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- PDB-3fbn: Structure of the Mediator submodule Med7N/31 -

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Basic information

Entry
Database: PDB / ID: 3fbn
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.007 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: Derived calculations / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)48,6334
Polymers48,6334
Non-polymers00
Water905
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)24,3162
Polymers24,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-19 kcal/mol
Surface area9970 Å2
MethodPISA, PQS
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)24,3162
Polymers24,3162
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-18 kcal/mol
Surface area9600 Å2
MethodPISA, PQS
3
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

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)97,2658
Polymers97,2658
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area18620 Å2
ΔGint-120 kcal/mol
Surface area29840 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

NCS oper:
IDCodeMatrixVector
1given(-0.929641, 0.089532, -0.357423), (0.067952, -0.911734, -0.405122), (-0.362146, -0.400906, 0.841501)64.775497, -7.80592, 10.5059
2given(-0.928988, 0.07547, -0.362334), (0.08278, -0.911819, -0.40216), (-0.360734, -0.403596, 0.840822)65.015999, -8.52041, 10.6024

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Components

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


Mass: 9286.294 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 2-83 / Mutation: L13Y, Y14S, P16T, P17S, P19S
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: 15030.014 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.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 3.55 Å3/Da / Density % sol: 65.4 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9177 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13576 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 82.46 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.7
Reflection shellResolution: 3→3.18 Å / Redundancy: 11 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 5.15 / Num. unique all: 2138 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FBI

3fbi


Resolution: 3.007→43.655 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU ML: 0.43 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 687 5.06 %RANDOM
Rwork0.178 ---
obs0.181 13575 98.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.428 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 228.74 Å2 / Biso mean: 105.711 Å2 / Biso min: 50.42 Å2
Baniso -1Baniso -2Baniso -3
1--17.355 Å2-0 Å20 Å2
2---17.355 Å20 Å2
3---34.711 Å2
Refinement stepCycle: LAST / Resolution: 3.007→43.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 0 5 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082465
X-RAY DIFFRACTIONf_angle_d1.0763351
X-RAY DIFFRACTIONf_chiral_restr0.071358
X-RAY DIFFRACTIONf_plane_restr0.005428
X-RAY DIFFRACTIONf_dihedral_angle_d17.61906
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A286X-RAY DIFFRACTIONPOSITIONAL
12C286X-RAY DIFFRACTIONPOSITIONAL0.696
21B653X-RAY DIFFRACTIONPOSITIONAL
22D653X-RAY DIFFRACTIONPOSITIONAL0.593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.007-3.240.3411440.2532322246690
3.24-3.5650.2621470.20126002747100
3.565-4.0810.2271280.15726202748100
4.081-5.140.1661320.13226442776100
5.14-43.660.241360.19627022838100
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)
10.83770.63750.69930.82740.61950.62660.2258-0.2166-0.07110.027-0.3077-0.17120.03120.09270.02240.7207-0.06780.03610.73810.0420.639130.2387-7.824216.5017
21.51720.89330.37311.84870.70270.34220.2282-0.12610.04210.4641-0.272-0.02940.1295-0.05370.04670.5942-0.0737-0.00990.68440.01420.453831.1217-5.663712.5829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain C
2X-RAY DIFFRACTION2chain B or chain D

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