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- PDB-6h02: Crystal structure of human Mediator subunit MED23 -

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Basic information

Entry
Database: PDB / ID: 6h02
TitleCrystal structure of human Mediator subunit MED23
Components
  • LAMA nanobody NB106
  • Mediator of RNA polymerase II transcription subunit 23
KeywordsTRANSCRIPTION / Human / Mediator / complex / subunit
Function / homology
Function and homology information


positive regulation of T cell extravasation / RSV-host interactions / core mediator complex / mediator complex / Generic Transcription Pathway / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression ...positive regulation of T cell extravasation / RSV-host interactions / core mediator complex / mediator complex / Generic Transcription Pathway / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / transcription regulator complex / transcription coactivator activity / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Mediator complex, subunit Med23 / Mediator complex subunit 23
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 23
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsClantin, B. / Monte, D. / Villeret, V.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyDS0401 France
European UnionINSTRUCT PID1235 France
Citation
Journal: Nat Commun / Year: 2018
Title: Crystal structure of human Mediator subunit MED23.
Authors: Monte, D. / Clantin, B. / Dewitte, F. / Lens, Z. / Rucktooa, P. / Pardon, E. / Steyaert, J. / Verger, A. / Villeret, V.
#1: Journal: Science / Year: 2002
Title: Transcription control by E1A and MAP kinase pathway via Sur2 mediator subunit.
Authors: Stevens, J.L. / Cantin, G.T. / Wang, G. / Shevchenko, A. / Shevchenko, A. / Berk, A.J.
#2: Journal: Mol. Cell / Year: 2005
Title: Mediator requirement for both recruitment and postrecruitment steps in transcription initiation.
Authors: Wang, G. / Balamotis, M.A. / Stevens, J.L. / Yamaguchi, Y. / Handa, H. / Berk, A.J.
#3: Journal: Mol. Cell / Year: 2012
Title: Mediator complex regulates alternative mRNA processing via the MED23 subunit.
Authors: Huang, Y. / Li, W. / Yao, X. / Lin, Q.J. / Yin, J.W. / Liang, Y. / Heiner, M. / Tian, B. / Hui, J. / Wang, G.
History
DepositionJul 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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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 23
B: LAMA nanobody NB106


Theoretical massNumber of molelcules
Total (without water)173,0482
Polymers173,0482
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS, microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-4 kcal/mol
Surface area59520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.650, 137.180, 90.110
Angle α, β, γ (deg.)90.000, 110.980, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 23 / Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 130 kDa component / ARC130 / Cofactor required for Sp1 transcriptional activation subunit 3 / CRSP complex subunit 3 / Mediator complex subunit 23 / Protein sur-2 homolog / hSur-2 / Transcriptional coactivator CRSP130 / Vitamin D3 receptor-interacting protein complex 130 kDa component / DRIP130


Mass: 158294.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human MED23 subunit with a C-terminal purification TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: MED23, ARC130, CRSP3, DRIP130, KIAA1216, SUR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ULK4
#2: Antibody LAMA nanobody NB106


Mass: 14753.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Lama nanobody generated against Human Mediator subunit MED23
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 6000 100mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 42643 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Redundancy: 20 % / Biso Wilson estimate: 76.02 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.143 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 20 % / Num. unique obs: 4250 / CC1/2: 0.887 / Rrim(I) all: 1.47 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→15 Å / SU ML: 0.3418 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.125
RfactorNum. reflection% reflection
Rfree0.2399 2010 4.79 %
Rwork0.199 --
obs0.201 41954 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 91.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11714 0 0 0 11714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001812017
X-RAY DIFFRACTIONf_angle_d0.469516328
X-RAY DIFFRACTIONf_chiral_restr0.03661834
X-RAY DIFFRACTIONf_plane_restr0.00382064
X-RAY DIFFRACTIONf_dihedral_angle_d8.70647187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.3461510.31892826X-RAY DIFFRACTION99.97
2.87-2.950.30681360.28772830X-RAY DIFFRACTION99.87
2.95-3.030.31881400.27832872X-RAY DIFFRACTION99.9
3.03-3.130.32561270.25252851X-RAY DIFFRACTION99.93
3.13-3.240.33451190.24992863X-RAY DIFFRACTION99.97
3.24-3.370.30631290.24022842X-RAY DIFFRACTION99.9
3.37-3.520.28331330.22742858X-RAY DIFFRACTION99.77
3.52-3.70.25841300.21392876X-RAY DIFFRACTION99.93
3.7-3.930.23021560.19912836X-RAY DIFFRACTION99.9
3.93-4.230.24931530.18882832X-RAY DIFFRACTION99.97
4.23-4.640.18791390.16512865X-RAY DIFFRACTION100
4.64-5.290.18661450.17542882X-RAY DIFFRACTION99.97
5.29-6.570.27321940.21532814X-RAY DIFFRACTION100
6.57-150.1911580.15452897X-RAY DIFFRACTION99.9
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)
11.229641403890.450392453090.1006161477841.27420577789-0.02704637208910.9501238943580.0703704251477-0.0196922216193-0.125374786860.026198756536-0.1014321475510.1833366125950.163429836719-0.331546374321-5.05108984882E-50.603424592507-0.09358390499730.02561061075270.734455104002-0.1679080375570.734576731216-41.710132833621.2980753944-5.8622629692
20.114033961428-0.332343847766-0.3165755965270.8209569878730.7596767682530.6502885062380.0803074756643-0.0151084415616-0.1262208879480.168342052745-0.2609969145720.3928627674920.214605721444-0.298043505375-5.17906889454E-50.75273489537-0.13885646010.1359052514940.818565876037-0.0764221984290.660617553997-25.609553902151.526288351241.1448446816
31.444383108390.626016934527-0.5990583788590.789159513452-0.1392288985990.8650089316660.225796478503-0.05556320050320.3954392350630.170280599798-0.07647967837780.196229480977-0.185874410086-0.006548247512342.42960275035E-50.6403681798320.01235506897540.03087697643140.559439106742-0.02265737364210.6119810285620.44041493046981.613406277134.999392984
40.6985212184360.4965669486780.1723774429430.4753931713810.4616604596030.7757688015010.0711924739748-0.080622500027-0.2310690689490.130096943917-0.0382704820563-0.08330021235440.1398548927150.01243198258431.31962650897E-50.6004877516780.0229221501838-0.07529566866340.5154850588490.0154469207140.5713440443181.0720113723741.535964054821.6746611104
50.0636071760421-0.08244337726530.04066006753870.117310745723-0.08324897496450.08590665634410.061249478723-0.0934441565977-0.18919898732-0.1186882895680.143713621475-0.5313749089080.3566612109050.0714895934696-0.000183694650470.7940462672820.0427841516140.002146813292951.08074455789-0.1643771879151.0563483486631.92353341944.51218240035.17454397982
60.231086762706-0.04335264512590.09937298214270.1132698993050.0837489753750.138622422159-0.1448966490260.00985069313831-0.1498338069970.1711165008040.2457816234320.0126732079309-0.0576481092292-0.205920883184-3.09962628746E-50.796815212967-0.06049994744380.07749632976240.65493985231-0.04543743195470.72368692675920.195008094747.55636534157.01693580784
70.007942167522740.03260187317880.03381810664330.1212971382360.1237072925910.122348994562-0.2236953612420.201134279261-0.5367995122160.227984999327-0.00255496917887-0.3597521395810.1725871649970.247163357504-0.0001609300963230.7880798373730.02205038098370.02750707413920.817358550043-0.07741153048030.85745233287923.503138123139.87934265323.67528324007
80.161767116277-0.0296224709335-0.05665182732150.07955702082130.03432207931970.024621103947-0.118526377880.1399076681150.0177289508945-0.3073758053170.0820637029005-0.208854428892-0.4141437949420.3367704076150.0001057080540290.664612115412-0.039677723182-0.002499376539240.679100013957-0.04874102210150.70903779664423.324041364350.20321062633.85020157561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 211 )
2X-RAY DIFFRACTION2chain 'A' and (resid 212 through 437 )
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 997 )
4X-RAY DIFFRACTION4chain 'A' and (resid 998 through 1334 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 60 )
7X-RAY DIFFRACTION7chain 'B' and (resid 61 through 83 )
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 123 )

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