[English] 日本語
Yorodumi
- PDB-3psi: Crystal Structure of the Spt6 core domain from Saccharomyces cere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3psi
TitleCrystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form Spt6(239-1451)
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / Transcription Elongation / Nucleus
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / nucleosome binding / transcription elongation factor complex / transcription antitermination ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / nucleosome binding / transcription elongation factor complex / transcription antitermination / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / euchromatin / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus
Similarity search - Function
Spt6, Death-like domain / Spt6, helix-hairpin-helix domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / YqgF/RNase H-like domain / : / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. ...Spt6, Death-like domain / Spt6, helix-hairpin-helix domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / YqgF/RNase H-like domain / : / 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 / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / Nucleic acid-binding proteins / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsClose, D. / Hill, C.P. / Johnson, S.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.
Authors: Close, D. / Johnson, S.J. / Sdano, M.A. / McDonald, S.M. / Robinson, H. / Formosa, T. / Hill, C.P.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)141,7191
Polymers141,7191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.747, 118.747, 214.408
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

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


Mass: 141719.000 Da / Num. of mol.: 1 / Fragment: Core Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: CRE2, G6169, SPT6, SSN20, YGR116W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23615

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Na-MES 13% PEG 4000 0.2 M MgCl2 12% Glycerol , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2005
RadiationMonochromator: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 27025 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.058 / Χ2: 1.599 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.426.60.56926711.003199.9
3.42-3.556.70.40826721.0881100
3.55-3.726.80.26826721.1541100
3.72-3.916.80.17626521.272199.8
3.91-4.166.80.11827031.44199.9
4.16-4.486.80.0826841.749199.7
4.48-4.936.80.06526992.025199.8
4.93-5.646.70.05827151.98199.6
5.64-7.16.80.04527491.922199.5
7.1-506.70.03228082.288196.8

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→45.67 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.49 / σ(F): 1.44 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3084 2836 7.44 %
Rwork0.2654 --
obs0.2687 27003 99.4 %
all-29013 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 125.003 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 523.2 Å2 / Biso mean: 170.0162 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.3792 Å2-0 Å20 Å2
2---1.3792 Å2-0 Å2
3---2.7584 Å2
Refinement stepCycle: LAST / Resolution: 3.3→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6877 0 0 0 6877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137016
X-RAY DIFFRACTIONf_angle_d1.5779487
X-RAY DIFFRACTIONf_chiral_restr0.0791049
X-RAY DIFFRACTIONf_plane_restr0.0111234
X-RAY DIFFRACTIONf_dihedral_angle_d10.1882651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.293-3.41060.36821960.32972427262398
3.4106-3.54710.34771960.316124772673100
3.5471-3.70850.32882010.306124842685100
3.7085-3.90390.35741970.282724562653100
3.9039-4.14840.29992010.272224952696100
4.1484-4.46840.26592000.22724822682100
4.4684-4.91760.25841990.213425162715100
4.9176-5.62810.29932040.274225132717100
5.6281-7.08650.35722030.297925462749100
7.0865-45.67420.30022130.25362597281097
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)
13.5497-1.1348-0.6937-0.0529-0.00885.274-0.38880.1813-0.20320.3059-0.3380.4492-0.0397-0.0262-0.45420.95420.2332-0.10550.1918-0.01760.623-69.170432.818844.0608
20.9735-1.946-0.89864.3165-1.19485.31630.8346-0.15870.3135-0.6951.1113-0.2640.4533-1.24191.09161.25520.0430.23660.9226-0.32950.8001-58.339962.466359.0512
36.69094.0511-5.00969.77541.92926.9030.41791.9041-0.80250.35332.55142.65181.813-2.61951.37942.2268-0.323-0.04640.60280.04912.4575-57.958782.941847.0921
41.2854-1.36010.13851.54440.07640.4790.24351.48461.19250.2505-0.3950.58590.18370.26790.07043.9015-1.15461.38540.4382-0.74196.1532-42.145289.304453.6816
56.3281-5.7749-8.30895.29957.59772.00051.3017-2.77591.82223.1519-3.19183.4441.18425.21990.21353.6581-0.36781.68131.05860.35073.8683-37.124682.405557.8838
64.3569-4.6265-2.89414.29311.15665.37071.611-1.34930.8101-0.48750.8521-1.5981-2.3586-1.2070.19182.1477-0.28370.37850.8041-0.19731.1301-48.830762.156942.6642
71.99150.16021.9982.87130.63881.99932.43260.8927-2.3149-1.41513.05320.33512.9801-4.27210.54561.5838-0.43371.59471.41940.26853.8822-26.253243.972227.7532
85.1169-1.3575-2.02260.21940.57420.7604-0.1391-1.28642.6376-0.70650.8559-0.0931-0.477-0.44950.01431.9201-0.38560.32251.37350.05380.8342-43.091644.883324.9731
91.9911-5.30962.89332.0021-4.91442.4095-3.8690.3081-2.7453-0.54111.84291.6836-2.93043.16820.42982.0414-0.06470.75231.4203-0.2619-0.1637-35.755142.634434.7652
105.13391.04722.75356.47674.21853.64080.1756-0.3892-0.54250.761.6387-0.6750.66270.34469.1071.7595-0.75681.41761.0278-0.20990.6971-46.353262.694233.0551
114.06213.34191.99452.75212.17027.88411.47660.35290.6481.62271.09321.4018-0.1867-3.0366.67590.0833-0.26962.02430.68542.03270.2686-54.189477.18738.4331
121.99482.0114-1.45341.99640.94020.9293-0.8665-2.19733.35663.16850.7522-5.1281-3.06083.23630.44663.45141.20750.34082.07620.63191.1238-51.16891.213141.1331
134.9643-0.14170.85310.5504-0.45930.4801-0.00311.2932-0.8595-1.2053-1.82630.7499-0.13591.09620.01974.5655-0.2327-1.520.48731.18013.2384-46.562987.665246.3924
142.0187-1.2963-0.52926.60272.57011.10140.3247-0.0313-0.45480.1306-0.1515-0.3813-0.22280.64550.00081.09110.3185-0.06940.80930.10720.6291-42.441311.950731.448
153.8965-0.8812-2.47711.3946-0.11680.962-0.65390.3418-1.16970.40870.48250.35250.32240.86050.1181.24380.39510.08950.2880.26730.8227-69.15439.859744.4213
160.21930.6573-1.8844-1.2511-0.5738-2.2076-0.7360.11320.62070.09720.3646-0.11450.3530.6832-0.22171.34770.3930.04660.9394-0.32141.1713-66.859215.312628.712
170.3762-1.8822-1.23572.04513.99655.04840.96390.6188-0.7985-2.0666-0.2396-1.5548-0.57783.18852.42441.03361.0811-0.3651.74520.26031.4272-25.070718.47946.3794
181.58770.9213-2.33470.153-1.20543.2959-1.32660.3397-1.45710.91930.7256-1.27240.9294-0.5511-0.05941.26130.2506-0.50341.31930.23191.3833-25.488820.11413.5191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 312:429)A312 - 429
2X-RAY DIFFRACTION2(chain A and resid 430:530)A430 - 530
3X-RAY DIFFRACTION3(chain A and resid 531:543)A531 - 543
4X-RAY DIFFRACTION4(chain A and resid 544:547)A544 - 547
5X-RAY DIFFRACTION5(chain A and resid 548:572)A548 - 572
6X-RAY DIFFRACTION6(chain A and resid 573:608)A573 - 608
7X-RAY DIFFRACTION7(chain A and resid 609:613)A609 - 613
8X-RAY DIFFRACTION8(chain A and resid 615:644)A615 - 644
9X-RAY DIFFRACTION9(chain A and resid 645:653)A645 - 653
10X-RAY DIFFRACTION10(chain A and resid 654:667)A654 - 667
11X-RAY DIFFRACTION11(chain A and resid 668:676)A668 - 676
12X-RAY DIFFRACTION12(chain A and resid 677:681)A677 - 681
13X-RAY DIFFRACTION13(chain A and resid 682:686)A682 - 686
14X-RAY DIFFRACTION14(chain A and resid 687:901)A687 - 901
15X-RAY DIFFRACTION15(chain A and resid 902:1070)A902 - 1070
16X-RAY DIFFRACTION16(chain A and resid 1071:1131)A1071 - 1131
17X-RAY DIFFRACTION17(chain A and resid 1133:1148)A1133 - 1148
18X-RAY DIFFRACTION18(chain A and resid 1149:1210)A1149 - 1210

+
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://pdbjlvh1.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