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- EMDB-13130: RNA Polymerase II dimer (Class 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-13130
TitleRNA Polymerase II dimer (Class 2)
Map dataSharpened and local resolution filtered map
Sample
  • Complex: RNA Polymerase II dimer
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
Function / homology
Function and homology information


RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 2 Promoter / B-WICH complex positively regulates rRNA expression / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / mRNA Splicing - Major Pathway / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes ...RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 2 Promoter / B-WICH complex positively regulates rRNA expression / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / mRNA Splicing - Major Pathway / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / Estrogen-dependent gene expression / TP53 Regulates Transcription of DNA Repair Genes / mRNA Capping / Formation of the Early Elongation Complex / Processing of Capped Intron-Containing Pre-mRNA / Formation of RNA Pol II elongation complex / mRNA Splicing - Minor Pathway / RNA Polymerase II Transcription Elongation / Transcriptional regulation by small RNAs / RNA Polymerase II Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA Pol II CTD phosphorylation and interaction with CE / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / Formation of TC-NER Pre-Incision Complex / nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / RPAP3/R2TP/prefoldin-like complex / organelle membrane / mRNA export from nucleus in response to heat stress / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II activity / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / translation initiation factor binding / transcription initiation from RNA polymerase II promoter / P-body / ribonucleoside binding / transcription by RNA polymerase II / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / fibrillar center / single-stranded DNA binding / single-stranded RNA binding / nucleic acid binding / nuclear speck / transcription, DNA-templated / protein dimerization activity / nucleotide binding / nucleolus / DNA binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA-directed RNA polymerase II subunit Rpb4-like / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 ...DNA-directed RNA polymerase II subunit Rpb4-like / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases H / 23 Kd subunits signature. / : / : / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, subunit H/Rpb5, conserved site / RPB5-like RNA polymerase subunit superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / S1 RNA binding domain / RNA-binding domain, S1 / Ribosomal protein S1-like RNA-binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb3/RpoA insert domain / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerases D / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, beta subunit, conserved site / RNA polymerases beta chain signature. / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, domain 6 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerase II subunit E / RNA polymerase II subunit K / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit J / RNA polymerase II subunit D / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB9
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig) / domestic pig (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAibara S / Dienemann C / Cramer P
Funding support Germany, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)CHROMATRANS 882357 Germany
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Structure of an inactive RNA polymerase II dimer.
Authors: Shintaro Aibara / Christian Dienemann / Patrick Cramer /
Abstract: Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two ...Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two other RNA polymerases dimerize. Here we present the cryo-electron microscopy (cryo-EM) structure of a mammalian Pol II dimer at 3.5 Å resolution. The structure differs from the Pol I dimer and reveals that one Pol II copy uses its RPB4-RPB7 stalk to penetrate the active centre cleft of the other copy, and vice versa, giving rise to a molecular handshake. The polymerase clamp domain is displaced and mobile, and the RPB7 oligonucleotide-binding fold mimics the DNA-RNA hybrid that occupies the cleft during active transcription. The Pol II dimer is incompatible with nucleic acid binding as required for transcription and may represent an inactive storage form of the polymerase.
History
DepositionJun 28, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ozo
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_13130.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened and local resolution filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 450 pix.
= 367.65 Å
0.82 Å/pix.
x 450 pix.
= 367.65 Å
0.82 Å/pix.
x 450 pix.
= 367.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.817 Å
Density
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-20.160208 - 39.0475
Average (Standard dev.)-0.00053653866 (±0.9347262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 367.65 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8170.8170.817
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z367.650367.650367.650
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-20.16039.048-0.001

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Supplemental data

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Mask #1

Fileemd_13130_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Local resolution filtered map

Fileemd_13130_additional_1.map
AnnotationLocal resolution filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Sharpened and local resolution filtered map, symmetry expanded

Fileemd_13130_additional_2.map
AnnotationSharpened and local resolution filtered map, symmetry expanded
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1

Fileemd_13130_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 2

Fileemd_13130_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Sample components

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Entire : RNA Polymerase II dimer

EntireName: RNA Polymerase II dimer
Components
  • Complex: RNA Polymerase II dimer
    • Protein or peptide: DNA-directed RNA polymerase subunitPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3Polymerase
    • Protein or peptide: RNA polymerase II subunit D
    • Protein or peptide: DNA-directed RNA polymerase II subunit EPolymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit FPolymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
    • Protein or peptide: RNA_pol_L_2 domain-containing protein
    • Protein or peptide: RNA polymerase II subunit K
  • Ligand: ZINC ION

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Supramolecule #1: RNA Polymerase II dimer

SupramoleculeName: RNA Polymerase II dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Sus scrofa domesticus (domestic pig)
Molecular weightTheoretical: 1.1 MDa

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Macromolecule #1: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 217.450078 KDa
SequenceString: MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ ...String:
MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ PEGDEDLTKE KGHGGCGRYQ PRIRRSGLEL YAEWKHVNED SQEKKILLSP ERVHEIFKRI SDEECFVLGM EP RYARPEW MIVTVLPVPP LSVRPAVVMQ GSARNQDDLT HKLADIVKIN NQLRRNEQNG AAAHVIAEDV KLLQFHVATM VDN ELPGLP RAMQKSGRPL KSLKQRLKGK EGRVRGNLMG KRVDFSARTV ITPDPNLSID QVGVPRSIAA NMTFAEIVTP FNID RLQEL VRRGNSQYPG AKYIIRDNGD RIDLRFHPKP SDLHLQTGYK VERHMCDGDI VIFNRQPTLH KMSMMGHRVR ILPWS TFRL NLSVTTPYNA DFDGDEMNLH LPQSLETRAE IQELAMVPRM IVTPQSNRPV MGIVQDTLTA VRKFTKRDVF LERGEV MNL LMFLSTWDGK VPQPAILKPR PLWTGKQIFS LIIPGHINCI RTHSTHPDDE DSGPYKHISP GDTKVVVENG ELIMGIL CK KSLGTSAGSL VHISYLEMGH DITRLFYSNI QTVINNWLLI EGHTIGIGDS IADSKTYQDI QNTIKKAKQD VIEVIEKA H NNELEPTPGN TLRQTFENQV NRILNDARDK TGSSAQKSLS EYNNFKSMVV SGAKGSKINI SQVIAVVGQQ NVEGKRIPF GFKHRTLPHF IKDDYGPESR GFVENSYLAG LTPTEFFFHA MGGREGLIDT AVKTAETGYI QRRLIKSMES VMVKYDATVR NSINQVVQL RYGEDGLAGE SVEFQNLATL KPSNKAFEKK FRFDYTNERA LRRTLQEDLV KDVLSNAHIQ NELEREFERM R EDREVLRV IFPTGDSKVV LPCNLLRMIW NAQKIFHINP RLPSDLHPIK VVEGVKELSK KLVIVNGDDP LSRQAQENAT LL FNIHLRS TLCSRRMAEE FRLSGEAFDW LLGEIESKFN QAIAHPGEMV GALAAQSLGE PATQMTLNTF HYAGVSAKNV TLG VPRLKE LINISKKPKT PSLTVFLLGQ SARDAERAKD ILCRLEHTTL RKVTANTAIY YDPNPQSTVV AEDQEWVNVY YEMP DFDVA RISPWLLRVE LDRKHMTDRK LTMEQIAEKI NAGFGDDLNC IFNDDNAEKL VLRIRIMNSD ENKMQEEEEV VDKMD DDVF LRCIESNMLT DMTLQGIEQI SKVYMHLPQT DNKKKIIITE DGEFKALQEW ILETDGVSLM RVLSEKDVDP VRTTSN DIV EIFTVLGIEA VRKALERELY HVISFDGSYV NYRHLALLCD TMTCRGHLMA ITRHGVNRQD TGPLMKCSFE ETVDVLM EA AAHGESDPMK GVSENIMLGQ LAPAGTGCFD LLLDAEKCKY GMEIPTNIPG LGAAGPTGMF FGSAPSPMGG ISPAMTPW N QGATPAYGAW SPSVGSGMTP GAAGFSPSAA SDASGFSPGY SPAWSPTPGS PGSPGPSSPY IPSPGGAMSP SYSPTSPAY EPRSPGGYTP QSPSYSPTSP SYSPTSPSYS PTSPNYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPNYS PTSPNYTPTS P SYSPTSPS YSPTSPNYTP TSPNYSPTSP SYSPTSPSYS PTSPSYSPSS PRYTPQSPTY TPSSPSYSPS SPSYSPTSPK YT PTSPSYS PSSPEYTPTS PKYSPTSPKY SPTSPKYSPT SPTYSPTTPK YSPTSPTYSP TSPVYTPTSP KYSPTSPTYS PTS PKYSPT SPTYSPTSPK GSTYSPTSPG YSPTSPTYSL TSPAISPDDS DEEN

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 134.041422 KDa
SequenceString: MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFE QIYLSKPTHW ERDGAPSPMM PNEARLRNLT YSAPLYVDIT KTVIKEGEEQ LQTQHQKTFI GKIPIMLRST Y CLLNGLTD ...String:
MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFE QIYLSKPTHW ERDGAPSPMM PNEARLRNLT YSAPLYVDIT KTVIKEGEEQ LQTQHQKTFI GKIPIMLRST Y CLLNGLTD RDLCELNECP LDPGGYFIIN GSEKVLIAQE KMATNTVYVF AKKDSKYAYT GECRSCLENS SRPTSTIWVS ML ARGGQGA KKSAIGQRIV ATLPYIKQEV PIIIVFRALG FVSDRDILEH IIYDFEDPEM MEMVKPSLDE AFVIQEQNVA LNF IGSRGA KPGVTKEKRI KYAKEVLQKE MLPHVGVSDF CETKKAYFLG YMVHRLLLAA LGRRELDDRD HYGNKRLDLA GPLL AFLFR GMFKNLLKEV RIYAQKFIDR GKDFNLELAI KTRIISDGLK YSLATGNWGD QKKAHQARAG VSQVLNRLTF ASTLS HLRR LNSPIGRDGK LAKPRQLHNT LWGMVCPAET PEGHAVGLVK NLALMAYISV GSQPSPILEF LEEWSMENLE EISPAA IAD ATKIFVNGCW VGIHKDPEQL MNTLRKLRRQ MDIIVSEVSM IRDIREREIR IYTDAGRICR PLLIVEKQKL LLKKRHI DQ LKEREYNNYS WQDLVASGVV EYIDTLEEET VMLAMTPDDL QEKEVAYCST YTHCEIHPSM ILGVCASIIP FPDHNQSP R NTYQSAMGKQ AMGVYITNFH VRMDTLAHVL YYPQKPLVTT RSMEYLRFRE LPAGINSIVA IASYTGYNQE DSVIMNRSA VDRGFFRSVF YRSYKEQESK KGFDQEEVFE KPTRETCQGM RHAIYDKLDD DGLIAPGVRV SGDDVIIGKT VTLPENEDEL EGTNRRYTK RDCSTFLRTS ETGIVDQVMV TLNQEGYKFC KIRVRSVRIP QIGDKFASRH GQKGTCGIQY RQEDMPFTCE G ITPDIIIN PHAIPSRMTI GHLIECLQGK VSANKGEIGD ATPFNDAVNV QKISNLLSDY GYHLRGNEVL YNGFTGRKIT SQ IFIGPTY YQRLKHMVDD KIHSRARGPI QILNRQPMEG RSRDGGLRFG EMERDCQIAH GAAQFLRERL FEASDPYQVH VCN LCGIMA IANTRTHTYE CRGCRNKTQI SLVRMPYACK LLFQELMSMS IAPRMMSV

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Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 31.439074 KDa
SequenceString: MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG ...String:
MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG FGKEHAKWNP TAGVAFEYDP DNALRHTVYP KPEEWPKSEY SELDEDESQA PYDPNGKPER FYYNVESCGS LR PETIVLS ALSGLKKKLS DLQTQLSHEI QSDVLTIN

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Macromolecule #4: RNA polymerase II subunit D

MacromoleculeName: RNA polymerase II subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 16.331255 KDa
SequenceString:
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQ KKLHKFELAC LANLCPETAE ESKALIPSLE GRFEDEELQQ ILDDIQTKRS FQY

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

MacromoleculeName: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 24.644318 KDa
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN QLPRIQAGDP VARYFGIKRG QVVKIIRPSE TAGRYITYRL VQ

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

MacromoleculeName: DNA-directed RNA polymerase II subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 14.477001 KDa
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIISD

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Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 19.314283 KDa
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF DPNSNPPCYK TMDEDIVIQQ DDEIRLKIVG TRVDKNDIFA I GSLMDDYL GLVS

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Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 17.162273 KDa
SequenceString:
MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG GLLMRLQGDA NNLHGFEVDS RVYLLMKKLA F

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Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 14.541221 KDa
SequenceString:
MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC GHRWTE

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Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 7.655123 KDa
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

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Macromolecule #11: RNA_pol_L_2 domain-containing protein

MacromoleculeName: RNA_pol_L_2 domain-containing protein / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 13.310284 KDa
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTN AITDLISELS LLEERFRVAI KDKQEGIE

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Macromolecule #12: RNA polymerase II subunit K

MacromoleculeName: RNA polymerase II subunit K / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: domestic pig (domestic pig)
Molecular weightTheoretical: 7.018244 KDa
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 10 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47091
FSC plot (resolution estimation)

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