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- EMDB-26547: Mediator-PIC Early (Tail A + Upstream DNA & Activator) -

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Basic information

Entry
Database: EMDB / ID: EMD-26547
TitleMediator-PIC Early (Tail A + Upstream DNA & Activator)
Map dataMediator-PIC Early (Tail A Upstream DNA)
Sample
  • Complex: Med-PICEarly (TailA+Activator & DNA Class 1)
    • DNA: DNA (38-MER)
    • DNA: DNA (37-MER)
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 15
    • 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: Regulatory protein GAL4
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 5
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 14
  • Ligand: ZINC ION
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter by galactose / 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 / galactose metabolic process / mediator complex / positive regulation of transcription from RNA polymerase II promoter by galactose / TFIIB-class transcription factor binding ...regulation of transcription from RNA polymerase II promoter by galactose / 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 / galactose metabolic process / mediator complex / positive regulation of transcription from RNA polymerase II promoter by galactose / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / transcription repressor complex / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / identical protein binding / 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 / Gal4 dimerisation domain / Gal4-like dimerisation domain / Mediator complex, subunit Med15, fungi / Gal11, coactivator domain ...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 / Gal4 dimerisation domain / Gal4-like dimerisation domain / 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) / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / : / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / Mediator complex subunit 16, N-terminal / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Coactivator CBP, KIX domain superfamily / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
Regulatory protein GAL4 / 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: 7.7 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) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 8, 2023-
Current statusMar 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26547.png

Downloads & links

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Map

FileDownload / File: emd_26547.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMediator-PIC Early (Tail A Upstream DNA)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.020282034 - 0.050172143
Average (Standard dev.)-0.0008630971 (±0.0025168045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26547_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_26547_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_26547_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Med-PICEarly (TailA+Activator & DNA Class 1)

EntireName: Med-PICEarly (TailA+Activator & DNA Class 1)
Components
  • Complex: Med-PICEarly (TailA+Activator & DNA Class 1)
    • DNA: DNA (38-MER)
    • DNA: DNA (37-MER)
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 15
    • 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: Regulatory protein GAL4
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 5
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 14
  • Ligand: ZINC ION

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Supramolecule #1: Med-PICEarly (TailA+Activator & DNA Class 1)

SupramoleculeName: Med-PICEarly (TailA+Activator & DNA Class 1) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2, #4-#6, #3, #8-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.666479 KDa
SequenceString:
(DA)(DC)(DC)(DG)(DG)(DA)(DG)(DG)(DA)(DC) (DA)(DG)(DT)(DC)(DC)(DT)(DC)(DC)(DC)(DG) (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA) (DC)(DG)(DT)(DC)(DG)(DT)(DA)(DC)(DG)

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Macromolecule #2: DNA (37-MER)

MacromoleculeName: DNA (37-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.42431 KDa
SequenceString:
(DC)(DG)(DT)(DA)(DC)(DG)(DA)(DC)(DG)(DT) (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DG) (DG)(DG)(DA)(DG)(DG)(DA)(DC)(DT)(DG) (DT)(DC)(DC)(DT)(DC)(DC)(DG)(DG)

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Macromolecule #3: Regulatory protein GAL4

MacromoleculeName: Regulatory protein GAL4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 16.895672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKLLSSIEQA CDICRLKKLK CSKEKPKCAK CLKNNWECRY SPKTKRSPLT RAHLTEVESR LERLEQLFLL IFPREDLDMI LKMDSLQDI KALLTGLFVQ DNVNKDAVTD RLASVETDMP LTLRQHRISA TSSSEESSNK GQRQLTVS

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Macromolecule #4: Mediator of RNA polymerase II transcription subunit 15

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 15
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: 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

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Macromolecule #5: Mediator of RNA polymerase II transcription subunit 2

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 2 / 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: 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

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Macromolecule #6: Mediator of RNA polymerase II transcription subunit 3

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
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

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Macromolecule #7: Mediator of RNA polymerase II transcription subunit 14

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 14
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 27.535459 KDa
SequenceString: MQLVVLTDVV ERLHKNFESE NFKIIALQPN EISFKYLSNN DEDDKDCTIK ISTNDDSIKN LTVQLSPSNP QHIIQPFLDN SKMDYHFIF SYLQFTSSLF KALKVILNER GGKFHESGSQ YSTMVNIGLH NLNEYQIVYY NPQAGTKITI CIELKTVLHN G RDKIQFHI ...String:
MQLVVLTDVV ERLHKNFESE NFKIIALQPN EISFKYLSNN DEDDKDCTIK ISTNDDSIKN LTVQLSPSNP QHIIQPFLDN SKMDYHFIF SYLQFTSSLF KALKVILNER GGKFHESGSQ YSTMVNIGLH NLNEYQIVYY NPQAGTKITI CIELKTVLHN G RDKIQFHI HFADVAHITT KSPAYPMMHQ VRNQVFMLDT KRLGTPESVK PANASHAIRL GNGVACDPSE IEPILMEIHN IL K

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Macromolecule #8: Mediator of RNA polymerase II transcription subunit 5

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 5 / type: protein_or_peptide / ID: 8 / 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

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Macromolecule #9: Mediator of RNA polymerase II transcription subunit 16

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 16
type: protein_or_peptide / ID: 9 / 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

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
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 FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199834

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