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- EMDB-22397: T module -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-22397
TitleT module
Map dataTail module of Mediator complex
Sample
  • Complex: T module complex
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 5
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 14
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16
    • Protein or peptide: MED15
    • Protein or peptide: Unknown peptide
KeywordsTranscription / Activation / PolII
Function / homology
Function and homology information


mediator complex / transcription coregulator activity / regulation of transcription by RNA polymerase II
Similarity search - Function
Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Mediator complex, subunit Med16 / Mediator complex subunit 16, N-terminal / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 5 / Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZhang HQ / Chen DC / Bushnell DA / Kornberg RD
CitationJournal: Mol Cell / Year: 2021
Title: Mediator structure and conformation change.
Authors: Heqiao Zhang / Dong-Hua Chen / Rayees U H Mattoo / David A Bushnell / Yannan Wang / Chao Yuan / Lin Wang / Chunnian Wang / Ralph E Davis / Yan Nie / Roger D Kornberg /
Abstract: Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription ...Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription machinery. Previous structural studies revealed a relatively small part of Mediator and none of the gene activator-binding regions. We have determined the cryo-EM structure of the Mediator at near-atomic resolution. The structure reveals almost all amino acid residues in ordered regions, including the major targets of activator proteins, the Tail module, and the Med1 subunit of the Middle module. Comparison of Mediator structures with and without pol II reveals conformational changes that propagate across the entire Mediator, from Head to Tail, coupling activator- and pol II-interacting regions.
History
DepositionAug 2, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jmn
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22397.png

Downloads & links

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Map

FileDownload / File: emd_22397.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTail module of Mediator complex
Voxel sizeX=Y=Z: 1.096 Å
Density
Contour LevelBy EMDB: 0.2 / Movie #1: 0.6
Minimum - Maximum-1.0963243 - 2.6104546
Average (Standard dev.)0.00080950215 (±0.036526732)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 526.07996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z526.080526.080526.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-1.0962.6100.001

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Supplemental data

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Sample components

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Entire : T module complex

EntireName: T module complex
Components
  • Complex: T module complex
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 5
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 14
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16
    • Protein or peptide: MED15
    • Protein or peptide: Unknown peptide

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Supramolecule #1: T module complex

SupramoleculeName: T module complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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Macromolecule #1: Mediator of RNA polymerase II transcription subunit 5

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 118.784406 KDa
Recombinant expressionOrganism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MVTVTDPLTA RLEAAIKAWS DFFSDAEHER LDPAIFADQS QTLFANHPLA PVPLADLLLR PTPSNRECVD QRTLQYLQVL QKQGRITTA AVLRALYKYS TAHTRAQTPD GKPKHGAGDS STNDADVGGS SKADLTSRMV RWRNSYMVEE DVLWRLARAV N HGTGIKTS ...String:
MVTVTDPLTA RLEAAIKAWS DFFSDAEHER LDPAIFADQS QTLFANHPLA PVPLADLLLR PTPSNRECVD QRTLQYLQVL QKQGRITTA AVLRALYKYS TAHTRAQTPD GKPKHGAGDS STNDADVGGS SKADLTSRMV RWRNSYMVEE DVLWRLARAV N HGTGIKTS HDVTEVAKVL ARWTALFAEV SAAISRDAFN SMNGLQVKDE SEDARNAFVL FYFAFCENQI VNETLSQPVC KD ICRKLLD SLDAFLPTLM HLTADITGRL EHFRSEVLAR YAPQEKKSMD MPSFMNDLSM SLESFQVPEL PVVNTRAGLY IYL GAALVG RPMIDDEALF SYLHNRYQGD LQAMAVHLIL ASFDLLANAV FRNEGAKTGH LLKSFLINKV PLILVQLVAY AATT MYPFN AEMCITEALN QVDINMFPTL SGMFDMPNNN SFNDSVRQDF CFACQLHGLL SQAAIETLLG DITYQSLPPE GRYVK EQLV QACLQEPDRT LKLIGELDNM NGNVGAAAQA IVEICRDLAS KPLSLDVLLL FDKPHKILHP LCELLDNWAG YEEDHG EYQ PVYEEFGSVL LLLLAFVYRY NLSTADLGIR SSGSFVAKLL NGVDRCQPLE QLSEQEKSHL GGWIHGLFDT EAGGLGD EL MSSCPPQDFY LLAPTLFHQI VNALSAGYLT DEMLKGGLEY LVDVLLLPAL VPALLYLSNL LWADNQPIQN AVIKILQP I LKPTSISNEA STMLSSVLNI VAKPLEHALK SYQRQDPECQ KIEPLLLAIA DNLAVSRRTG GADHTELESW CSAQITNPA TGALIHGGLA AAVRTTIQQL VQWAQNPTLN SMNGMPAPYT HRQTLAAQQI LGPHRLLGII LDELKSSPEP GIAYDVVTTM ICAPDVRNS TISSPSTQSN NSSDHNDQAQ NHQSQDAKHK HPHRLTLRDA LRLEAHDFRA HLRADPVLAE TVVRLYRRVE A QLTPLALP LPPAAAAAPA VGVNVGVDAA TAAAAAAAAA MMPDALGLGV VGGVELGGME GAIAAAVAAA NGSGTGGAGG DG TQGGAGD AGMGLDGQQQ GQGGSSAGDM GLGGGTADDI FSGLSGPDDF GADFGSWSMD LS

UniProtKB: Mediator of RNA polymerase II transcription subunit 5

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Macromolecule #2: Mediator of RNA polymerase II transcription subunit 14

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 14
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 133.223094 KDa
Recombinant expressionOrganism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MEARAHGALP NNYDRERFIN GVGGDDKALK RKLEEPLSDI TKELDTVIAQ SDVAVADPKG QLCPDADVPD EMEHITDGIL PLNLLLIRL AEFSHSKLEE LVTMLASKPV PQHAVNGNGS HSTLVEDASP ESQEKKRLLL NTIQDLHSRW VKALVITEWA R NAEKVGKL ...String:
MEARAHGALP NNYDRERFIN GVGGDDKALK RKLEEPLSDI TKELDTVIAQ SDVAVADPKG QLCPDADVPD EMEHITDGIL PLNLLLIRL AEFSHSKLEE LVTMLASKPV PQHAVNGNGS HSTLVEDASP ESQEKKRLLL NTIQDLHSRW VKALVITEWA R NAEKVGKL IDIRTHLFKK LELYPQVLND FINLKRDMAW AKVPSPDLKT ALHILTHGEV TWMPDFNFLD PPPLTTEETL RW INDMNLA LHARLQLEEH DKLPPPFKNY TIDSGRVTFR VRGEFEVDLS ISEEDFSEQF WFINFRFDFS PAPAELTPAV RYW MTEKVN NILKTEGLGG CYKYLHEFTL TQKIAELHRQ AIALNKGRWA NSLRVEKLNR NLGIHYWANR LHSQNLKSWI IIGV HSGED PQGLEEPKPS YLMVQWFREG VEQFIDIPFS QEKLSIEEIL EFVTAKHVGY LLFSLFRKFD GKPRFTQGKK ARLEL NVWT QKPEDYYLSM QLLDDEDLKI QVNPWMGDFI TTPSTGPWNR TLNSLGNPAE EGSKELENFR YIYIISVLKA QGKSHG WSV VRSPISQDEL RSIVHSESAS SRETFQAAWT RFVDWDPQWY AMRSMSLAGD QWWLVEVTSQ RQSISGNRLV FFTKMAP CF SEERLTDGFF NGLRDHSRRL IAEITNLREL YPGITPSQLR KLIDPTRQPP VLPVKASKIL GDFGGADAQS IAWLKDPV W LIYRGSACDT RVSDSPQQKR TQPVLDVFEA YLDVTDRRRF QTLNPRLDRD ILYNPYTGRF MFRLRAKMGV PVVPLLGIR VRQLQRLLDF LEGLRRVGDD AVPERVTLRE IVFSYGATRK RDSTNQPKVR PWRVRLDLTK EEGVGVVLEK GNPHLRVINR LEDLVNSQK FYSLATYLTL SLPLFRAFQQ LENAWQTAQE NGRGSCFILH LSLDKHTIRF VLPGHQRQIS LLIQPHEKEG K LVWEVGRP RHDPELLNEN CEFNRVLKER VWTISGSGFK GLVTGAAAEP DEGIERLLVL ISDAVLHLST SQPATAPPQP PQ AQPSQQV QQVQQQQVVS QLQPQAQQPR SAMPHASVGQ QQPHGAPAPM ARFPPQQQQI FQQQRPPQPQ PNMHGGQISQ PNM HGGPKP QLQGQHGQPG QMVAAPQQQG QRPGTGTAAG MGRSNAPLVV LD

UniProtKB: Mediator of RNA polymerase II transcription subunit 14

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Macromolecule #3: Mediator of RNA polymerase II transcription subunit 16

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 16
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 123.395898 KDa
Recombinant expressionOrganism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MALLMEGGDP MSVDGSSTMP AHMRVMPDMG ITGAPMTLDD VDLFGDAVMN NALDALPPAP GHPPPSRALQ RRIAELRARG CCQGIAWSR QGTIASISAD GMSIELRFLR TNPENGDWEL TDAALSLSVA LVPASSPSAT SSSGSGTSNT TVISAGAPFV H LAWAPSVH ...String:
MALLMEGGDP MSVDGSSTMP AHMRVMPDMG ITGAPMTLDD VDLFGDAVMN NALDALPPAP GHPPPSRALQ RRIAELRARG CCQGIAWSR QGTIASISAD GMSIELRFLR TNPENGDWEL TDAALSLSVA LVPASSPSAT SSSGSGTSNT TVISAGAPFV H LAWAPSVH TSSFELAAID APGRITIFLF TQNINKPYLS RKWDTDPVDD LHAVVGCYWL PLPFNVSYVA NWVQTDYRYE PI LSPAWGP IHPNHTKSAL VCVTTNGLLK MLFPQNNNRI EETSIELESV TASDDLITHA AIGADRNTLL IALAMGSKQL RVV RVGIQW WLPQVDKQQM PPSVPLRPSL RESRVAVTTL LDPEQQQSDG DAPIAQLTHL EILPSPLGET PQTVLPPVIL AVRS YLPQE GSLYAAHQEP FTVIDRWELF TDQPKAFHPA FEQLGAKNSA SSQPSAMQTL RKLDPVVIPG KVVVTVNTLQ FGRVV CFGF SDGTLQYRDR FTMNEVYTEQ ATTNITSPLQ VGFQWETEGP CLQMAFAPTN CSFVQVSEDG SVKWVKLRYP VDDPNM TLQ GPKLKAVAAS LAVASVGANI AGPNIHNHCD DVMAIARPLA KKFKDFPTAW VREFVTMFKI TVDYSEEAHH DQLMRNS LL QFCLSILNHF GFNGDFQPRT FSGKFANLAL AVRNIVVLIT IASNAPNTIK EKLSPLDEPE VVDALASCAK WGFDLLAW L TDRLLALSTD QTIKAMLADQ KRFPDLARYL HSKNDVSLHL LLCSSTRGLL SAVCRRLQVV ESLAHRATVY YESRYAVDP AAAAQKTLPP LYHAYVKMQR VVTASLVKAS DFDKLLTALS RDIQTAYIQT FSGVATQIRQ HASGSGGQPL TEQQQQQCNE QFIKKAQSH VELDMLLGQN PPPGFREVLA CFFGNIFPAF RATVDPRSVF FADWSLLEEI VAEDERTLKR RREGGGRYVD V FKRVELCG RGQVLPRGRI VASVKTERAE AVPMVPSQSQ SSHQAASQAQ GQQSQQQQGA TPAPNATPSV PISQLNPPTG PT QPPNSSG NTANANPNTG TNANTLGGSV PGLQGFVPVT ANLAVNASQW RRCVRCAAVM EDVWGQRPGF TFVLTQQRRC ACG GGWGLV PRGD

UniProtKB: Mediator of RNA polymerase II transcription subunit 16

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Macromolecule #4: MED15

MacromoleculeName: MED15 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 175.252594 KDa
Recombinant expressionOrganism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MAANIPQFPN GQMAMLQQQQ QQAQQQAIAA NQQYMNVFIL NNLRGSGTNL PGTWQAQIPP QQLLSERFQK THILYTNIML ASNGGDPQR CAVAALNLEK QIFQNAQDKA SYDQAMAKKI SEVMKRRESN GPALQNQVIT DAQRQAQIQQ QIQLAQAQQR Q QQQLMLNR ...String:
MAANIPQFPN GQMAMLQQQQ QQAQQQAIAA NQQYMNVFIL NNLRGSGTNL PGTWQAQIPP QQLLSERFQK THILYTNIML ASNGGDPQR CAVAALNLEK QIFQNAQDKA SYDQAMAKKI SEVMKRRESN GPALQNQVIT DAQRQAQIQQ QIQLAQAQQR Q QQQLMLNR MAAQGLTQPP QPAFQPMQNP GQVPVIPQQM GINVAVPGML PNAPSQPQLA MQMGQPRPGA IPVDLNQLSN QD RMRIHEE VMRRVNSTTE NSKMQIRQLM QQRLTPAQIS EANASGKDLV YLYFQNQVVQ VFRATMLQAQ EKAQQVAQVQ QAL LMQQRQ GIQGAGMPGV PPQGQVNPAL MNALGQQPAI SDAPMLGPNL TNEPQMGLLA QQPGQMIVPT NPAAVPGRPV TAGP QLGAI PPQPTPGNPQ APNQTPRPGQ LQQPFGMPQV NNPAAAAAAA AAAAAVQQPP QAQPGMRPPG PRTMPGQPGA ITTVA GPQP TSQSPAMNTL NAPMRQPPVA MTQATTQPVN PANAPMAGAT LNAQFNHQNN ARPLSMQGNM NNQAMAGMGA AANMNA NNN PMKEFMARLQ EQQRATAAAG FQGPKPGQVI GMPGQFPGGP MNALNQPGMF NQNSKPNAMV PPTAQAAALQ QQQQQAN AA DMANIYKIIQ TPQGQNMMNN MDIHQMILQE INKHLGGRLP PNITKWAHLR QFLAAQPNAL PSEIVQRIMS YQILQFKN F WKRASQPNAV GGIPQPVSNV PVSQFAGMNQ PVAPPPGVQV PQSISQVSPQ DIEGLRKNPK FANLTDDQLA EWIRKVKQQ SFIKKAWEIH NNQSNAAQNQ ATNSSLIGQQ KPGMTVPPTP TTAQPTSSVV QTAQSRPQGP QPTPTPQGPQ GVQPQAAQPK PTPSPAANV TTAPPATTGM SAASVQAANI RPSMPQQQQQ PAPQPQAPQP PPPQQQQQQQ QQQQQQQQQQ QQQVPQPPQN S RQAPMDPS PAMATKSLKR PSPDDSAEDT PAQQNITPMQ RAPSQAAQVA PNAPNAASGE PPKLSPELQK LRNLASEAQL EV SKEHLQP ILMTPADQQE TREKIAQVKL KMNQIRSMGL LPKWYYLTND DNRARQFFRG RFKVVKQFTD GEAMTQLRDT FTI TKEELN QYDNLLGSML RDMMMSRVNQ QQAAMMNQQQ QTQQQTTQPT PATLANQQAA ALRQAQQRVA PPPPKPVQQP PAQQ QQPHQ PAQPAQQQFQ PGVQPTPAPA PEYFGDQRLT AANLVLPPRK KPKVSGNQTS PSANQQLAAG SPQVQALSPV ATRKP EPQV KPQAQIPQQQ QQQQQQQQQQ QQQQQPQAPP APQFKCPEPG CTSLVAFPSE EALNAHRQEE HLKPAENPLA FMQEQM ASV LALDAQGRAK ASPKPSGQDV STPVPTAPPM SASLSKQGQT PRLQAATPMS RNLSMQRQGS ASGGKPGENM PTPGKSA GG KGKEGATPQQ MEDVWPQGTI DPANLFANLG GTLDAGTATI SGSIITDFAA YRSSTPKDTP ESSSSSKDSG VSEPNSDI N ENANLEIDLF WSNIDDGLLM DINNISMDGA AGSMGGSSGN AGGLVDISQF VEDPWGVDSA NFSLDDFGRE LDKGFGFLD GTLGEGQQES GQGQGQGQPE VMVIE

UniProtKB: Uncharacterized protein

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Macromolecule #5: Unknown peptide

MacromoleculeName: Unknown peptide / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 4.443468 KDa
Recombinant expressionOrganism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 281144
FSC plot (resolution estimation)

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