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- EMDB-26543: Mediator-PIC Early (Tail A) -

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Basic information

Entry
Database: EMDB / ID: EMD-26543
TitleMediator-PIC Early (Tail A)
Map dataMed-PIC Tail A - Unsharpened
Sample
  • Complex: Mediator-PIC Early
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 2
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 3
    • 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 15
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16
KeywordsDivergent transcription / Mediator / RNA Polymerase II / PIC / Pre-Initiation / Activation / Transcription Factor / Gal4 / Gal4VP16 / TRANSCRIPTION
Function / homology
Function and homology information


TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / TFIIB-class transcription factor binding / replicative senescence / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding ...TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / positive regulation of invasive growth in response to glucose limitation / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / TFIIB-class transcription factor binding / replicative senescence / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / response to endoplasmic reticulum stress / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / cellular response to heat / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol
Similarity search - Function
Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Mediator complex, subunit Med15, fungi / Gal11, coactivator domain / Mediator complex subunit 15, KIX domain / Mediator complex subunit 15 ...Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Mediator complex, subunit Med15, fungi / Gal11, coactivator domain / Mediator complex subunit 15, KIX domain / Mediator complex subunit 15 / KIX domain / Gal11 activator-binding domain (ABD1) / : / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / Coactivator CBP, KIX domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 15 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 3 / Mediator of RNA polymerase II transcription subunit 5 / Mediator of RNA polymerase II transcription subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGorbea Colon JJ / Chen S-F / Tsai KL / Murakami K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233-01 United States
CitationJournal: Mol Cell / Year: 2023
Title: Structural basis of a transcription pre-initiation complex on a divergent promoter.
Authors: Jose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami /
Abstract: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single ...Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
History
DepositionMar 29, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26543.png

Downloads & links

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Map

FileDownload / File: emd_26543.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMed-PIC Tail A - Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 280 pix.
= 386.4 Å		1.38 Å/pix.
x 280 pix.
= 386.4 Å		1.38 Å/pix.
x 280 pix.
= 386.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.022876464 - 0.057277236
Average (Standard dev.)-0.00016899385 (±0.0019421249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26543_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Med-PIC Tail A - Sharpened (Relion)

Fileemd_26543_additional_1.map
AnnotationMed-PIC Tail A - Sharpened (Relion)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Med-PIC Tail A - Sharpened (DeepEMhancer)

Fileemd_26543_additional_2.map
AnnotationMed-PIC Tail A - Sharpened (DeepEMhancer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Med-PIC Tail A - Half 2

Fileemd_26543_half_map_1.map
AnnotationMed-PIC Tail A - Half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Med-PIC Tail A - Half 1

Fileemd_26543_half_map_2.map
AnnotationMed-PIC Tail A - Half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mediator-PIC Early

EntireName: Mediator-PIC Early
Components
  • Complex: Mediator-PIC Early
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 2
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 3
    • 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 15
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16

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Supramolecule #1: Mediator-PIC Early

SupramoleculeName: Mediator-PIC Early / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Mediator of RNA polymerase II transcription subunit 2

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 47.75427 KDa
SequenceString: MVVQNSPVSS VHTANFSERG SNTRTMTYKN KLTVCFDDIL KVGAEMMMQQ QLKNVQLDSY LVNGFSQSQQ KLLKEKVKLF HGILDDLET SLSQSSSYLE TLTALGKEKE KEREEAEKKR AEQENMRKVR EQEELKKRQE LEEASQQQQL QQNSKEKNGL G LNFSTTAP ...String:
MVVQNSPVSS VHTANFSERG SNTRTMTYKN KLTVCFDDIL KVGAEMMMQQ QLKNVQLDSY LVNGFSQSQQ KLLKEKVKLF HGILDDLET SLSQSSSYLE TLTALGKEKE KEREEAEKKR AEQENMRKVR EQEELKKRQE LEEASQQQQL QQNSKEKNGL G LNFSTTAP ANTTDANGSK ENYQELGSLQ SSSQTQLENA NAANNGAAFS PLTTTRIQSQ QAQPSDVMFN DLNSMDISMF SG LDSTGFD STAFNATVDE TKGFDDNDSG NNYNDINISS IENNINNNIN STKNGKDNNN ESNKNNNGDE KNKNNNEDNE NNN NSSEKN NNNNNNNNNN NDDNGNNNNN NSGNDNNNTT NNDSNNKNNS ITTGNDNENI VNNDLPTTVV SNPGDNPPPA DNGE EYLTL NDFNDLNIDW STTGDNGELD LSGFNI

UniProtKB: Mediator of RNA polymerase II transcription subunit 2

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Macromolecule #2: Mediator of RNA polymerase II transcription subunit 3

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 43.116039 KDa
SequenceString: MDSIIPAGVK LDDLQVILAK NENETRDKVC KQINEARDEI LPLRLQFNEF IQIMANIDQE GSKQADRMAK YLHIRDKILQ LNDRFQTLS SHLEALQPLF STVPEYLKTA DNRDRSFQLL EPLSTYNKNG NAVCSTATVV STNHSAAAST PTTTATPHAN P ITHAHSLS ...String:
MDSIIPAGVK LDDLQVILAK NENETRDKVC KQINEARDEI LPLRLQFNEF IQIMANIDQE GSKQADRMAK YLHIRDKILQ LNDRFQTLS SHLEALQPLF STVPEYLKTA DNRDRSFQLL EPLSTYNKNG NAVCSTATVV STNHSAAAST PTTTATPHAN P ITHAHSLS NPNSTATMQH NPLAGKRGPK SGSTMGTPTV HNSTAAAPIA APKKPRKPRQ TKKAKAQAQA QAQAQAQVYA QQ STVQTPI TASMAAALPN PTPSMINSVS PTNVMGTPLT NMMSPMGNAY SMGAQNQGGQ VSMSQFNGSG NGSNPNTNTN SNN TPLQSQ LNLNNLTPAN ILNMSMNNDF QQQQQQQQQQ QQPQPQYNMN MGMNNMNNGG KELDSLDLNN LELGGLNMDF L

UniProtKB: Mediator of RNA polymerase II transcription subunit 3

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Macromolecule #3: Mediator of RNA polymerase II transcription subunit 5

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 128.91875 KDa
SequenceString: MEKESVYNLA LKCAERQLTS MEFSNLYKEF FNEKFPSLIQ EEEEDTTTTA NINEVKKASD LVDTPSNNTA ATADTTHLHE ALDIVCSDF VKILNLEKPL ILADYIVEVL LVNYNSDMIK CFLPKLNSVR NSLLLAHFFS KSCSFFAKLS DTLIIDQVRK D LGNVIVPN ...String:
MEKESVYNLA LKCAERQLTS MEFSNLYKEF FNEKFPSLIQ EEEEDTTTTA NINEVKKASD LVDTPSNNTA ATADTTHLHE ALDIVCSDF VKILNLEKPL ILADYIVEVL LVNYNSDMIK CFLPKLNSVR NSLLLAHFFS KSCSFFAKLS DTLIIDQVRK D LGNVIVPN ILSLDMNSMN KELIAIVSKL LQTTLKLSPS PILLTSAGCK NGSFTLLNQL SQTNKLLFKR VSQTFEAKLH FK DTKPFLN KDSTNEFVGS PSLTSPQYIP SPLSSTKPPG SVNSAAKYKD MKLLRYYKNI WLNNKIINWE ISNPDFLSKY SAI TSSIFQ ESFNSVQNLD QLLTDLIETS FTCFAQFVSN KQYHQANSNL TLLERKWVIF ITKHLPLLIL ENSSRSPRVV TNAL DNIDE KVVKAIRIYF TEKDDNKTNN EDLFDDYPST SLDIRHDFIK GLIMLNLQPA SVINNYLRED QMIDTSILPT RDDLF VRNL QGIQEVVHNT NSFIISSLDT LELESITESI THDSSNGLFQ VLHNFESVAP TKQREIVKAF LSIFEDAIKE LNYNRI AKI CALLFFNFSH SLTTILSFSS PAALMKTLIK FVDLSRNGRN GSNGNDESSE YETINISLSF SWAILLIINL TQTYGIS VV DVALKYPELS IKNSFIINFI SNLPNVSDKY YLEESNVNDS DMLTKSHNTV QSWLCDLFVN GSITDQLIQN IETRQLAN L IPFIVKQVLL SVEIGVLTDI SSLIGGFEYF LQPLLLVGLI KTFYWLEQFL SCVKNDTISE DILQGIFNLL NTLFNPVTL NEDSKAFHTA VLRLNAIPLL KVLRKFRVQS QSNYGIYSSD AQGDPNLEPL IAKLVAVLNV SPVYDVDPRI INSENDYSRK QLGYGKFLI LNENPINKIM TNQINSFWSL HSSTYYNLDY LFELIELVTP KSFLFDVLKT LEYKLATYGV PGSENKRGSL D SEHVFDYF FYFLVLYDVK TAEEASQLIE YMENDAKKSK GDVDIKGEDL HEKNDSAEVR QETQPKAEAT QDDDFDMLFG EN DTSTQAY EEEEENEDND GNNRTNNVPM IKAEETPSKT NKISILKRHS FAVLLHERKL LNDLALENGE ITKTENEKFI SYH DKYLCM LKTCVF

UniProtKB: Mediator of RNA polymerase II transcription subunit 5

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Macromolecule #4: Mediator of RNA polymerase II transcription subunit 14

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 14
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 123.500695 KDa
SequenceString: MTTTIGSPQM LANEERLSNE MHALKNRSEQ NGQEQQGPVK NTQLHGPSAT DPETTATQKE SLEMVPKDTS AATMTSAPPP ALPHVEINQ VSLALVIRNL TVFTMKELAQ YMKTNVHTQA NEPNSAKKIR FLQLIIFLRT QFLKLYVLVK WTRTIKQNNF H VLIDLLNW ...String:
MTTTIGSPQM LANEERLSNE MHALKNRSEQ NGQEQQGPVK NTQLHGPSAT DPETTATQKE SLEMVPKDTS AATMTSAPPP ALPHVEINQ VSLALVIRNL TVFTMKELAQ YMKTNVHTQA NEPNSAKKIR FLQLIIFLRT QFLKLYVLVK WTRTIKQNNF H VLIDLLNW FRTTNMNVNN CIWALKSSLN SMTNAKLPNV DLVTALEVLS LGRPNLPTHN FKLSGVSNSM DMVDGMAKVP IG LILQRLK DLNLTVSIKI ALMNIPKPLN SYHIKNGRIY FTVPNEFEIQ LSTVNRQSPL FFVDLKLLFN TEAEQTVSAV TEA TSTNGD SENNEENSSS NGNNLPLNKP RLEKLINEIL LKSNDPLLSL YNFLHKYVLT LQLYMVHREF LKLANGGKFS KSNL IHNYD SKKSTITVRY WLNGKMDSKG KITIGIQRTT ESLILKWDNQ SASRAKNMPV IYNNIVSNIE GILDEIMFNH ARIIR SELL ARDIFQEDEE NSDVLLFQLP TTCVSMAPIQ LKIDLLSGQF YFRNPTPLLS NYASKINRAE GPEELARILQ QLKLDK IIH VLTTMFENTG WSCSRIIKID KPIRTQVNTG GESVVKKEDN KYAIAGNSTT NSDVSLLLQR DLFIRLPHWP LNWYLIL SI ISSKTSCVVE KRIGKIVSQR GKWNLKYLDN SNVMTVKLES ITYQKIMILQ RTILNRIINH MLIDSLNQLE IRNKICSS E MINEQKLPQY IIQGSNTNDN ISIITLELES FLEGSKALNS ILESSMFLRI DYSNSQIRLY AKFKRNTMMI QCQIDKLYI HFVQEEPLAF YLEESFTNLG IIVQYLTKFR QKLMQLVVLT DVVERLHKNF ESENFKIIAL QPNEISFKYL SNNDEDDKDC TIKISTNDD SIKNLTVQLS PSNPQHIIQP FLDNSKMDYH FIFSYLQFTS SLFKALKVIL NERGGKFHES GSQYSTMVNI G LHNLNEYQ IVYYNPQAGT KITICIELKT VLHNGRDKIQ FHIHFADVAH ITTKSPAYPM MHQVRNQVFM LDTKRLGTPE SV KPANASH AIRLGNGVAC DPSEIEPILM EIHNILKVDS NSSSS

UniProtKB: Mediator of RNA polymerase II transcription subunit 14

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Macromolecule #5: Mediator of RNA polymerase II transcription subunit 15

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 15
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 120.432242 KDa
SequenceString: MSAAPVQDKD TLSNAERAKN VNGLLQVLMD INTLNGGSSD TADKIRIHAK NFEAALFAKS SSKKEYMDSM NEKVAVMRNT YNTRKNAVT AAAANNNIKP VEQHHINNLK NSGNSANNMN VNMNLNPQMF LNQQAQARQQ VAQQLRNQQQ QQQQQQQQQR R QLTPQQQQ ...String:
MSAAPVQDKD TLSNAERAKN VNGLLQVLMD INTLNGGSSD TADKIRIHAK NFEAALFAKS SSKKEYMDSM NEKVAVMRNT YNTRKNAVT AAAANNNIKP VEQHHINNLK NSGNSANNMN VNMNLNPQMF LNQQAQARQQ VAQQLRNQQQ QQQQQQQQQR R QLTPQQQQ LVNQMKVAPI PKQLLQRIPN IPPNINTWQQ VTALAQQKLL TPQDMEAAKE VYKIHQQLLF KARLQQQQAQ AQ AQANNNN NGLPQNGNIN NNINIPQQQQ MQPPNSSANN NPLQQQSSQN TVPNVLNQIN QIFSPEEQRS LLQEAIETCK NFE KTQLGS TMTEPVKQSF IRKYINQKAL RKIQALRDVK NNNNANNNGS NLQRAQNVPM NIIQQQQQQN TNNNDTIATS ATPN AAAFS QQQNASSKLY QMQQQQQAQA QAQAQAQAQA QAQAQAQAAQ AAQAQAQAQA QAQAQAQAQA QAQAQAQAQA QAQAQ AHAQ HQPSQQPQQA QQQPNPLHGL TPTAKDVEVI KQLSLDASKT NLRLTDVTNS LSNEEKEKIK MKLKQGQKLF VQVSNF APQ VYIITKNENF LKEVFQLRIF VKEILEKCAE GIFVVKLDTV DRLIIKYQKY WESMRIQILR RQAILRQQQQ MANNNGN PG TTSTGNNNNI ATQQNMQQSL QQMQHLQQLK MQQQQQQQQQ QQQQQQQQQQ QQQQHIYPSS TPGVANYSAM ANAPGNNI P YMNHKNTSSM DFLNSMENTP KVPVSAAATP SLNKTINGKV NGRTKSNTIP VTSIPSTNKK LSISNAASQQ PTPRSASNT AKSTPNTNPS PLKTQTKNGT PNPNNMKTVQ SPMGAQPSYN SAIIENAFRK EELLLKDLEI RKLEISSRFK HRQEIFKDSP MDLFMSTLG DCLGIKDEEM LTSCTIPKAV VDHINGSGKR KPTKAAQRAR DQDSIDISIK DNKLVMKSKF NKSNRSYSIA L SNVAAIFK GIGGNFKDLS TLVHSSSPST SSNMDVGNPR KRKASVLEIS PQDSIASVLS PDSNIMSDSK KIKVDSPDDP FM TKSGATT SEKQEVTNEA PFLTSGTSSE QFNVWDWNNW TSAT

UniProtKB: Mediator of RNA polymerase II transcription subunit 15

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Macromolecule #6: Mediator of RNA polymerase II transcription subunit 16

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 16
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 111.423422 KDa
SequenceString: MMLGEHLMSW SKTGIIAYSD SQSSNANICL TFLESINGIN WRFHTPQKYV LHPQLHEVQY QESSSTLSTH STTTSVNGST TAGVGSTPN FGGNSNKSPP QFFYNISSIH WNNWFSLPGD MLAVCDELGN MTMLITGQRP DRATTYEKLT MVFQDNVYKI Y NHVMPLKP ...String:
MMLGEHLMSW SKTGIIAYSD SQSSNANICL TFLESINGIN WRFHTPQKYV LHPQLHEVQY QESSSTLSTH STTTSVNGST TAGVGSTPN FGGNSNKSPP QFFYNISSIH WNNWFSLPGD MLAVCDELGN MTMLITGQRP DRATTYEKLT MVFQDNVYKI Y NHVMPLKP VDKLKPMNIE RKQTRKEYNT SILEFRWLTS SKSVIVSQFC AFDSSSNTYR SRAQQVPPYG VYHPPFIKYA CL AIRKNGQ IDFWYQFSNS KDHKKITLQL LDTSNQRFKD LQWLEFARIT PMNDDQCMLI TTYSKLSKNI SFYKLHVNWN LNA TKPNVL NDPSLKIQFI LSTTLDPTDD EGHVLKLENL HVVSKSSIEK DPSPEILVLY NVCDTSKSLV KRYRLAPTQL SAEY LVILK PDLNIDRNNS TNQIFQSRRY NLRRHSDIVL DKKVTLITSE MFDAFVSFYF EDGTIESYNQ NDWKLETERL ISQSQ LGKF KNIIASPLSA GFNYGKLPLP PSVEWMKVSP SMCGVIVKQY NKKWPQFYAA VQKNYADPEK DSINATALAF GYVKSL HKQ ISAEDLTIAA KTHILRISFL DRKRAKEFIT TLLKSLYSFF NISPDAPKEI MDKIITSRPL QKIMLLQLEL GSCFSQE NI EEMARVILYL KNVLFAFNGV ARNFHFAIEQ ISNNSNQQQN PKLFQTIFSK QDLIHSLIPV AKWFVKFITY LTQEILIL I NDPTNKEYTL VHGIFGAKMS RTLILSILNE IKKVTQIVAK FPETSYPILN ESSTFLKLVL SESPVDFEKF ETFLVDVNN KFIALCEQQP SQEREFSLLV KAEIPPEYAK VGDFLLQYAN NAVISHANAA AVYFADTSGL KISNSEFFNP EIFHLLQPLE EGLIIDTDK LPIKNRTSKS FSKLLYDDVT CDKLSVSEIS DGKLKRCSRC GSVTRAGNII SSDKTIVPTS IQTKRWPTMY T RLCICSGM LFEMDG

UniProtKB: Mediator of RNA polymerase II transcription subunit 16

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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

Concentration.1 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
80.0 mMKOAcPotassium acetate
20.0 mMHEPESHEPES
5.0 mMDTTDithiothreitol
2.0 mMMg(OAc)2Magnesium acetate
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 40900 / Average exposure time: 3.4 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1102984
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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