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- PDB-6yan: Mammalian 48S late-stage translation initiation complex with hist... -

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Basic information

Entry
Database: PDB / ID: 6yan
TitleMammalian 48S late-stage translation initiation complex with histone 4 mRNA
Components
  • (40S ribosomal protein ...) x 16
  • (Ribosomal protein ...) x 16
  • 18S ribosomal RNA
  • 60s ribosomal protein l41
  • Eukaryotic translation initiation factor 2 subunit 1
  • Ribosomal_S10 domain-containing protein
  • eukaryotic translation initiation factor 2 subunit gamma
  • histone 4 (H4) mRNA
  • initiator methionylated tRNA
KeywordsTRANSLATION / initiation complex / 48S / eukaryotic initiation factor 1A / rabbit
Function / homology
Function and homology information


ribosomal subunit / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / cytoplasmic stress granule / cytosolic small ribosomal subunit / small ribosomal subunit / cell differentiation / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal subunit / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / cytoplasmic stress granule / cytosolic small ribosomal subunit / small ribosomal subunit / cell differentiation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleolus / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit ...Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / S15/NS1, RNA-binding / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / Ribosomal protein L41 / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S26e signature. / S1 domain profile. / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S27a / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / 40S Ribosomal protein S10 / Ribosomal protein S6/S6e/A/B/2, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / YVTN repeat-like/Quinoprotein amine dehydrogenase / Plectin/S10 domain / Ribosomal protein S6e / Ribosomal protein S6e / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Ribosomal protein S1-like RNA-binding domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / S1 RNA binding domain / Ribosomal protein S8e / S1 domain / Single Sheet / Dna Ligase; domain 1 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / Ribosomal protein S10, conserved site / KH domain / Ribosomal protein L30 signature. / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Few Secondary Structures / Irregular / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S2 / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit 1 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsBochler, A. / Simonetti, A. / Guca, E. / Hashem, Y.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
European Research Council (ERC)759120European Union
French National Research AgencyANR-14-ACHN-0024 France
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into the Mammalian Late-Stage Initiation Complexes.
Authors: Angelita Simonetti / Ewelina Guca / Anthony Bochler / Lauriane Kuhn / Yaser Hashem /
Abstract: In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. ...In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
History
DepositionMar 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
l: 60s ribosomal protein l41
C: 40S ribosomal protein SA
D: ribosomal protein eS1
E: 40S ribosomal protein uS5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S5
I: 40S ribosomal protein S6
J: ribosomal protein eS7
K: 40S ribosomal protein S8
L: Ribosomal protein S9 (Predicted)
M: 40S ribosomal protein eS10
N: Ribosomal protein S11
O: 40S ribosomal protein S12
P: ribosomal protein uS15
Q: 40S ribosomal protein uS11
S: ribosomal protein uS9
T: ribosomal protein eS17
V: 40S ribosomal protein eS19
W: Ribosomal_S10 domain-containing protein
X: 40S ribosomal protein S21
Y: Ribosomal protein S15a
Z: 40S ribosomal protein uS12
a: 40S ribosomal protein S24
b: 40S ribosomal protein eS26
c: 40S ribosomal protein S27
d: ribosomal protein eS28
e: ribosomal protein uS14
f: ribosomal protein eS31
g: ribosomal protein RACK1
h: ribosomal protein eS25
i: 40S ribosomal protein eS30
2: 18S ribosomal RNA
3: histone 4 (H4) mRNA
A: Eukaryotic translation initiation factor 2 subunit 1
B: eukaryotic translation initiation factor 2 subunit gamma
U: 40S ribosomal protein uS13
R: Ribosomal protein S15
1: initiator methionylated tRNA


Theoretical massNumber of molelcules
Total (without water)1,273,88039
Polymers1,273,88039
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 1 types, 1 molecules l

#1: Protein/peptide 60s ribosomal protein l41 / / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

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40S ribosomal protein ... , 16 types, 16 molecules CEGIKMOQVXZabciU

#2: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 23360.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#4: Protein 40S ribosomal protein uS5 /


Mass: 24814.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUT9*PLUS
#6: Protein 40S ribosomal protein S4 /


Mass: 29658.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#8: Protein 40S ribosomal protein S6 /


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55, UniProt: A0A5K1UJS7*PLUS
#10: Protein 40S ribosomal protein S8 /


Mass: 23902.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#12: Protein 40S ribosomal protein eS10 /


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#14: Protein 40S ribosomal protein S12 /


Mass: 13766.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#16: Protein 40S ribosomal protein uS11 /


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#19: Protein 40S ribosomal protein eS19 /


Mass: 15812.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#21: Protein 40S ribosomal protein S21 /


Mass: 8896.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#23: Protein 40S ribosomal protein uS12 /


Mass: 15757.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#24: Protein 40S ribosomal protein S24 /


Mass: 14575.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TS40
#25: Protein 40S ribosomal protein eS26 /


Mass: 11315.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#26: Protein 40S ribosomal protein S27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#32: Protein 40S ribosomal protein eS30 /


Mass: 6741.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#37: Protein 40S ribosomal protein uS13 /


Mass: 16642.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3

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Ribosomal protein ... , 16 types, 16 molecules DFHJLNPSTYdefghR

#3: Protein ribosomal protein eS1 /


Mass: 24944.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN72
#5: Protein Ribosomal protein S3 /


Mass: 25158.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#7: Protein Ribosomal protein S5 /


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#9: Protein ribosomal protein eS7 /


Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#11: Protein Ribosomal protein S9 (Predicted) / Ribosome


Mass: 21266.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#13: Protein Ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#15: Protein ribosomal protein uS15 /


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#17: Protein ribosomal protein uS9 /


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#18: Protein ribosomal protein eS17 /


Mass: 14578.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#22: Protein Ribosomal protein S15a / Ribosome


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#27: Protein ribosomal protein eS28 /


Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#28: Protein ribosomal protein uS14 /


Mass: 6364.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#29: Protein ribosomal protein eS31 /


Mass: 8358.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#30: Protein ribosomal protein RACK1 /


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#31: Protein ribosomal protein eS25 /


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#38: Protein Ribosomal protein S15 /


Mass: 15873.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2

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Protein , 3 types, 3 molecules WAB

#20: Protein Ribosomal_S10 domain-containing protein


Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9CX53, UniProt: G1SIZ2*PLUS
#35: Protein Eukaryotic translation initiation factor 2 subunit 1


Mass: 30633.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T2G4
#36: Protein eukaryotic translation initiation factor 2 subunit gamma


Mass: 45862.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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RNA chain , 3 types, 3 molecules 231

#33: RNA chain 18S ribosomal RNA /


Mass: 601015.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: U at position 1244 is modified / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: RNA chain histone 4 (H4) mRNA


Mass: 11685.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#39: RNA chain initiator methionylated tRNA


Mass: 24376.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: adenine at position 37 is modified (threonyl-carbomoyl-adenosine (t6A))
Source: (natural) Oryctolagus cuniculus (rabbit)

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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
IDNameTypeEntity IDParent-IDSource
1LS48S IC with histone 4 mRNACOMPLEXall0MULTIPLE SOURCES
2LS48S ICRIBOSOME#1-#33, #35-#391NATURAL
3histone 4 mRNACOMPLEX#341RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Mus musculus (house mouse)10090
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 26 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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