchromatin ...transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / cellular response to stress / nucleosome binding / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / euchromatin / G1/S transition of mitotic cell cycle / nucleosome assembly / histone binding / negative regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 ...: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / : / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / SH2 domain / SHC Adaptor Protein / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Transcription elongation factor SPT6
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsDengl, S. / Mayer, A. / Sun, M. / Cramer, P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and in vivo requirement of the yeast Spt6 SH2 domain
Authors: Dengl, S. / Mayer, A. / Sun, M. / Cramer, P.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription elongation factor SPT6
B: Transcription elongation factor SPT6
C: Transcription elongation factor SPT6
D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,03410
Polymers49,7064
Non-polymers3286
Water7,891438
1
A: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5683
Polymers12,4271
Non-polymers1412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4502
Polymers12,4271
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5683
Polymers12,4271
Non-polymers1412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription elongation factor SPT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4502
Polymers12,4271
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.499, 54.499, 253.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
Transcription elongation factor SPT6 / Chromatin elongation factor SPT6


Mass: 12426.574 Da / Num. of mol.: 4 / Fragment: SH2 domain / Mutation: L1309M, L1317M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0L04774g, SPT6 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 (DE3) CodonPlus RIL / References: UniProt: Q6FLB1
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES pH 7.0, 1 M succinic acid, 1% (v/v) PEG 2000 MME, 5 mM Tris(2-Carboxyethyl) phosphine hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97973, 0.97987, 0.90810
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979731
20.979871
30.90811
ReflectionResolution: 1.9→20 Å / Num. all: 33162 / Num. obs: 33162 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.052 / Net I/σ(I): 42.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 3223 / Rsym value: 0.129 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 1648 random
Rwork0.196 --
all-33162 -
obs-33162 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 20 438 3730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005

+
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