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- EMDB-71479: Extra Med5/16 of PIC-Med-SWI/SNF -

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Basic information

Entry
Database: EMDB / ID: EMD-71479
TitleExtra Med5/16 of PIC-Med-SWI/SNF
Map datasharpened map
Sample
  • Complex: Extra Med5/16 of PIC-Med-SWI/SNF
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 5
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16
KeywordsSWI/SNF / PIC / TRANSCRIPTION
Function / homology
Function and homology information


regulation of establishment of protein localization to chromosome / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription by RNA polymerase II / transcription coregulator activity / cellular response to heat / RNA polymerase II-specific DNA-binding transcription factor binding ...regulation of establishment of protein localization to chromosome / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription by RNA polymerase II / transcription coregulator activity / cellular response to heat / RNA polymerase II-specific DNA-binding transcription factor binding / 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
Similarity search - Function
Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYang C / Nagai S / Chen D-H
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure of Extra Med5/16 of PIC-Med-SWI/SNF
Authors: Yang C / Nagai S / Chen D-H
History
DepositionJun 26, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71479.png

Downloads & links

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Map

FileDownload / File: emd_71479.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0262
Minimum - Maximum-0.08379066 - 0.16159244
Average (Standard dev.)0.00030858134 (±0.0048992066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71479_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_71479_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71479_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71479_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Extra Med5/16 of PIC-Med-SWI/SNF

EntireName: Extra Med5/16 of PIC-Med-SWI/SNF
Components
  • Complex: Extra Med5/16 of PIC-Med-SWI/SNF
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 5
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 16

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Supramolecule #1: Extra Med5/16 of PIC-Med-SWI/SNF

SupramoleculeName: Extra Med5/16 of PIC-Med-SWI/SNF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2 MDa

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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: Saccharomyces cerevisiae (brewer's yeast)
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 #2: Mediator of RNA polymerase II transcription subunit 16

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 16
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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

BufferpH: 7.5
Details: 40 mM Hepes-KOH pH 7.5, 100 mM potassium acetate, 2 mM magnesium acetate and 5 mM DTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.0 sec. / Average electron dose: 40.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 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

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Details: 3D auto-refine in Relion / Number images used: 67550
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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