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- PDB-9qeq: Structure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex -

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Entry
Database: PDB / ID: 9qeq
TitleStructure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex
Components
  • (DNA-directed RNA polymerase ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 3
  • (RNA polymerase ...) x 2
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Transcription elongation factor ...) x 3
  • (U1 small nuclear ribonucleoprotein ...) x 2
  • Non-template DNA
  • Pre-mRNA
  • Small nuclear ribonucleoprotein-associated protein
  • Template DNA
  • U1 snRNA
KeywordsSPLICING / Transcription / elongation / cryo-EM
Function / homology
Function and homology information


negative regulation of protein refolding / regulation of isotype switching / negative regulation of DNA-templated transcription, elongation / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / DSIF complex ...negative regulation of protein refolding / regulation of isotype switching / negative regulation of DNA-templated transcription, elongation / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / DSIF complex / U7 snRNP / histone pre-mRNA 3'end processing complex / regulation of transcription elongation by RNA polymerase II / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / protein methylation / U12-type spliceosomal complex / nucleosome organization / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / blastocyst formation / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / small nuclear ribonucleoprotein complex / nuclear lumen / telomerase holoenzyme complex / SMN-Sm protein complex / P granule / telomerase RNA binding / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / positive regulation of DNA-templated transcription, elongation / negative regulation of chaperone-mediated autophagy / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / transcription elongation-coupled chromatin remodeling / 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 / spliceosomal complex assembly / regulation of RNA splicing / mRNA Splicing - Minor Pathway / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / U5 snRNP / mRNA transport / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase III / transcription by RNA polymerase I / spliceosomal snRNP assembly / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / U1 snRNA binding / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III
Similarity search - Function
snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / HHH domain 9 / HHH domain / : / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 ...snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / HHH domain 9 / HHH domain / : / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / : / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Small ribonucleoprotein associated, SmB/SmN / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Small nuclear ribonucleoprotein D1 / RuvA domain 2-like / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / NusG, N-terminal domain superfamily / : / Sm domain profile. / LSM domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / DNA-directed RNA polymerase subunit beta / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit ...: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / DNA-directed RNA polymerase subunit beta / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / RNA polymerase II subunit D / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit E / Transcription elongation factor SPT5 / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein A / DNA-directed RNA polymerase II subunit RPB9 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Transcription elongation factor SPT4 / Small nuclear ribonucleoprotein-associated protein / Transcription elongation factor SPT6
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa domesticus (domestic pig)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/30 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structure of a transcribing Pol II-DSIF-SPT6-U1 snRNP complex
Authors: Zhang, L. / Batters, C. / Aibara, S. / Gordiyenko, Y. / Zumer, K. / Schmitzova, J. / Maier, K. / Cramer, P. / Zhang, S.
History
DepositionMar 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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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 subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: RNA polymerase II subunit D
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase subunit
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: RNA polymerase II, I and III subunit K
M: Transcription elongation factor SPT6
N: Non-template DNA
P: Pre-mRNA
T: Template DNA
Y: Transcription elongation factor SPT4
Z: Transcription elongation factor SPT5
a: U1 snRNA
b: U1 small nuclear ribonucleoprotein 70 kDa
c: U1 small nuclear ribonucleoprotein A
e: Small nuclear ribonucleoprotein Sm D2
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein E
h: Small nuclear ribonucleoprotein G
i: Small nuclear ribonucleoprotein Sm D3
j: Small nuclear ribonucleoprotein-associated protein
k: Small nuclear ribonucleoprotein Sm D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,132,73737
Polymers1,132,19028
Non-polymers5489
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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DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCEGIK

#1: Protein DNA-directed RNA polymerase subunit


Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig)
References: UniProt: A0A8D1DPV6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig)
References: UniProt: A0A0B8RVL1, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit C


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LCH3
#5: Protein DNA-directed RNA polymerase II subunit E / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LSI7
#7: Protein DNA-directed RNA polymerase subunit


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1VKG7
#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) Sus scrofa domesticus (domestic pig) / References: UniProt: P60899
#11: Protein DNA-directed RNA polymerase II subunit RPB11-a


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: F1RKE4

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RNA polymerase ... , 2 types, 2 molecules DL

#4: Protein RNA polymerase II subunit D


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1VM56
#12: Protein RNA polymerase II, I and III subunit K


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1TRS6

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DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ

#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit F / RPB6 homolog


Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1VEK9
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LCB2
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1VYD0

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Transcription elongation factor ... , 3 types, 3 molecules MYZ

#13: Protein Transcription elongation factor SPT6 / hSPT6 / Histone chaperone suppressor of Ty6 / Tat-cotransactivator 2 protein / Tat-CT2 protein


Mass: 199330.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT6H, KIAA0162, SPT6H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7KZ85
#17: Protein Transcription elongation factor SPT4 / DRB sensitivity-inducing factor small subunit / DSIF small subunit


Mass: 13508.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT4H1, QtsA-10763 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4R941
#18: Protein Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 121145.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli (E. coli) / References: UniProt: O00267

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DNA chain , 2 types, 2 molecules NT

#14: DNA chain Non-template DNA


Mass: 14932.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain Template DNA


Mass: 14672.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 2 types, 2 molecules Pa

#15: RNA chain Pre-mRNA


Mass: 21967.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#19: RNA chain U1 snRNA


Mass: 52697.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 2795782232

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U1 small nuclear ribonucleoprotein ... , 2 types, 2 molecules bc

#20: Protein U1 small nuclear ribonucleoprotein 70 kDa / U1 snRNP 70 kDa / U1-70K / snRNP70


Mass: 51683.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08621
#21: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 31319.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09012

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules efghik

#22: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#23: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#24: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#25: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308
#26: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#28: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314

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Protein , 1 types, 1 molecules j

#27: Protein Small nuclear ribonucleoprotein-associated protein


Mass: 23686.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q66K91

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Non-polymers , 2 types, 9 molecules

#29: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#30: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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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

ComponentName: Transcribing Pol II-DSIF-SPT6-U1 snRNP complex / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 20 mM Hepes, 100 mM NaCl, 3 mM MgCl2, 0.5 mM TCEP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warpparticle selection
2SerialEMimage acquisition
4RELIONCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
13PHENIX1.21.2_5419:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52065 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00457729
ELECTRON MICROSCOPYf_angle_d0.55479129
ELECTRON MICROSCOPYf_dihedral_angle_d15.84110435
ELECTRON MICROSCOPYf_chiral_restr0.0418939
ELECTRON MICROSCOPYf_plane_restr0.0049292

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