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- PDB-6s0k: Ribosome nascent chain in complex with SecA -

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Entry
Database: PDB / ID: 6s0k
TitleRibosome nascent chain in complex with SecA
Components
  • (50S ribosomal protein ...) x 30
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Cytoskeleton protein RodZ
  • Protein translocase subunit SecA
  • tRNA-CCA
KeywordsRIBOSOME / Ribosome nascent chain in complex with SecA
Function / homology
Function and homology information


protein import / intracellular protein transmembrane transport / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / protein targeting / ribosome assembly ...protein import / intracellular protein transmembrane transport / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / protein targeting / ribosome assembly / polysomal ribosome / translational termination / assembly of large subunit precursor of preribosome / DNA-templated transcription, termination / helicase activity / translation repressor activity, mRNA regulatory element binding / DNA-binding transcription repressor activity / regulation of cell growth / response to reactive oxygen species / large ribosomal subunit rRNA binding / ribosome biogenesis / cytosolic large ribosomal subunit / large ribosomal subunit / ribosome binding / ribosomal large subunit assembly / 5S rRNA binding / protein-DNA complex / response to radiation / negative regulation of translation / tRNA binding / transferase activity / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / zinc ion binding / ATP binding / plasma membrane / metal ion binding / cytosol / cytoplasm
Ribosomal protein L2, conserved site / Ribosomal protein L36 superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal ...Ribosomal protein L2, conserved site / Ribosomal protein L36 superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L29/L35 superfamily / Ribosomal protein L10 / L21-like superfamily / Ribosomal L18e/L15P superfamily / SecA, Wing/Scaffold superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / SecA, preprotein cross-linking domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L35, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, short-form / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein L29 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / SecA conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L13 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L11, N-terminal domain / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / SecA preprotein cross-linking domain / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal protein L9, N-terminal domain / Ribosomal L25p family / Ribosomal protein L35 / Ribosomal L32p protein family / SEC-C motif / Ribosomal Proteins L2, C-terminal domain / Ribosomal L28 family / Ribosomal protein L9, C-terminal domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal L29 protein / Ribosomal prokaryotic L21 protein / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L3 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal Protein L26/L24, KOW domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L11, RNA binding domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L30p/L7e / Ribosomal protein L6 / Ribosomal protein L36 / Ribosomal protein L20
50S ribosomal protein L23 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L22 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L24 ...50S ribosomal protein L23 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L22 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L5 / 50S ribosomal protein L25 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L27 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / 50S ribosomal protein L36 / 50S ribosomal protein L35 / 50S ribosomal protein L34 / 50S ribosomal protein L33 / 50S ribosomal protein L32 / 50S ribosomal protein L29 / 50S ribosomal protein L28 / 50S ribosomal protein L20 / 50S ribosomal protein L19 / 50S ribosomal protein L11 / 50S ribosomal protein L15 / 50S ribosomal protein L10 / Protein translocase subunit SecA / gb:1476653947:
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJomaa, A. / Wang, S. / Shan, S. / Ban, N.
Funding support Switzerland, United States, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
National Institutes of Health/National Center for Research Resources United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA.
Authors: Shuai Wang / Ahmad Jomaa / Mateusz Jaskolowski / Chien-I Yang / Nenad Ban / Shu-Ou Shan /
Abstract: Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent ...Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release

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Assembly

Deposited unit
2: tRNA-CCA
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
a: 50S ribosomal protein L30
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
h: Protein translocase subunit SecA
k: Cytoskeleton protein RodZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,472,245104
Polymers1,470,52735
Non-polymers1,71869
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area172550 Å2
ΔGint-1976 kcal/mol
Surface area527360 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 2AB

#1: RNA chain tRNA-CCA


Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain 23S ribosomal RNA /


Mass: 934972.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1476653947

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50S ribosomal protein ... , 30 types, 30 molecules CDEFGHIJKLMNOPQRSTUVWXYZabcdef

#4: Protein/peptide 50S ribosomal protein L2 / / ribosomal protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#5: Protein/peptide 50S ribosomal protein L3 / / ribosomal protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#6: Protein/peptide 50S ribosomal protein L4 / / ribosomal protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#7: Protein/peptide 50S ribosomal protein L5 / / ribosomal protein uL5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#8: Protein/peptide 50S ribosomal protein L6 / / ribosomal protein uL6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#9: Protein/peptide 50S ribosomal protein L9 / / ribosomal protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#10: Protein/peptide 50S ribosomal protein L10 /


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A073UC57
#11: Protein/peptide 50S ribosomal protein L11 / / ribosomal protein uL11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#12: Protein/peptide 50S ribosomal protein L13 / / ribosomal protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#13: Protein/peptide 50S ribosomal protein L14 / / ribosomal protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#14: Protein/peptide 50S ribosomal protein L15 / / ribosomal protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#15: Protein/peptide 50S ribosomal protein L16 / / ribosomal protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#16: Protein/peptide 50S ribosomal protein L17 / / ribosomal protein uL17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#17: Protein/peptide 50S ribosomal protein L18 / / ribosomal protein uL18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#18: Protein/peptide 50S ribosomal protein L19 / / ribosomal protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#19: Protein/peptide 50S ribosomal protein L20 / / ribosomal protein bL20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#20: Protein/peptide 50S ribosomal protein L21 / / ribosomal protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#21: Protein/peptide 50S ribosomal protein L22 / / ribosomal protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#22: Protein/peptide 50S ribosomal protein L23 / / ribosomal protein uL23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#23: Protein/peptide 50S ribosomal protein L24 / / ribosomal protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#24: Protein/peptide 50S ribosomal protein L25 / / ribosomal protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#25: Protein/peptide 50S ribosomal protein L27 / / ribosomal protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#26: Protein/peptide 50S ribosomal protein L28 / / ribosomal protein bL28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#27: Protein/peptide 50S ribosomal protein L29 / / ribosomal protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#28: Protein/peptide 50S ribosomal protein L30 / / ribosomal protein uL30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#29: Protein/peptide 50S ribosomal protein L32 / / ribosomal protein bL32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#30: Protein/peptide 50S ribosomal protein L33 / / ribosomal protein bL33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#31: Protein/peptide 50S ribosomal protein L34 / / ribosomal protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#32: Protein/peptide 50S ribosomal protein L35 / / Ribosomal protein A / ribosomal protein bL35


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#33: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B / ribosomal protein bL36


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q6

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Protein/peptide , 2 types, 2 molecules hk

#34: Protein/peptide Protein translocase subunit SecA


Mass: 95155.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secA, azi, div / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037YQ84
#35: Protein/peptide Cytoskeleton protein RodZ /


Mass: 5823.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rodZ, SAMEA3472055_00952 / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 69 molecules

#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 68 / Source method: obtained synthetically / Formula: Mg / Magnesium
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Zinc

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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
1ribosome nascent chain in complex with SecARIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 350MULTIPLE SOURCES
2ribosomeRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 351NATURAL
3SecACOMPLEX341RECOMBINANT
4nascent chainCOMPLEX351RECOMBINANT
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)

Ncbi tax-ID: 562 / Organism: Escherichia coli (E. coli)

IDEntity assembly-ID
12
23
34
Source (recombinant)

Ncbi tax-ID: 562 / Organism: Escherichia coli (E. coli)

IDEntity assembly-ID
13
24
Buffer solutionpH: 7.4
SpecimenDetails: prepared using in-vitro translation system / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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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: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37334 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 5GAG

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