[English] 日本語
Yorodumi
- EMDB-31878: Back track state of human RNA Polymerase I Elongation Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31878
TitleBack track state of human RNA Polymerase I Elongation Complex
Map data
Sample
  • Complex: back track state of human RNA Polymerase I Elongation Complex
    • Protein or peptide: x 13 types
    • RNA: x 1 types
    • DNA: x 2 types
  • Ligand: x 2 types
KeywordsRNA Polymerase I / transcription / back track state / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


RNA polymerase I transcription regulator complex / negative regulation of protein localization to nucleolus / nucleologenesis / neural crest formation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / RNA polymerase I general transcription initiation factor binding ...RNA polymerase I transcription regulator complex / negative regulation of protein localization to nucleolus / nucleologenesis / neural crest formation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / RNA polymerase I general transcription initiation factor binding / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase I preinitiation complex assembly / Abortive elongation of HIV-1 transcript in the absence of Tat / nucleobase-containing compound metabolic process / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / Viral Messenger RNA Synthesis / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase III activity / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / rRNA transcription / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Processing of Capped Intron-Containing Pre-mRNA / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / cell surface receptor protein tyrosine kinase signaling pathway / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / embryo implantation / mRNA Splicing - Major Pathway / protein-DNA complex / cellular response to leukemia inhibitory factor / DNA-templated transcription initiation / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / chromosome / Estrogen-dependent gene expression / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / protein stabilization / chromatin binding / nucleolus / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RPA43, OB domain / RPA43 OB domain in RNA Pol I / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / Pol I subunit A12, C-terminal zinc ribbon ...DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RPA43, OB domain / RPA43 OB domain in RNA Pol I / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / Pol I subunit A12, C-terminal zinc ribbon / : / RNA polymerase I, Rpa2 specific domain / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Zinc finger TFIIS-type signature. / 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 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature.
Similarity search - Domain/homology
DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA1 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit RPA43 ...DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA1 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerase I subunit RPA49 / DNA-directed RNA polymerase I subunit RPA2 / DNA-directed RNA polymerase I subunit RPA12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsZhao D / Liu W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2021
Title: Structure of the human RNA polymerase I elongation complex.
Authors: Dan Zhao / Weida Liu / Ke Chen / Zihan Wu / Huirong Yang / Yanhui Xu /
Abstract: Eukaryotic RNA polymerase I (Pol I) transcribes ribosomal DNA and generates RNA for ribosome synthesis. Pol I accounts for the majority of cellular transcription activity and dysregulation of Pol I ...Eukaryotic RNA polymerase I (Pol I) transcribes ribosomal DNA and generates RNA for ribosome synthesis. Pol I accounts for the majority of cellular transcription activity and dysregulation of Pol I transcription leads to cancers and ribosomopathies. Despite extensive structural studies of yeast Pol I, structure of human Pol I remains unsolved. Here we determined the structures of the human Pol I in the pre-translocation, post-translocation, and backtracked states at near-atomic resolution. The single-subunit peripheral stalk lacks contacts with the DNA-binding clamp and is more flexible than the two-subunit stalk in yeast Pol I. Compared to yeast Pol I, human Pol I possesses a more closed clamp, which makes more contacts with DNA. The Pol I structure in the post-cleavage backtracked state shows that the C-terminal zinc ribbon of RPA12 inserts into an open funnel and facilitates "dinucleotide cleavage" on mismatched DNA-RNA hybrid. Critical disease-associated mutations are mapped on Pol I regions that are involved in catalysis and complex organization. In summary, the structures provide new sights into human Pol I complex organization and efficient proofreading.
History
DepositionAug 31, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7vbc
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31878.png

Downloads & links

-
Map

FileDownload / File: emd_31878.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.575 / Movie #1: 0.5
Minimum - Maximum-2.3440902 - 3.9767025
Average (Standard dev.)-0.0008271679 (±0.11168464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0541.0541.054
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z337.280337.280337.280
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.3443.977-0.001

-
Supplemental data

-
Sample components

+
Entire : back track state of human RNA Polymerase I Elongation Complex

EntireName: back track state of human RNA Polymerase I Elongation Complex
Components
  • Complex: back track state of human RNA Polymerase I Elongation Complex
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA1
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA2
    • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC1
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC2
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA34
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA43
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA49
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA12
    • RNA: RNA (5'-R(P*UP*GP*CP*UP*GP*A)-3')
    • DNA: DNA (5'-D(P*AP*GP*GP*AP*CP*AP*GP*CP*GP*TP*GP*TP*CP*AP*GP*CP*AP*AP*TP*A)-3')
    • DNA: DNA (5'-D(*GP*TP*AP*CP*TP*GP*TP*CP*CP*TP*CP*TP*GP*G)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: back track state of human RNA Polymerase I Elongation Complex

SupramoleculeName: back track state of human RNA Polymerase I Elongation Complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: DNA-directed RNA polymerase I subunit RPA1

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 194.911859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLISKNMPWR RLQGISFGMY SAEELKKLSV KSITNPRYLD SLGNPSANGL YDLALGPADS KEVCSTCVQD FSNCSGHLGH IELPLTVYN PLLFDKLYLL LRGSCLNCHM LTCPRAVIHL LLCQLRVLEV GALQAVYELE RILNRFLEEN PDPSASEIRE E LEQYTTEI ...String:
MLISKNMPWR RLQGISFGMY SAEELKKLSV KSITNPRYLD SLGNPSANGL YDLALGPADS KEVCSTCVQD FSNCSGHLGH IELPLTVYN PLLFDKLYLL LRGSCLNCHM LTCPRAVIHL LLCQLRVLEV GALQAVYELE RILNRFLEEN PDPSASEIRE E LEQYTTEI VQNNLLGSQG AHVKNVCESK SKLIALFWKA HMNAKRCPHC KTGRSVVRKE HNSKLTITFP AMVHRTAGQK DS EPLGIEE AQIGKRGYLT PTSAREHLSA LWKNEGFFLN YLFSGMDDDG MESRFNPSVF FLDFLVVPPS RYRPVSRLGD QMF TNGQTV NLQAVMKDVV LIRKLLALMA QEQKLPEEVA TPTTDEEKDS LIAIDRSFLS TLPGQSLIDK LYNIWIRLQS HVNI VFDSE MDKLMMDKYP GIRQILEKKE GLFRKHMMGK RVDYAARSVI CPDMYINTNE IGIPMVFATK LTYPQPVTPW NVQEL RQAV INGPNVHPGA SMVINEDGSR TALSAVDMTQ REAVAKQLLT PATGAPKPQG TKIVCRHVKN GDILLLNRQP TLHRPS IQA HRARILPEEK VLRLHYANCK AYNADFDGDE MNAHFPQSEL GRAEAYVLAC TDQQYLVPKD GQPLAGLIQD HMVSGAS MT TRGCFFTREH YMELVYRGLT DKVGRVKLLS PSILKPFPLW TGKQVVSTLL INIIPEDHIP LNLSGKAKIT GKAWVKET P RSVPGFNPDS MCESQVIIRE GELLCGVLDK AHYGSSAYGL VHCCYEIYGG ETSGKVLTCL ARLFTAYLQL YRGFTLGVE DILVKPKADV KRQRIIEEST HCGPQAVRAA LNLPEAASYD EVRGKWQDAH LGKDQRDFNM IDLKFKEEVN HYSNEINKAC MPFGLHRQF PENSLQMMVQ SGAKGSTVNT MQISCLLGQI ELEGRRPPLM ASGKSLPCFE PYEFTPRAGG FVTGRFLTGI K PPEFFFHC MAGREGLVDT AVKTSRSGYL QRCIIKHLEG LVVQYDLTVR DSDGSVVQFL YGEDGLDIPK TQFLQPKQFP FL ASNYEVI MKSQHLHEVL SRADPKKALH HFRAIKKWQS KHPNTLLRRG AFLSYSQKIQ EAVKALKLES ENRNGRSPGT QEM LRMWYE LDEESRRKYQ KKAAACPDPS LSVWRPDIYF ASVSETFETK VDDYSQEWAA QTEKSYEKSE LSLDRLRTLL QLKW QRSLC EPGEAVGLLA AQSIGEPSTQ MTLNTFHFAG RGEMNVTLGI PRLREILMVA SANIKTPMMS VPVLNTKKAL KRVKS LKKQ LTRVCLGEVL QKIDVQESFC MEEKQNKFQV YQLRFQFLPH AYYQQEKCLR PEDILRFMET RFFKLLMESI KKKNNK ASA FRNVNTRRAT QRDLDNAGEL GRSRGEQEGD EEEEGHIVDA EAEEGDADAS DAKRKEKQEE EVDYESEEEE EREGEEN DD EDMQEERNPH REGARKTQEQ DEEVGLGTEE DPSLPALLTQ PRKPTHSQEP QGPEAMERRV QAVREIHPFI DDYQYDTE E SLWCQVTVKL PLMKINFDMS SLVVSLAHGA VIYATKGITR CLLNETTNNK NEKELVLNTE GINLPELFKY AEVLDLRRL YSNDIHAIAN TYGIEAALRV IEKEIKDVFA VYGIAVDPRH LSLVADYMCF EGVYKPLNRF GIRSNSSPLQ QMTFETSFQF LKQATMLGS HDELRSPSAC LVVGKVVRGG TGLFELKQPL

UniProtKB: DNA-directed RNA polymerase I subunit RPA1

+
Macromolecule #2: DNA-directed RNA polymerase I subunit RPA2

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 128.379219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDPGSRWRNL PSGPSLKHLT DPSYGIPREQ QKAALQELTR AHVESFNYAV HEGLGLAVQA IPPFEFAFKD ERISFTILDA VISPPTVPK GTICKEANVY PAECRGRRST YRGKLTADIN WAVNGISKGI IKQFLGYVPI MVKSKLCNLR NLPPQALIEH H EEAEEMGG ...String:
MDPGSRWRNL PSGPSLKHLT DPSYGIPREQ QKAALQELTR AHVESFNYAV HEGLGLAVQA IPPFEFAFKD ERISFTILDA VISPPTVPK GTICKEANVY PAECRGRRST YRGKLTADIN WAVNGISKGI IKQFLGYVPI MVKSKLCNLR NLPPQALIEH H EEAEEMGG YFIINGIEKV IRMLIMPRRN FPIAMIRPKW KTRGPGYTQY GVSMHCVREE HSAVNMNLHY LENGTVMLNF IY RKELFFL PLGFALKALV SFSDYQIFQE LIKGKEDDSF LRNSVSQMLR IVMEEGCSTQ KQVLNYLGEC FRVKLNVPDW YPN EQAAEF LFNQCICIHL KSNTEKFYML CLMTRKLFAL AKGECMEDNP DSLVNQEVLT PGQLFLMFLK EKLEGWLVSI KIAF DKKAQ KTSVSMNTDN LMRIFTMGID LTKPFEYLFA TGNLRSKTGL GLLQDSGLCV VADKLNFIRY LSHFRCVHRG ADFAK MRTT TVRRLLPESW GFLCPVHTPD GEPCGLMNHL TAVCEVVTQF VYTASIPALL CNLGVTPIDG APHRSYSECY PVLLDG VMV GWVDKDLAPG IADSLRHFKV LREKRIPPWM EVVLIPMTGK PSLYPGLFLF TTPCRLVRPV QNLALGKEEL IGTMEQI FM NVAIFEDEVF AGVTTHQELF PHSLLSVIAN FIPFSDHNQS PRNMYQCQMG KQTMGFPLLT YQDRSDNKLY RLQTPQSP L VRPSMYDYYD MDNYPIGTNA IVAVISYTGY DMEDAMIVNK ASWERGFAHG SVYKSEFIDL SEKIKQGDSS LVFGIKPGD PRVLQKLDDD GLPFIGAKLQ YGDPYYSYLN LNTGESFVMY YKSKENCVVD NIKVCSNDTG SGKFKCVCIT MRVPRNPTIG DKFASRHGQ KGILSRLWPA EDMPFTESGM VPDILFNPHG FPSRMTIGML IESMAGKSAA LHGLCHDATP FIFSEENSAL E YFGEMLKA AGYNFYGTER LYSGISGLEL EADIFIGVVY YQRLRHMVSD KFQVRTTGAR DRVTNQPIGG RNVQGGIRFG EM ERDALLA HGTSFLLHDR LFNCSDRSVA HVCVKCGSLL SPLLEKPPPS WSAMRNRKYN CTLCSRSDTI DTVSVPYVFR YFV AELAAM NIKVKLDVV

UniProtKB: DNA-directed RNA polymerase I subunit RPA2

+
Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.301672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAASQAVEEM RSRVVLGEFG VRNVHTTDFP GNYSGYDDAW DQDRFEKNFR VDVVHMDENS LEFDMVGIDA AIANAFRRIL LAEVPTMAV EKVLVYNNTS IVQDEILAHR LGLIPIHADP RLFEYRNQGD EEGTEIDTLQ FRLQVRCTRN PHAAKDSSDP N ELYVNHKV ...String:
MAASQAVEEM RSRVVLGEFG VRNVHTTDFP GNYSGYDDAW DQDRFEKNFR VDVVHMDENS LEFDMVGIDA AIANAFRRIL LAEVPTMAV EKVLVYNNTS IVQDEILAHR LGLIPIHADP RLFEYRNQGD EEGTEIDTLQ FRLQVRCTRN PHAAKDSSDP N ELYVNHKV YTRHMTWIPL GNQADLFPEG TIRPVHDDIL IAQLRPGQEI DLLMHCVKGI GKDHAKFSPV ATASYRLLPD IT LLEPVEG EAAEELSRCF SPGVIEVQEV QGKKVARVAN PRLDTFSREI FRNEKLKKVV RLARVRDHYI FSVESTGVLP PDV LVSEAI KVLMGKCRRF LDELDAVQMD

UniProtKB: DNA-directed RNA polymerases I and III subunit RPAC1

+
Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.584223 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQSGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQSGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN QLPRIQAGDP VARYFGIKRG QVVKIIRPSE TAGRYITYRL VQ

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

+
Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.491026 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIITD

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

+
Macromolecule #6: 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: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.162273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG GLLMRLQGDA NNLHGFEVDS RVYLLMKKLA F

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

+
Macromolecule #7: 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: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.655123 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

+
Macromolecule #8: DNA-directed RNA polymerases I and III subunit RPAC2

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.259222 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEEDQELERK ISGLKTSMAE GERKTALEMV QAAGTDRHCV TFVLHEEDHT LGNSLRYMIM KNPEVEFCGY TTTHPSESKI NLRIQTRGT LPAVEPFQRG LNELMNVCQH VLDKFEASIK DYKDQKASRN ESTF

UniProtKB: DNA-directed RNA polymerases I and III subunit RPAC2

+
Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.018244 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

+
Macromolecule #10: DNA-directed RNA polymerase I subunit RPA34

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA34 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.065523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEPQAGDAA RFSCPPNFTA KPPASESPRF SLEALTGPDT ELWLIQAPAD FAPECFNGRH VPLSGSQIVK GKLAGKRHRY RVLSSCPQA GEATLLAPST EAGGGLTCAS APQGTLRILE GPQQSLSGSP LQPIPASPPP QIPPGLRPRF CAFGGNPPVT G PRSALAPN ...String:
MEEPQAGDAA RFSCPPNFTA KPPASESPRF SLEALTGPDT ELWLIQAPAD FAPECFNGRH VPLSGSQIVK GKLAGKRHRY RVLSSCPQA GEATLLAPST EAGGGLTCAS APQGTLRILE GPQQSLSGSP LQPIPASPPP QIPPGLRPRF CAFGGNPPVT G PRSALAPN LLTSGKKKKE MQVTEAPVTQ EAVNGHGALE VDMALGSPEM DVRKKKKKKN QQLKEPEAAG PVGTEPTVET LE PLGVLFP STTKKRKKPK GKETFEPEDK TVKQEQINTE PLEDTVLSPT KKRKRQKGTE GMEPEEGVTV ESQPQVKVEP LEE AIPLPP TKKRKKEKGQ MAMMEPGTEA MEPVEPEMKP LESPGGTMAP QQPEGAKPQA QAALAAPKKK TKKEKQQDAT VEPE TEVVG PELPDDLEPQ AAPTSTKKKK KKKERGHTVT EPIQPLEPEL PGEGQPEARA TPGSTKKRKK QSQESRMPET VPQEE MPGP PLNSESGEEA PTGRDKKRKQ QQQQPV

UniProtKB: DNA-directed RNA polymerase I subunit RPA34

+
Macromolecule #11: DNA-directed RNA polymerase I subunit RPA43

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA43 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.490379 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGCSEAPR PAAASDGSLV GQAGVLPCLE LPTYAAACAL VNSRYSCLVA GPHQRHIALS PRYLNRKRTG IREQLDAELL RYSESLLGV PIAYDNIKVV GELGDIYDDQ GHIHLNIEAD FVIFCPEPGQ KLMGIVNKVS SSHIGCLVHG CFNASIPKPE Q LSAEQWQT ...String:
MAAGCSEAPR PAAASDGSLV GQAGVLPCLE LPTYAAACAL VNSRYSCLVA GPHQRHIALS PRYLNRKRTG IREQLDAELL RYSESLLGV PIAYDNIKVV GELGDIYDDQ GHIHLNIEAD FVIFCPEPGQ KLMGIVNKVS SSHIGCLVHG CFNASIPKPE Q LSAEQWQT MEINMGDELE FEVFRLDSDA AGVFCIRGKL NITSLQFKRS EVSEEVTENG TEEAAKKPKK KKKKKDPETY EV DSGTTKL ADDADDTPME ESALQNTNNA NGIWEEEPKK KKKKKKHQEV QDQDPVFQGS DSSGYQSDHK KKKKKRKHSE EAE FTPPLK CSPKRKGKSN FL

UniProtKB: DNA-directed RNA polymerase I subunit RPA43

+
Macromolecule #12: DNA-directed RNA polymerase I subunit RPA49

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA49 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.330234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAEVLPSAR WQYCGAPDGS QRAVLVQFSN GKLQSPGNMR FTLYENKDST NPRKRNQRIL AAETDRLSYV GNNFGTGALK CNTLCRHFV GILNKTSGQM EVYDAELFNM QPLFSDVSVE SELALESQTK TYREKMDSCI EAFGTTKQKR ALNTRRMNRV G NESLNRAV ...String:
MAAEVLPSAR WQYCGAPDGS QRAVLVQFSN GKLQSPGNMR FTLYENKDST NPRKRNQRIL AAETDRLSYV GNNFGTGALK CNTLCRHFV GILNKTSGQM EVYDAELFNM QPLFSDVSVE SELALESQTK TYREKMDSCI EAFGTTKQKR ALNTRRMNRV G NESLNRAV AKAAETIIDT KGVTALVSDA IHNDLQDDSL YLPPCYDDAA KPEDVYKFED LLSPAEYEAL QSPSEAFRNV TS EEILKMI EENSHCTFVI EALKSLPSDV ESRDRQARCI WFLDTLIKFR AHRVVKRKSA LGPGVPHIIN TKLLKHFTCL TYN NGRLRN LISDSMKAKI TAYVIILALH IHDFQIDLTV LQRDLKLSEK RMMEIAKAMR LKISKRRVSV AAGSEEDHKL GTLS LPLPP AQTSDRLAKR RKIT

UniProtKB: DNA-directed RNA polymerase I subunit RPA49

+
Macromolecule #13: DNA-directed RNA polymerase I subunit RPA12

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA12 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.917695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSVMDLANTC SSFQSDLDFC SDCGSVLPLP GAQDTVTCIR CGFNINVRDF EGKVVKTSVV FHQLGTAMPM SVEEGPECQG PVVDRRCPR CGHEGMAYHT RQMRSADEGQ TVFYTCTNCK FQEKEDS

UniProtKB: DNA-directed RNA polymerase I subunit RPA12

+
Macromolecule #14: RNA (5'-R(P*UP*GP*CP*UP*GP*A)-3')

MacromoleculeName: RNA (5'-R(P*UP*GP*CP*UP*GP*A)-3') / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.892173 KDa
SequenceString:
UGCUGA

+
Macromolecule #15: DNA (5'-D(P*AP*GP*GP*AP*CP*AP*GP*CP*GP*TP*GP*TP*CP*AP*GP*CP*AP*AP...

MacromoleculeName: DNA (5'-D(P*AP*GP*GP*AP*CP*AP*GP*CP*GP*TP*GP*TP*CP*AP*GP*CP*AP*AP*TP*A)-3')
type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.192031 KDa
SequenceString:
(DA)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DT) (DG)(DT)(DC)(DA)(DG)(DC)(DA)(DA)(DT)(DA)

+
Macromolecule #16: DNA (5'-D(*GP*TP*AP*CP*TP*GP*TP*CP*CP*TP*CP*TP*GP*G)-3')

MacromoleculeName: DNA (5'-D(*GP*TP*AP*CP*TP*GP*TP*CP*CP*TP*CP*TP*GP*G)-3')
type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.262764 KDa
SequenceString:
(DG)(DT)(DA)(DC)(DT)(DG)(DT)(DC)(DC)(DT) (DC)(DT)(DG)(DG)

+
Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152653
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more