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- PDB-9t5h: RNA polymerase II bound to Gdown1 and RPAP2 -

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Entry
Database: PDB / ID: 9t5h
TitleRNA polymerase II bound to Gdown1 and RPAP2
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA-directed RNA polymerase subunit
  • Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
KeywordsTRANSCRIPTION / cytoplasm / polymerase / biogenesis
Function / homology
Function and homology information


maintenance of ER location / RNA polymerase II CTD heptapeptide repeat phosphatase activity / snRNA transcription / RNA polymerase core enzyme binding / microfibril binding / PERK-mediated unfolded protein response / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex ...maintenance of ER location / RNA polymerase II CTD heptapeptide repeat phosphatase activity / snRNA transcription / RNA polymerase core enzyme binding / microfibril binding / PERK-mediated unfolded protein response / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / 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 / Cytosolic sensors of pathogen-associated DNA / transcription elongation factor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / Viral Messenger RNA Synthesis / I band / Signaling by FGFR2 IIIa TM / MicroRNA (miRNA) biogenesis / protein-serine/threonine phosphatase / LRR domain binding / DNA-templated transcription elongation / 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 / 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 / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / protein serine/threonine phosphatase activity / termination of RNA polymerase II transcription / RNA polymerase II complex binding / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription by RNA polymerase III / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / nuclear-transcribed mRNA catabolic process / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / mRNA Polyadenylation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase I complex / RNA polymerase III complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription elongation by RNA polymerase I / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / transcription-coupled nucleotide-excision repair / translation initiation factor binding / Inhibition of DNA recombination at telomere / positive regulation of RNA splicing / Dengue Virus-Host Interactions / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / P-body / transcription elongation by RNA polymerase II / DNA-templated transcription termination / protein-DNA complex / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / mRNA transcription by RNA polymerase II / fibrillar center / Activation of anterior HOX genes in hindbrain development during early embryogenesis / ribonucleoside binding / kinase binding / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-directed RNA polymerase activity / nuclear envelope / transcription by RNA polymerase II / chromosome
Similarity search - Function
DNA-directed RNA polymerase II subunit GRINL1 / Putative GRINL1B complex locus protein 2 / : / Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core ...DNA-directed RNA polymerase II subunit GRINL1 / Putative GRINL1B complex locus protein 2 / : / Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb1 C-terminal repeat / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / HRDC-like superfamily / 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 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. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / 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. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / 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 / 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 Rpb2, domain 2 superfamily / 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 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 / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit GRINL1A / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC4 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit GRINL1A / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHlavata, A. / Bernecky, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Structure of cytoplasmic RNA polymerase II.
Authors: Annamaria Hlavata / Benjamin Neuditschko / Ulla Schellhaas / Clemens Plaschka / Franz Herzog / Carrie Bernecky /
Abstract: RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how ...RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated assembly factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contains Gdown1 and three biogenesis factors - RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex reveals how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis reveals how RPAP2 tethers GPN1-GPN3 to the complex and how the assembly of the RPAP2-GPN1-GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a molecular switch regulating biogenesis factor association, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes.
History
DepositionNov 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
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 II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11-a
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA-directed RNA polymerase II subunit GRINL1A
N: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)629,27920
Polymers628,88614
Non-polymers3926
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AN

#1: Protein DNA-directed RNA polymerase subunit


Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562
References: UniProt: A0AAG2TJB2, DNA-directed RNA polymerase
#14: Protein Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 / RNA polymerase II-associated protein 2


Mass: 69614.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562
References: UniProt: Q8IXW5, protein-serine/threonine phosphatase

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules BCDGIKM

#2: Protein DNA-directed RNA polymerase II subunit RPB2 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA ...3'-5' exoribonuclease / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA polymerase II subunit 2 / RNA polymerase II subunit B2 / RNA-directed RNA polymerase II subunit RPB2


Mass: 134071.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562
References: UniProt: P30876, DNA-directed RNA polymerase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, RNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa ...RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA-directed RNA polymerase II subunit C / RPB31


Mass: 31478.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: P19387
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa ...RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa subunit / RPB16


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: O15514
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa ...RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa subunit / RPB19


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: P62487
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: P36954
#11: Protein DNA-directed RNA polymerase II subunit RPB11-a / RNA polymerase II subunit B11-a / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA ...RNA polymerase II subunit B11-a / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA polymerase II 13.3 kDa subunit


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: P52435
#13: Protein DNA-directed RNA polymerase II subunit GRINL1A / DNA-directed RNA polymerase II subunit M / Glutamate receptor-like protein 1A


Mass: 41803.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K562 / References: UniProt: P0CAP2

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

#5: 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: K562 / References: UniProt: P19388
#6: 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: K562 / References: UniProt: P61218
#8: 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: K562 / References: UniProt: P52434
#10: 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: K562 / References: UniProt: P62875
#12: 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: K562 / References: UniProt: P53803

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Non-polymers , 1 types, 6 molecules

#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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
IDNameTypeDetails (eV)Entity IDParent-IDSource
1RNA polymerase II bound to Gdown1 and RPAP2COMPLEXComplex isolated from cytoplasmic extract through a tag on endogenously expressed Gdown1#1-#140NATURAL
2RNA polymerase IICOMPLEX#1-#121NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.63 MDaNO
210.52 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Buffer solutionpH: 8.2 / Details: pH at 4 degrees Celsius
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
32 mMmagnesium chlorideMgCl21
42 mMdithiothreitolC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 300 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 75 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
2PHENIX1.21.2_5419model refinement
5Warp1.0.9CTF correction
6RELION3.1CTF correction
7RELION5CTF correction
13RELION3.1final Euler assignment
14RELION5final Euler assignment
16RELION3.13D reconstruction
17RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 886711 / Symmetry type: POINT
RefinementCross valid method: NONE

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