[English] 日本語
Yorodumi
- PDB-5oho: Crystal structure of the KOWx-KOW4 domain of human DSIF -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5oho
TitleCrystal structure of the KOWx-KOW4 domain of human DSIF
ComponentsTranscription elongation factor SPT5
KeywordsTRANSCRIPTION / RNA polymerase II / transcription elongation
Function / homologySpt5 transcription elongation factor, N-terminal / Formation of RNA Pol II elongation complex / Transcription elongation factor Spt5 / RNA Polymerase II Pre-transcription Events / Spt5 C-terminal domain / NusG, N-terminal domain superfamily / KOW motif / Early transcription elongation factor of RNA pol II, NGN section / Spt5 transcription elongation factor, acidic N-terminal / Formation of the Early Elongation Complex ...Spt5 transcription elongation factor, N-terminal / Formation of RNA Pol II elongation complex / Transcription elongation factor Spt5 / RNA Polymerase II Pre-transcription Events / Spt5 C-terminal domain / NusG, N-terminal domain superfamily / KOW motif / Early transcription elongation factor of RNA pol II, NGN section / Spt5 transcription elongation factor, acidic N-terminal / Formation of the Early Elongation Complex / Translation protein SH3-like domain superfamily / Formation of HIV elongation complex in the absence of HIV Tat / Formation of the HIV-1 Early Elongation Complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Formation of HIV-1 elongation complex containing HIV-1 Tat / Pausing and recovery of Tat-mediated HIV elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / Tat-mediated HIV elongation arrest and recovery / Tat-mediated elongation of the HIV-1 transcript / Ribosomal protein L2, domain 2 / NusG, N-terminal / Pausing and recovery of HIV elongation / KOW / RNA Pol II CTD phosphorylation and interaction with CE / RNA Polymerase II Transcription Elongation / mRNA Capping / RNA polymerase II transcribes snRNA genes / Transcription elongation factor Spt5, NGN domain / TP53 Regulates Transcription of DNA Repair Genes / HIV elongation arrest and recovery / negative regulation of DNA-templated transcription, elongation / DSIF complex / positive regulation of DNA-templated transcription, elongation / negative regulation of mRNA polyadenylation / positive regulation of viral transcription / positive regulation of macroautophagy / 7-methylguanosine mRNA capping / transcription elongation from RNA polymerase II promoter / transcription by RNA polymerase II / mRNA binding / chromatin binding / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / DNA binding / nucleoplasm / nucleus / Transcription elongation factor SPT5
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 1.601 Å resolution
AuthorsBernecky, C. / Plitzko, J.M. / Cramer, P.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Authors: Carrie Bernecky / Jürgen M Plitzko / Patrick Cramer
Abstract: During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA ...During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 17, 2017 / Release: Sep 13, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 13, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription elongation factor SPT5
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1987
Polyers25,7942
Non-polymers4045
Water4,576254
1
A: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0813
Polyers12,8971
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1174
Polyers12,8971
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)50.286, 54.403, 73.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

-
Components

#1: Protein/peptide Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 12896.992 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): RIL / References: UniProt:O00267
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Formula: C3H8O3 / Glycerol
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl / Chloride
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 / Density percent sol: 36.51
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 1.0 M tri-sodium citrate dihydrate

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X06SA / Synchrotron site: SLS / Beamline: X06SA / Wavelength: 1.00003056744
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Collection date: Dec 1, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003056744 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 31.67 Å2 / D resolution high: 1.6 Å / D resolution low: 43.635 Å / Number obs: 50856 / Observed criterion sigma I: -3 / CC half: 0.999 / Rmerge I obs: 0.047 / Rrim I all: 0.051 / Chi squared: 1.273 / NetI over sigmaI: 15.88 / Redundancy: 6.76 / Percent possible obs: 99.7
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber unique obsCC halfRrim I allRedundancyPercent possible all
1.3361.6001.7000.94081200.4851.4526.46698.700
0.6941.7001.8202.10077700.8100.7497.00299.900
0.3301.8201.9604.79071890.9490.3576.84599.900
0.1611.9602.1509.88066400.9880.1756.561100.000
0.1012.1502.40017.18060020.9950.1097.052100.000
0.0702.4002.77024.14052980.9970.0766.731100.000
0.0432.7703.39038.77044760.9990.0466.60999.900
0.0333.3904.78051.14034460.9990.0356.81399.900
0.0274.78043.63553.72019150.9990.0296.81099.800

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
XDSdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefineMethod to determine structure: SAD / Overall SU ML: 0.22 / Cross valid method: FREE R-VALUE / Sigma F: 1.36 / Overall phase error: 24.55
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 114.99 Å2 / B iso mean: 42.3488 Å2 / B iso min: 23.11 Å2
Least-squares processR factor R free: 0.2213 / R factor R work: 0.1745 / R factor obs: 0.1767 / Highest resolution: 1.601 Å / Lowest resolution: 43.635 Å / Number reflection R free: 2507 / Number reflection obs: 50852 / Percent reflection R free: 4.93 / Percent reflection obs: 99.73
Refine hist #finalHighest resolution: 1.601 Å / Lowest resolution: 43.635 Å / B iso mean ligand: 55 / B iso mean solvent: 54.35 / Number residues total: 226
Number of atoms included #finalProtein: 1812 / Nucleic acid: 0 / Ligand: 25 / Solvent: 254 / Total: 2091
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061917
X-RAY DIFFRACTIONf_angle_d0.8622586
X-RAY DIFFRACTIONf_chiral_restr0.057287
X-RAY DIFFRACTIONf_plane_restr0.005335
X-RAY DIFFRACTIONf_dihedral_angle_d18.1491158
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 18

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.60120.39220.33711.63201582559271796.0000
1.63200.35980.32521.665314426752819100.0000
1.66530.29840.28991.701513627202856100.0000
1.70150.28830.26431.741114226982840100.0000
1.74110.32040.25761.784612826882816100.0000
1.78460.27690.24441.832914126712812100.0000
1.83290.32580.23281.886813727092846100.0000
1.88680.28630.20741.947716426492813100.0000
1.94770.22960.19072.017314427162860100.0000
2.01730.20390.18422.098112827102838100.0000
2.09810.20240.18402.193612726902817100.0000
2.19360.25250.19432.309211427092823100.0000
2.30920.25070.20392.453916226762838100.0000
2.45390.26910.20922.643314326942837100.0000
2.64330.24410.18602.909311926982817100.0000
2.90930.20300.16273.330115726862843100.0000
3.33010.16950.12864.195112227192841100.0000
4.19510.19490.153843.651814126782819100.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.69931.2923-0.71622.39030.54131.20870.08020.0951-0.2758-0.26170.1182-0.1443-0.26080.03680.00000.29110.0289-0.07160.2818-0.02880.297315.702764.725622.8543
20.9783-0.0767-0.48051.3642-0.81001.29000.04340.67800.1180-0.2106-0.0015-0.3255-0.25100.6816-0.00020.27410.0052-0.01080.4026-0.01900.316222.563566.238921.3771
30.12500.2612-0.03580.3080-0.18400.07160.1964-0.26610.66390.5720-0.13150.46110.21780.0194-0.00210.4309-0.0430-0.01980.3961-0.02450.44126.016464.498027.3113
41.67410.22510.15172.86201.15141.78150.09800.2670-0.39700.32490.1067-0.26010.54720.1426-0.00090.44460.0353-0.06780.2984-0.01150.31174.460249.757717.2323
52.11312.01120.02201.97080.68782.27730.18380.3737-0.30800.18450.1699-0.68310.49010.50370.02950.35920.1019-0.10800.3117-0.05630.389610.417252.634217.1767
64.21442.0111-0.38004.33062.34113.0584-0.06290.01880.2825-0.5283-0.1017-0.0401-0.1468-0.0014-0.00430.1765-0.01210.00290.3280-0.07780.2834-6.704860.133037.7925
71.0031-0.7903-0.36820.46620.27400.06680.35350.2975-0.6039-0.02280.2500-0.77591.17010.25890.00220.7475-0.0486-0.14470.3813-0.02850.4442-3.790446.859430.3823
83.60011.9657-0.15593.07352.56083.8996-0.18260.1194-0.25890.0218-0.04410.10460.2537-0.1433-0.00030.2753-0.0277-0.00360.23330.00890.2148-18.607544.297636.7247
90.0291-0.0077-0.05620.0502-0.00610.1466-0.1413-0.5745-0.9396-0.31550.80410.6355-0.1998-0.58580.00330.43780.0024-0.19740.35400.04340.6655-26.307157.075432.1734
101.87390.1344-0.49041.01830.84720.8414-0.3398-0.09580.2461-0.23860.06770.14470.1212-0.4423-0.00020.3206-0.0178-0.04890.2821-0.01600.3271-19.828648.684239.0040
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A534A5531chain 'A' and (resid 534 through 553 )
2A554A5742chain 'A' and (resid 554 through 574 )
3A575A5843chain 'A' and (resid 575 through 584 )
4A585A6174chain 'A' and (resid 585 through 617 )
5A618A6465chain 'A' and (resid 618 through 646 )
6B534B5746chain 'B' and (resid 534 through 574 )
7B575B5847chain 'B' and (resid 575 through 584 )
8B585B6258chain 'B' and (resid 585 through 625 )
9B626B6309chain 'B' and (resid 626 through 630 )
10B631B64610chain 'B' and (resid 631 through 646 )

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

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