+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22397 | |||||||||
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Title | T module | |||||||||
Map data | Tail module of Mediator complex | |||||||||
Sample |
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Keywords | Transcription / Activation / PolII | |||||||||
Function / homology | Function and homology information mediator complex / transcription coregulator activity / regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||
Authors | Zhang HQ / Chen DC / Bushnell DA / Kornberg RD | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22397.map.gz | 398.7 MB | EMDB map data format | |
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Header (meta data) | emd-22397-v30.xml emd-22397.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22397_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_22397.png | 130 KB | ||
Filedesc metadata | emd-22397.cif.gz | 8.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22397 | HTTPS FTP |
-Validation report
Summary document | emd_22397_validation.pdf.gz | 521 KB | Display | EMDB validaton report |
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Full document | emd_22397_full_validation.pdf.gz | 520.5 KB | Display | |
Data in XML | emd_22397_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_22397_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22397 | HTTPS FTP |
-Related structure data
Related structure data | 7jmnMC 6xp5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22397.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tail module of Mediator complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.096 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : T module complex
Entire | Name: T module complex |
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Components |
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-Supramolecule #1: T module complex
Supramolecule | Name: T module complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
-Macromolecule #1: Mediator of RNA polymerase II transcription subunit 5
Macromolecule | Name: Mediator of RNA polymerase II transcription subunit 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 118.784406 KDa |
Recombinant expression | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Sequence | String: 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 |
-Macromolecule #2: Mediator of RNA polymerase II transcription subunit 14
Macromolecule | Name: Mediator of RNA polymerase II transcription subunit 14 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 133.223094 KDa |
Recombinant expression | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Sequence | String: 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 |
-Macromolecule #3: Mediator of RNA polymerase II transcription subunit 16
Macromolecule | Name: Mediator of RNA polymerase II transcription subunit 16 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 123.395898 KDa |
Recombinant expression | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Sequence | String: 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 |
-Macromolecule #4: MED15
Macromolecule | Name: MED15 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 175.252594 KDa |
Recombinant expression | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Sequence | String: 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 |
-Macromolecule #5: Unknown peptide
Macromolecule | Name: Unknown peptide / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Molecular weight | Theoretical: 4.443468 KDa |
Recombinant expression | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |