[English] 日本語
Yorodumi
- PDB-6gme: Structure of H. sapiens SPT6 tandem SH2 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gme
TitleStructure of H. sapiens SPT6 tandem SH2 domain
ComponentsSPT6 tandem SH2 domain,Transcription elongation factor SPT6
KeywordsTRANSCRIPTION / SH2 domain / Pol II interaction / Kinase target / Transcription factor
Function / homology
Function and homology information


regulation of isotype switching / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / regulation of mRNA processing / nucleosome organization / blastocyst formation / transcription elongation-coupled chromatin remodeling / mRNA transport / nucleosome binding / RNA Polymerase II Transcription Elongation ...regulation of isotype switching / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / regulation of mRNA processing / nucleosome organization / blastocyst formation / transcription elongation-coupled chromatin remodeling / mRNA transport / nucleosome binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / RNA splicing / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / mRNA processing / histone binding / DNA binding / RNA binding / nucleoplasm
Similarity search - Function
HHH domain 9 / HHH 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 ...HHH domain 9 / HHH 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 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsVos, S.M. / Farnung, L. / Cramer, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
Volkswagen Foundation Germany
European Molecular Biology OrganizationALTF 745-2014 Germany
European Research Council693023 Germany
CitationJournal: Nature / Year: 2018
Title: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6.
Authors: Seychelle M Vos / Lucas Farnung / Marc Boehning / Christoph Wigge / Andreas Linden / Henning Urlaub / Patrick Cramer /
Abstract: Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here ...Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation.
History
DepositionMay 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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: SPT6 tandem SH2 domain,Transcription elongation factor SPT6
B: SPT6 tandem SH2 domain,Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)45,7932
Polymers45,7932
Non-polymers00
Water3,297183
1
A: SPT6 tandem SH2 domain,Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)22,8961
Polymers22,8961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SPT6 tandem SH2 domain,Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)22,8961
Polymers22,8961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.020, 81.100, 51.370
Angle α, β, γ (deg.)90.00, 115.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein SPT6 tandem SH2 domain,Transcription elongation factor SPT6 / hSPT6 / Histone chaperone suppressor of Ty6 / Tat-cotransactivator 2 protein / Tat-CT2 protein


Mass: 22896.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT6H, SUPT6H, KIAA0162, SPT6H / Plasmid: 438-C / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7KZ85
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 200 mM MgCl2, 21-25 % (v/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.802→46.21 Å / Num. obs: 33254 / % possible obs: 94.91 % / Redundancy: 6.1 % / Biso Wilson estimate: 29.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1034 / Rpim(I) all: 0.04554 / Rrim(I) all: 0.1133 / Net I/σ(I): 11.88
Reflection shellResolution: 1.802→1.867 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2484 / CC1/2: 0.395 / % possible all: 71.59

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(1.13_2998: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PSJ

3psj


Resolution: 1.802→46.21 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.44
RfactorNum. reflection% reflection
Rfree0.2231 1663 5 %
Rwork0.1907 --
obs0.1923 33242 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.802→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 0 183 3254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063147
X-RAY DIFFRACTIONf_angle_d0.7494245
X-RAY DIFFRACTIONf_dihedral_angle_d17.5591887
X-RAY DIFFRACTIONf_chiral_restr0.052441
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8023-1.85540.32281030.32591959X-RAY DIFFRACTION71
1.8554-1.91520.30721200.29332280X-RAY DIFFRACTION82
1.9152-1.98370.27711360.25922577X-RAY DIFFRACTION94
1.9837-2.06310.2561440.22772752X-RAY DIFFRACTION100
2.0631-2.1570.28091450.22422740X-RAY DIFFRACTION100
2.157-2.27070.2281430.20962724X-RAY DIFFRACTION99
2.2707-2.4130.26521450.20852756X-RAY DIFFRACTION99
2.413-2.59930.25961440.19572733X-RAY DIFFRACTION99
2.5993-2.86080.23031440.20112732X-RAY DIFFRACTION99
2.8608-3.27470.22371440.18132726X-RAY DIFFRACTION98
3.2747-4.12540.19781460.15262779X-RAY DIFFRACTION99
4.1254-46.54250.18181490.17482821X-RAY DIFFRACTION99
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)
11.7833-0.5565-0.6380.15020.09551.7038-0.2146-0.5254-0.69850.51960.4019-0.63370.60560.134-0.00780.43170.0438-0.04520.3899-0.03770.553435.898749.576632.1225
22.5412-0.3588-0.58542.1625-2.012.1942-0.06940.1464-1.0128-0.27350.2857-0.46570.7061-0.21160.02070.3489-0.02550.01490.3326-0.12250.484229.288547.9926.756
33.0676-0.69370.23423.162-0.69190.23670.00171.1841-0.801-0.7050.252-0.26520.25450.38620.09110.3623-0.01460.07340.5051-0.14660.432923.594448.074519.3741
42.5458-0.43980.75472.77-1.45440.9088-0.03850.3407-0.1061-0.6993-0.0553-0.28680.16270.3232-0.03230.3135-0.00010.05720.2612-0.04340.205628.108761.770224.4864
50.9154-0.1841-0.44580.45230.61461.38670.054-0.53150.0726-0.01030.02290.32960.25750.4910.00040.32880.04790.01340.3716-0.0670.32222.46864.719944.062
60.9570.234-0.66360.7233-0.35230.837-0.2914-0.7583-0.24470.71050.29930.07670.60710.1812-0.00010.44390.07720.06690.36660.03830.284414.027863.454652.6627
71.20180.31450.06120.37960.85361.2656-0.1598-0.3677-0.19330.36810.04880.16610.24370.0153-0.00040.30150.03860.02460.297-0.02380.24916.609664.774544.1827
80.46570.18980.42361.30320.10861.4691-0.237-0.166-0.10230.16280.02730.21640.3038-0.18280.00050.24210.01710.02970.2189-0.02830.215511.510963.008240.8825
90.4604-0.40660.00430.8091-0.71080.6416-0.03940.15410.0207-0.25130.0060.121-0.2435-0.01270.00010.2499-0.019-0.03060.2359-0.00340.220514.131365.915527.5978
100.7675-0.56190.63031.45050.63261.9489-0.1793-0.40030.12880.01690.03770.3855-0.3414-0.791-00.33870.0763-0.00960.40890.02860.31019.03972.647236.5242
111.4925-0.4560.43930.21620.23882.1353-0.9104-1.07780.8686-0.21270.5001-0.1399-1.6995-0.2314-0.04980.67060.0625-0.02270.7174-0.1110.5836-2.994553.034334.8939
120.6194-0.23890.35540.25790.06610.4672-0.0972-0.2030.25880.41330.42590.6797-0.4155-0.35610.00010.25190.00840.02130.25770.08270.4059-2.262345.913929.0736
133.0911-0.33320.50822.32972.08722.0637-0.2940.19970.7219-0.61090.17060.0895-0.4039-0.01890.00410.2741-0.0168-0.05010.28540.04740.41913.717151.361826.9018
142.5914-0.4135-0.03083.65830.99030.9894-0.1910.79730.2914-0.82490.1577-0.0541-0.1808-0.21720.00360.3768-0.0435-0.02030.40020.05120.4019.271550.986319.3305
152.2326-0.6084-0.86782.35351.35740.9806-0.08480.1531-0.0496-0.5693-0.01610.1527-0.0009-0.5395-0.01710.2966-0.0238-0.04310.27690.02480.21225.048637.63625.1721
161.03070.29630.04290.5629-0.73721.1-0.0599-0.6196-0.00760.06030.1392-0.1652-0.285-0.872400.32030.0708-0.00850.4690.01510.318310.50635.167444.9752
172.2822-0.78590.37920.74240.14691.4038-0.3669-1.68950.75330.55240.4147-0.156-0.3122-0.65820.01440.37480.1026-0.04170.5566-0.07080.290818.997336.353953.5842
183.4171.01671.11452.04070.49273.3074-0.1128-0.38390.22230.1951-0.0005-0.2369-0.12030.0146-0.00050.21690.0164-0.00340.2464-0.01210.208419.112436.024143.2612
192.32820.5859-0.46473.50111.73972.31140.13410.1079-0.15320.02160.1963-0.48490.47811.07130.00940.32630.0447-0.01630.3658-0.03720.241321.926730.128333.6743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1338 through 1359 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1360 through 1376 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1377 through 1407 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1408 through 1427 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1428 through 1439 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1440 through 1453 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1454 through 1470 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1471 through 1490 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1491 through 1503 )
10X-RAY DIFFRACTION10chain 'A' and (resid 1504 through 1519 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1338 through 1349 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1350 through 1359 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1360 through 1376 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1377 through 1407 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1408 through 1427 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1428 through 1439 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1440 through 1453 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1454 through 1490 )
19X-RAY DIFFRACTION19chain 'B' and (resid 1491 through 1519 )

+
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