[English] 日本語
Yorodumi
- PDB-3fbi: Structure of the Mediator submodule Med7N/31 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fbi
TitleStructure of the Mediator submodule Med7N/31
Components
  • Mediator of RNA polymerase II transcription subunit 31
  • Mediator of RNA polymerase II transcription subunit 7
KeywordsTRANSCRIPTION / proline-rich stretches / right-handed four-helix bundle / protein-protein complex / nucleus / transcription regulation / Activator
Function / homology
Function and homology information


meiotic gene conversion / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / DNA recombination / transcription by RNA polymerase II / DNA repair ...meiotic gene conversion / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / DNA recombination / transcription by RNA polymerase II / DNA repair / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Helix Hairpins - #1520 / Mediator of RNA polymerase II, submodule Med31 (Soh1) / Mediator complex, subunit Med31 / Mediator of RNA polymerase II, subunit Med31 superfamily / Mediator complex, subunit Med7 superfmaily / SOH1 / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Helix Hairpins ...Helix Hairpins - #1520 / Mediator of RNA polymerase II, submodule Med31 (Soh1) / Mediator complex, subunit Med31 / Mediator of RNA polymerase II, subunit Med31 superfamily / Mediator complex, subunit Med7 superfmaily / SOH1 / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Helix Hairpins / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKoschubs, T. / Seizl, M. / Lariviere, L. / Kurth, F. / Baumli, S. / Martin, D.E. / Cramer, P.
CitationJournal: Embo J. / Year: 2009
Title: Identification, structure, and functional requirement of the Mediator submodule Med7N/31
Authors: Koschubs, T. / Seizl, M. / Lariviere, L. / Kurth, F. / Baumli, S. / Martin, D.E. / Cramer, P.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 7
B: Mediator of RNA polymerase II transcription subunit 31
C: Mediator of RNA polymerase II transcription subunit 7
D: Mediator of RNA polymerase II transcription subunit 31


Theoretical massNumber of molelcules
Total (without water)49,2804
Polymers49,2804
Non-polymers00
Water543
1
A: Mediator of RNA polymerase II transcription subunit 7
B: Mediator of RNA polymerase II transcription subunit 31


Theoretical massNumber of molelcules
Total (without water)24,6402
Polymers24,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-24 kcal/mol
Surface area10040 Å2
MethodPISA
2
C: Mediator of RNA polymerase II transcription subunit 7
D: Mediator of RNA polymerase II transcription subunit 31


Theoretical massNumber of molelcules
Total (without water)24,6402
Polymers24,6402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-19 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.620, 174.620, 117.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A and (resseq 20:41 or resseq 60:72)
21CHAIN C and (resseq 20:41 or resseq 60:72)
12CHAIN B and (resseq 20:96)
22CHAIN D and (resseq 20:96)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRALAALAAA20 - 4120 - 41
121THRTHRPROPROAA60 - 7260 - 72
211TYRTYRALAALACC20 - 4120 - 41
221THRTHRPROPROCC60 - 7260 - 72
112ASNASNILEILEBB20 - 9620 - 96
212ASNASNILEILEDD20 - 9620 - 96

NCS ensembles :
ID
1
2

-
Components

#1: Protein Mediator of RNA polymerase II transcription subunit 7 / Mediator complex subunit 7


Mass: 9422.249 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 2-83
Source method: isolated from a genetically manipulated source
Details: cloned residues 1-83
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MED7 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q08278
#2: Protein Mediator of RNA polymerase II transcription subunit 31 / Mediator complex subunit 31 / Hpr1 suppressor protein 1


Mass: 15217.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MED31, SOH1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P38633
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50mM MES pH 5.6, 1.8M Li2SO4, 10mM MgCl2, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 17033 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 74.219 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.8
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 4.1 / Num. measured obs: 48263 / Num. unique all: 5275 / Num. unique obs: 5275 / % possible all: 98

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.9 Å / D res low: 20 Å / FOM : 0.38 / Reflection: 15335
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.2360.5020.0211.362
2Se600.2180.3610.1331.319
3Se600.4380.1350.0150.983
4Se600.1160.5740.0580.952
5Se600.5080.040.0190.419
6Se21.2120.4580.0230.0210.145
Phasing MAD shell
Resolution (Å)FOM Reflection
9.65-200.5832
6.36-9.650.531291
5.06-6.360.51632
4.32-5.060.461892
3.83-4.320.412130
3.48-3.830.362343
3.21-3.480.282513
2.99-3.210.222702
Phasing dmFOM : 0.65 / FOM acentric: 0.66 / FOM centric: 0.55 / Reflection: 15336 / Reflection acentric: 14259 / Reflection centric: 1077
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-19.9690.950.970.88649539110
5.2-8.30.890.910.7420761864212
4.1-5.20.880.890.7225872388199
3.6-4.10.770.780.6125952433162
3.1-3.60.530.540.3245994344255
2.9-3.10.310.310.1428302691139

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.11phasing
RESOLVE2.11phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.969 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / σ(F): 2.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 860 5.05 %RANDOM
Rwork0.195 ---
obs0.197 17033 99.83 %-
all-17062 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.171 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 213.53 Å2 / Biso mean: 85.619 Å2 / Biso min: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.366 Å20 Å20 Å2
2---1.366 Å20 Å2
3---2.732 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 0 3 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072510
X-RAY DIFFRACTIONf_angle_d1.0413420
X-RAY DIFFRACTIONf_chiral_restr0.064361
X-RAY DIFFRACTIONf_plane_restr0.006439
X-RAY DIFFRACTIONf_dihedral_angle_d18.274931
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A286X-RAY DIFFRACTIONPOSITIONAL0.756
12C286X-RAY DIFFRACTIONPOSITIONAL0.756
21B653X-RAY DIFFRACTIONPOSITIONAL0.634
22D653X-RAY DIFFRACTIONPOSITIONAL0.634
LS refinement shellResolution: 2.8001→2.975 Å
RfactorNum. reflection
Rfree0.3403 142
Rwork0.3074 -
obs-2655
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)
11.12841.57470.51061.1140.82310.48460.1712-0.2975-0.05720.2085-0.297-0.15060.13090.07910.12390.5079-0.0199-0.03290.47350.03320.41229.890293.095835.0318
20.84141.21710.43712.32070.60610.41230.1654-0.03650.08450.4437-0.2657-0.04970.0929-0.02610.09040.3281-0.0899-0.06110.3699-0.02130.351131.400695.246732.257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A OR BA0
2X-RAY DIFFRACTION2CHAIN B OR DB0

+
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