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- PDB-4h63: Structure of the Schizosaccharomyces pombe Mediator head module -

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Basic information

Entry
Database: PDB / ID: 4h63
TitleStructure of the Schizosaccharomyces pombe Mediator head module
Components(Mediator of RNA polymerase II transcription subunit ...) x 6
KeywordsTRANSCRIPTION / MEDIATOR COMPLEX / NUCLEUS
Function / homology
Function and homology information


core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1710 / Aspartate Aminotransferase, domain 1 - #120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2600 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2610 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2620 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2630 / Helix Hairpins - #3490 / Single helix bin / Mediator complex, subunit Med6, fungi / Hypothetical Protein Pfu-838710-001 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1710 / Aspartate Aminotransferase, domain 1 - #120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2600 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2610 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2620 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2630 / Helix Hairpins - #3490 / Single helix bin / Mediator complex, subunit Med6, fungi / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Aspartate Aminotransferase, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / Helix Hairpins / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 6
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.4 Å
AuthorsLariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P.
CitationJournal: Nature / Year: 2012
Title: Structure of the Mediator head module.
Authors: Lariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Mediator of RNA polymerase II transcription subunit 6
H: Mediator of RNA polymerase II transcription subunit 8
K: Mediator of RNA polymerase II transcription subunit 11
Q: Mediator of RNA polymerase II transcription subunit 17
R: Mediator of RNA polymerase II transcription subunit 18
V: Mediator of RNA polymerase II transcription subunit 22


Theoretical massNumber of molelcules
Total (without water)150,5266
Polymers150,5266
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33130 Å2
ΔGint-253 kcal/mol
Surface area53260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.600, 145.600, 241.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Mediator of RNA polymerase II transcription subunit ... , 6 types, 6 molecules FHKQRV

#1: Protein Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6 / RNA polymerase II mediator complex protein pmc5


Mass: 21163.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h / Gene: med6, pmc5, SPAC1002.15c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9US45
#2: Protein Mediator of RNA polymerase II transcription subunit 8 / Cell separation protein sep15 / Mediator complex subunit 8


Mass: 23360.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h / Gene: med8, sep15, SPBC21.04 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O94646
#3: Protein Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


Mass: 12644.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h / Gene: med11, SPAC644.10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9P6Q0
#4: Protein Mediator of RNA polymerase II transcription subunit 17 / Mediator complex subunit 17 / Suppressor of RNA polymerase B 4 homolog


Mass: 53877.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h / Gene: med17, SPBC31F10.04c, srb4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P87306
#5: Protein Mediator of RNA polymerase II transcription subunit 18 / Cell separation protein sep11 / Mediator complex subunit 18 / RNA polymerase II mediator complex protein pmc6


Mass: 24214.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h / Gene: med18, pmc6, sep11, SPAC5D6.05 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O14198
#6: Protein Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Suppressor of RNA polymerase B 6 homolog


Mass: 15264.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h / Gene: med22, SPAC29A4.07, srb6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O14010

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.91 Å3/Da / Density % sol: 74.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, 1 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99977 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99977 Å / Relative weight: 1
ReflectionResolution: 3.4→126.093 Å / Num. all: 41454 / Num. obs: 41454 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 82.19 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 15.16
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.04124 / Mean I/σ(I) obs: 0.64 / Num. unique all: 3007 / Rsym value: 0.04124 / % possible all: 99.9

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHARPphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.4→126.093 Å / Cor.coef. Fo:Fc: 0.9154 / Cor.coef. Fo:Fc free: 0.9116 / SU R Cruickshank DPI: 1.136 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 2100 5.07 %RANDOM
Rwork0.2319 ---
all0.2332 41453 --
obs0.2332 41453 99.99 %-
Displacement parametersBiso mean: 165.62 Å2
Baniso -1Baniso -2Baniso -3
1-7.3829 Å20 Å20 Å2
2--7.3829 Å20 Å2
3----14.7659 Å2
Refine analyzeLuzzati coordinate error obs: 1.139 Å
Refinement stepCycle: LAST / Resolution: 3.4→126.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9254 0 0 0 9254
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099445HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1312785HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion3.5
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3219 152 5.06 %
Rwork0.2719 2849 -
all0.2746 3001 -
obs--99.99 %
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)
10.3415-0.62380.42343.3348-2.57233.2465-0.0911-0.0560.12570.14090.09030.10790.15230.10110.00090.09930.35730.06850.0495-0.0305-0.117451.549432.18292.005
20.3242-0.2492-0.96151.313-1.88572.34470.0013-0.11080.23520.04250.0697-0.0575-0.01640.2234-0.071-0.04090.26080.11120.0627-0.08390.043855.13751.698166.1434
30.578-0.41470.75121.23-0.91861.7849-0.0330.12810.0041-0.08960.0924-0.05590.07580.1898-0.05950.11570.1833-0.0199-0.1220.1556-0.000143.639562.939336.52
40.7627-1.04350.85041.5807-1.40821.0704-0.08280.07810.1087-0.18380.031-0.00020.08620.25520.05180.30390.0834-0.0908-0.10260.12220.099521.872287.622839.5767
5-0.90840.5245-2.63760.9084-1.928900.0150.01120.0545-0.0408-0.0041-0.0472-0.01680.0362-0.0109-0.11880.0050.0258-0.17940.0885-0.036255.6492105.964831.5041
60.6044-1.40980.62383.2169-1.0140.9043-0.19740.1581-0.1124-0.03430.1914-0.09770.15060.28290.00610.00520.18570.0289-0.07610.1839-0.01440.138469.30740.7575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ F|10 - F|158 }F10 - 158
2X-RAY DIFFRACTION2{ H|3 - H|200 }H3 - 200
3X-RAY DIFFRACTION3{ K|15 - K|112 }K15 - 112
4X-RAY DIFFRACTION4{ Q|99 - Q|537 }Q99 - 537
5X-RAY DIFFRACTION5{ R|1 - R|207 }R1 - 207
6X-RAY DIFFRACTION6{ V|5 - V|121 }V5 - 121

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