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- EMDB-18367: RNA polymerase II bound to Alu RNA left arm -

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Basic information

Entry
Database: EMDB / ID: EMD-18367
TitleRNA polymerase II bound to Alu RNA left arm
Map dataLocally filtered, unsharpened map
Sample
  • Complex: RNA Polymerase II bound to Alu RNA left arm
    • Complex: RNA polymerase II
      • Protein or peptide: x 12 types
    • Complex: Alu RNA Left Arm
      • RNA: x 1 types
Keywordstranscription inhibition / noncoding RNA / RNA polymerase II / Alu RNA / TRANSCRIPTION
Function / homology
Function and homology information


Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA ...Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / nuclear lumen / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / fibrillar center / : / : / : / DNA-directed RNA polymerase / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily ...DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerase subunit / RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB9
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsTluckova K / Bernecky C
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Science FundP34185 Austria
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Mechanism of mammalian transcriptional repression by noncoding RNA.
Authors: Katarína Tlučková / Beata Kaczmarek / Anita Salmazo / Carrie Bernecky /
Abstract: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here ...Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.
History
DepositionAug 31, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18367.png

Downloads & links

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Map

FileDownload / File: emd_18367.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally filtered, unsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 428 pix.
= 427.52 Å		1 Å/pix.
x 428 pix.
= 427.52 Å		1 Å/pix.
x 428 pix.
= 427.52 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99888 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.023132062 - 0.07356925
Average (Standard dev.)0.00009071394 (±0.0013172047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions428428428
Spacing428428428
CellA=B=C: 427.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18367_msk_1.map
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Additional map: 8A-filtered, unsharpened map

Fileemd_18367_additional_1.map
Annotation8A-filtered, unsharpened map
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Additional map: Sharpened map (auto B-factor)

Fileemd_18367_additional_2.map
AnnotationSharpened map (auto B-factor)
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Additional map: Unsharpened map

Fileemd_18367_additional_3.map
AnnotationUnsharpened map
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Half map: Half map 1

Fileemd_18367_half_map_1.map
AnnotationHalf map 1
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Half map: Half map 2

Fileemd_18367_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : RNA Polymerase II bound to Alu RNA left arm

EntireName: RNA Polymerase II bound to Alu RNA left arm
Components
  • Complex: RNA Polymerase II bound to Alu RNA left arm
    • Complex: RNA polymerase II
      • Protein or peptide: DNA-directed RNA Polymerase II subunit POLR2A
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2B
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2C
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2D
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2E
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2F
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2G
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2H
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2I
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2L
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2J
      • Protein or peptide: DNA-directed RNA polymerase II subunit POLR2K
    • Complex: Alu RNA Left Arm
      • RNA: Alu RNA Left Arm

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Supramolecule #1: RNA Polymerase II bound to Alu RNA left arm

SupramoleculeName: RNA Polymerase II bound to Alu RNA left arm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 36 KDa

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Sus scrofa domesticus (domestic pig)

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Supramolecule #3: Alu RNA Left Arm

SupramoleculeName: Alu RNA Left Arm / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13 / Details: In vitro transcribed RNA
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA-directed RNA Polymerase II subunit POLR2A

MacromoleculeName: DNA-directed RNA Polymerase II subunit POLR2A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString: MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIEL AKPVFHVGFL VKTMKVLRCV CFFCSKLLVD SNNPKIKDIL AKSKGQPKKR LTHVYDLCKG KNICEGGEEM DNKFGVEQPE ...String:
MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIEL AKPVFHVGFL VKTMKVLRCV CFFCSKLLVD SNNPKIKDIL AKSKGQPKKR LTHVYDLCKG KNICEGGEEM DNKFGVEQPE GDEDLTKEKG HGGCGRYQPR IRRSGLELYA EWKHVNEDSQ EKKILLSPER VHEIFKRISD EECFVLGMEP RYARPEWMIV TVLPVPPLSV RPAVVMQGSA RNQDDLTHKL ADIVKINNQL RRNEQNGAAA HVIAEDVKLL QFHVATMVDN ELPGLPRAMQ KSGRPLKSLK QRLKGKEGRV RGNLMGKRVD FSARTVITPD PNLSIDQVGV PRSIAANMTF AEIVTPFNID RLQELVRRGN SQYPGAKYII RDNGDRIDLR FHPKPSDLHL QTGYKVERHM CDGDIVIFNR QPTLHKMSMM GHRVRILPWS TFRLNLSVTT PYNADFDGDE MNLHLPQSLE TRAEIQELAM VPRMIVTPQS NRPVMGIVQD TLTAVRKFTK RDVFLERGEV MNLLMFLSTW DGKVPQPAIL KPRPLWTGKQ IFSLIIPGHI NCIRTHSTHP DDEDSGPYKH ISPGDTKVVV ENGELIMGIL CKKSLGTSAG SLVHISYLEM GHDITRLFYS NIQTVINNWL LIEGHTIGIG DSIADSKTYQ DIQNTIKKAK QDVIEVIEKA HNNELEPTPG NTLRQTFENQ VNRILNDARD KTGSSAQKSL SEYNNFKSMV VSGAKGSKIN ISQVIAVVGQ QNVEGKRIPF GFKHRTLPHF IKDDYGPESR GFVENSYLAG LTPTEFFFHA MGGREGLIDT AVKTAETGYI QRRLIKSMES VMVKYDATVR NSINQVVQLR YGEDGLAGES VEFQNLATLK PSNKAFEKKF RFDYTNERAL RRTLQEDLVK DVLSNAHIQN ELEREFERMR EDREVLRVIF PTGDSKVVLP CNLLRMIWNA QKIFHINPRL PSDLHPIKVV EGVKELSKKL VIVNGDDPLS RQAQENATLL FNIHLRSTLC SRRMAEEFRL SGEAFDWLLG EIESKFNQAI AHPGEMVGAL AAQSLGEPAT QMTLNTFHYA GVSAKNVTLG VPRLKELINI SKKPKTPSLT VFLLGQSARD AERAKDILCR LEHTTLRKVT ANTAIYYDPN PQSTVVAEDQ EWVNVYYEMP DFDVARISPW LLRVELDRKH MTDRKLTMEQ IAEKINAGFG DDLNCIFNDD NAEKLVLRIR IMNSDENKMQ EEEEVVDKMD DDVFLRCIES NMLTDMTLQG IEQISKVYMH LPQTDNKKKI IITEDGEFKA LQEWILETDG VSLMRVLSEK DVDPVRTTSN DIVEIFTVLG IEAVRKALER ELYHVISFDG SYVNYRHLAL LCDTMTCRGH LMAITRHGVN RQDTGPLMKC SFEETVDVLM EAAAHGESDP MKGVSENIML GQLAPAGTGC FDLLLDAEKC KYGMEIPTNI PGLGAAGPTG MFFGSAPSPM GGISPAMTPW NQGATPAYGA WSPSVGSGMT PGAAGFSPSA ASDASGFSPG YSPAWSPTPG SPGSPGPSSP YIPSPGGAMS PSYSPTSPAY EPRSPGGYTP QSPSYSPTSP SYSPTSPSYS PTSPNYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPNYSP TSPNYTPTSP SYSPTSPSYS PTSPNYTPTS PNYSPTSPSY SPTSPSYSPT SPSYSPSSPR YTPQSPTYTP SSPSYSPSSP SYSPTSPKYT PTSPSYSPSS PEYTPTSPKY SPTSPKYSPT SPKYSPTSPT YSPTTPKYSP TSPTYSPTSP VYTPTSPKYS PTSPTYSPTS PKYSPTSPTY SPTSPKGSTY SPTSPGYSPT SPTYSLTSPA ISPDDSDEEN

UniProtKB: DNA-directed RNA polymerase subunit

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Macromolecule #2: DNA-directed RNA polymerase II subunit POLR2B

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString: MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFEQ IYLSKPTHWE RDGAPSPMMP NEARLRNLTY SAPLYVDITK TVIKEGEEQL QTQHQKTFIG KIPIMLRSTY CLLNGLTDRD ...String:
MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFEQ IYLSKPTHWE RDGAPSPMMP NEARLRNLTY SAPLYVDITK TVIKEGEEQL QTQHQKTFIG KIPIMLRSTY CLLNGLTDRD LCELNECPLD PGGYFIINGS EKVLIAQEKM ATNTVYVFAK KDSKYAYTGE CRSCLENSSR PTSTIWVSML ARGGQGAKKS AIGQRIVATL PYIKQEVPII IVFRALGFVS DRDILEHIIY DFEDPEMMEM VKPSLDEAFV IQEQNVALNF IGSRGAKPGV TKEKRIKYAK EVLQKEMLPH VGVSDFCETK KAYFLGYMVH RLLLAALGRR ELDDRDHYGN KRLDLAGPLL AFLFRGMFKN LLKEVRIYAQ KFIDRGKDFN LELAIKTRII SDGLKYSLAT GNWGDQKKAH QARAGVSQVL NRLTFASTLS HLRRLNSPIG RDGKLAKPRQ LHNTLWGMVC PAETPEGHAV GLVKNLALMA YISVGSQPSP ILEFLEEWSM ENLEEISPAA IADATKIFVN GCWVGIHKDP EQLMNTLRKL RRQMDIIVSE VSMIRDIRER EIRIYTDAGR ICRPLLIVEK QKLLLKKRHI DQLKEREYNN YSWQDLVASG VVEYIDTLEE ETVMLAMTPD DLQEKEVAYC STYTHCEIHP SMILGVCASI IPFPDHNQSP RNTYQSAMGK QAMGVYITNF HVRMDTLAHV LYYPQKPLVT TRSMEYLRFR ELPAGINSIV AIASYTGYNQ EDSVIMNRSA VDRGFFRSVF YRSYKEQESK KGFDQEEVFE KPTRETCQGM RHAIYDKLDD DGLIAPGVRV SGDDVIIGKT VTLPENEDEL EGTNRRYTKR DCSTFLRTSE TGIVDQVMVT LNQEGYKFCK IRVRSVRIPQ IGDKFASRHG QKGTCGIQYR QEDMPFTCEG ITPDIIINPH AIPSRMTIGH LIECLQGKVS ANKGEIGDAT PFNDAVNVQK ISNLLSDYGY HLRGNEVLYN GFTGRKITSQ IFIGPTYYQR LKHMVDDKIH SRARGPIQIL NRQPMEGRSR DGGLRFGEME RDCQIAHGAA QFLRERLFEA SDPYQVHVCN LCGIMAIANT RTHTYECRGC RNKTQISLVR MPYACKLLFQ ELMSMSIAPR MMSV

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase II subunit POLR2C

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString: MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL ISNSPRVIPV TSRNRDNDPS DYVEQDDILI VKLRKGQELR LRAYAKKGFG ...String:
MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL ISNSPRVIPV TSRNRDNDPS DYVEQDDILI VKLRKGQELR LRAYAKKGFG KEHAKWNPTA GVAFEYDPDN ALRHTVYPKP EEWPKSEYSE LDEDESQAPY DPNGKPERFY YNVESCGSLR PETIVLSALS GLKKKLSDLQ TQLSHEIQSD VLTIN

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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Macromolecule #4: DNA-directed RNA polymerase II subunit POLR2D

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2D / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHKFELACL ANLCPETAEE SKALIPSLEG RFEDEELQQI LDDIQTKRSF QY

UniProtKB: RNA polymerase II subunit D

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Macromolecule #5: DNA-directed RNA polymerase II subunit POLR2E

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2E / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD MAPKYILEQF LQQELLINIT EHELVPEHVV MTKEEVTELL ARYKLRENQL ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD MAPKYILEQF LQQELLINIT EHELVPEHVV MTKEEVTELL ARYKLRENQL PRIQAGDPVA RYFGIKRGQV VKIIRPSETA GRYITYRLVQ

UniProtKB: DNA-directed RNA polymerase II subunit E

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Macromolecule #6: DNA-directed RNA polymerase II subunit POLR2F

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2F / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDPL LIAMKELKAR KIPIIIRRYL PDGSYEDWGV DELIISD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #7: DNA-directed RNA polymerase II subunit POLR2G

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2G / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVVT QVNKVGLFTE IGPMSCFISR HSIPSEMEFD PNSNPPCYKT MDEDIVIQQD DEIRLKIVGT RVDKNDIFAI GSLMDDYLGL VS

UniProtKB: DNA-directed RNA polymerase subunit

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Macromolecule #8: DNA-directed RNA polymerase II subunit POLR2H

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2H / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFEY VMYGKVYRIE GDETSTEAAT RLSAYVSYGG LLMRLQGDAN NLHGFEVDSR VYLLMKKLAF

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

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Macromolecule #9: DNA-directed RNA polymerase II subunit POLR2I

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2I / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKCG HKEAVFFQSH SARAEDAMRL YYVCTAPHCG HRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #10: DNA-directed RNA polymerase II subunit POLR2L

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2L / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

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Macromolecule #11: DNA-directed RNA polymerase II subunit POLR2J

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2J / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTNA ITDLISELSL LEERFRVAIK DKQEGIE

UniProtKB: DNA-directed RNA polymerase II subunit RPB11-a

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Macromolecule #12: DNA-directed RNA polymerase II subunit POLR2K

MacromoleculeName: DNA-directed RNA polymerase II subunit POLR2K / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Thymus
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

UniProtKB: RNA polymerase II, I and III subunit K

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Macromolecule #13: Alu RNA Left Arm

MacromoleculeName: Alu RNA Left Arm / type: rna / ID: 13
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GGCCGGGCGC GGUGGCUCAC GCCUGUAAUC CCAGCACUUU GGGAGGCCGA GGCGGGCGGA UCACAAGGUC AGGAGAUCGA GACCAUCCUG GCUAACACAG UGAAACCCCG UCUCUACU

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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

Concentration0.2 mg/mL
BufferpH: 7.25
Component:
ConcentrationNameFormula
5.0 mMHEPES
50.0 mMNaClNaCl
0.01 mMZnCl2ZnCl2
10.0 mMDTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.07 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 16470 / Average exposure time: 2.14 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 1402832
Startup modelType of model: EMDB MAP
EMDB ID:

3218

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 152647
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementOverall B value: 40.63

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