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- PDB-7ob9: Cryo-EM structure of human RNA Polymerase I in elongation state -

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Basic information

Entry
Database: PDB / ID: 7ob9
TitleCryo-EM structure of human RNA Polymerase I in elongation state
Components
  • (DNA-directed RNA polymerase I subunit ...) x 6
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA non-template strand
  • DNA template strand
  • RNA
KeywordsTRANSCRIPTION / RNA polymerase I / human / rRNA transcription / DNA-dependent RNA polymerase / elongation state
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 / RPAP3/R2TP/prefoldin-like complex / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase I ...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 / RPAP3/R2TP/prefoldin-like complex / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase I / 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 / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / RNA Polymerase I Transcription Termination / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / 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 / termination of RNA polymerase I transcription / 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 / mRNA Splicing - Minor Pathway / nucleolar large rRNA transcription by RNA polymerase I / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / rRNA transcription / transcription by RNA polymerase III / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / RNA polymerase II activity / 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 / cellular response to leukemia inhibitory factor / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / protein-DNA complex / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / ribonucleoside binding / Formation of TC-NER Pre-Incision Complex / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / single-stranded DNA binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / nucleic acid binding / protein stabilization / protein dimerization activity / chromatin binding / nucleolus / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm
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 subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / 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 / DNA-directed RNA polymerase subunit Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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, 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 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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 / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / 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 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / 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. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / 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 / DNA (> 10) / RNA / RNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMisiaszek, A.D. / Girbig, M. / Mueller, C.W.
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Cryo-EM structures of human RNA polymerase I.
Authors: Agata D Misiaszek / Mathias Girbig / Helga Grötsch / Florence Baudin / Brice Murciano / Aleix Lafita / Christoph W Müller /
Abstract: RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the ...RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the cryo-EM structure of elongating human Pol I at 2.7 Å resolution. In the exit tunnel, we observe a double-stranded RNA helix that may support Pol I processivity. Our structure confirms that human Pol I consists of 13 subunits with only one subunit forming the Pol I stalk. Additionally, the structure of human Pol I in complex with the initiation factor RRN3 at 3.1 Å resolution reveals stalk flipping upon RRN3 binding. We also observe an inactivated state of human Pol I bound to an open DNA scaffold at 3.3 Å resolution. Lastly, the high-resolution structure of human Pol I allows mapping of disease-related mutations that can aid understanding of disease etiology.
History
DepositionApr 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit RPA1
B: DNA-directed RNA polymerase I subunit RPA2
C: DNA-directed RNA polymerases I and III subunit RPAC1
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase I subunit RPA43
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase I subunit RPA12
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerases I and III subunit RPAC2
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
N: DNA-directed RNA polymerase I subunit RPA34
M: DNA-directed RNA polymerase I subunit RPA49
R: RNA
S: DNA non-template strand
T: DNA template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)639,01623
Polymers638,60016
Non-polymers4177
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area87420 Å2
ΔGint-450 kcal/mol
Surface area178570 Å2

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Components

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DNA-directed RNA polymerase I subunit ... , 6 types, 6 molecules ABGINM

#1: Protein DNA-directed RNA polymerase I subunit RPA1 / RNA polymerase I subunit A1 / A190 / DNA-directed RNA polymerase I largest subunit / DNA-directed ...RNA polymerase I subunit A1 / A190 / DNA-directed RNA polymerase I largest subunit / DNA-directed RNA polymerase I subunit A / RNA polymerase I 194 kDa subunit / RPA194


Mass: 195069.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: O95602, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase I subunit RPA2 / RNA polymerase I subunit 2 / DNA-directed RNA polymerase I 135 kDa polypeptide / RPA135


Mass: 128379.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9H9Y6, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerase I subunit F / Twist neighbor protein


Mass: 37490.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q3B726
#8: Protein DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerase I subunit H / Zinc ribbon domain-containing protein 1


Mass: 13917.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9P1U0
#12: Protein DNA-directed RNA polymerase I subunit RPA34 / A34.5 / Antisense to ERCC-1 protein / ASE-1 / CD3-epsilon-associated protein / CD3E-associated ...A34.5 / Antisense to ERCC-1 protein / ASE-1 / CD3-epsilon-associated protein / CD3E-associated protein / DNA-directed RNA polymerase I subunit G / RNA polymerase I-associated factor PAF49


Mass: 55065.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: O15446
#13: Protein DNA-directed RNA polymerase I subunit RPA49 / RNA polymerase I subunit A49 / DNA-directed RNA polymerase I subunit E / RNA polymerase I- ...RNA polymerase I subunit A49 / DNA-directed RNA polymerase I subunit E / RNA polymerase I-associated factor 1 / RNA polymerase I-associated factor 53


Mass: 47330.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9GZS1

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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#3: Protein DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerases I and III subunit AC1 / AC40 / DNA-directed RNA polymerases I and III 40 kDa ...RNA polymerases I and III subunit AC1 / AC40 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / RPA40 / RPA39 / RPC40


Mass: 39301.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: O15160
#10: Protein DNA-directed RNA polymerases I and III subunit RPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerase I subunit D / RNA ...RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerase I subunit D / RNA polymerase I 16 kDa subunit / RPA16 / RPC16 / hRPA19


Mass: 15259.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P0DPB6

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#4: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / DNA-directed RNA polymerase II subunit E / RPB5 homolog / XAP4


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Variant: pSer44Phe / References: UniProt: P19388
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA- ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPB6 homolog / RPC15


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P61218
#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA- ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / and III 17.1 kDa polypeptide / RPB17 / RPB8 homolog / hRPB8


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P52434
#9: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA polymerase II 7.6 kDa subunit / RPB7.6 / RPB10 homolog


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P62875
#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II ...RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II subunit K / RNA polymerase II 7.0 kDa subunit / RPB7.0 / RPB10alpha


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P53803

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RNA chain , 1 types, 1 molecules R

#14: RNA chain RNA


Mass: 9275.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)

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DNA chain , 2 types, 2 molecules ST

#15: DNA chain DNA non-template strand


Mass: 13265.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#16: DNA chain DNA template strand


Mass: 13274.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)

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Non-polymers , 2 types, 7 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Zn
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1RNA polymerase ICOMPLEXRNA Polymerase 1 in elongation state#1-#160MULTIPLE SOURCES
2RNA polymerase ICOMPLEXUpper moving module, used to produce Map B1 through RELION multi-body#1-#131NATURAL
3RNA and DNACOMPLEXRNA and DNA#14-#161RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)UnitsExperimental value
110.60 MDaNO
21MEGADALTONSNO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
115 mMHEPESC8H18N2O4S1
280 mMammonium sulfate(NH4)2SO41
35 mMmagnesium chlorideMgCl21
410 mMdithiothreitolC4H10O2S21
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Human RNA Polymerase I with 1.5 molar excess of the synthetic nucleic acid template
Specimen supportDetails: NanoClean plasma cleaner (Fischione Instruments, Model 1070)
Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K / Details: blot force 3, blot time 0 s, wait time 0 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10053

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.13_2998refinement
PHENIX1.13_2998refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Warp1.0.6CTF correction
5RELION3.1CTF correction
8UCSF Chimera1.11.2model fitting
9Coot0.9model fitting
11cryoSPARC3.1initial Euler assignment
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
16PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2164189
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198822 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingDetails: Initial rigid body fitting with UCSF Chimera followed by manual model fitting in Coot.
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
17AEI

7aei

C1
27AEI

7aei

E1
37AEI

7aei

F1
47AEI

7aei

H1
57AEI

7aei

J1
67AEI

7aei

K1
77AEI

7aei

L1
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.012837245
ELECTRON MICROSCOPYf_angle_d1.098250658
ELECTRON MICROSCOPYf_chiral_restr0.06455636
ELECTRON MICROSCOPYf_plane_restr0.00866323
ELECTRON MICROSCOPYf_dihedral_angle_d13.31422487

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