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- PDB-8qu1: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1 -

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Basic information

Entry
Database: PDB / ID: 8qu1
Titlemt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1
Components
  • (39S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • mitochondrial tRNAVal
KeywordsRIBOSOME / Mitochondria / Assembly / GTPBP8
Function / homology
Function and homology information


rRNA import into mitochondrion / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / Mitochondrial protein degradation / cellular response to leukemia inhibitory factor / fibrillar center ...rRNA import into mitochondrion / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / Mitochondrial protein degradation / cellular response to leukemia inhibitory factor / fibrillar center / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / mRNA binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ribosomal protein L37/S30 / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Ribosomal protein L35, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily ...Ribosomal protein L37/S30 / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Ribosomal protein L35, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10 / Ribosomal protein L10P / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L13, conserved site / Ribosomal protein L13 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L24 signature. / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L24/L26, conserved site / Ribosomal Proteins L2, RNA binding domain / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L2 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L15 / Ribosomal protein L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L25/L23 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L26/L24, KOW domain
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL28m ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein uL11m
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsValentin Gese, G. / Cipullo, M. / Rorbach, J. / Hallberg, B.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: GTPBP8 plays a role in mitoribosome formation in human mitochondria
Authors: Cipullo, M. / Valentin Gese, G. / Gopalakrishna, S. / Krueger, A. / Lobo, V. / Pirozhkova, M.A. / Marks, J. / Palenkova, P. / Shiriaev, D. / Liu, Y. / Misic, J. / Cai, Y. / Nguyen, M. / ...Authors: Cipullo, M. / Valentin Gese, G. / Gopalakrishna, S. / Krueger, A. / Lobo, V. / Pirozhkova, M.A. / Marks, J. / Palenkova, P. / Shiriaev, D. / Liu, Y. / Misic, J. / Cai, Y. / Nguyen, M. / Abdelbagi, A. / Li, X. / Minczuk, M. / Hafner, M. / Benhalevy, D. / Sarshad, A.A. / Attanasov, I. / Hallberg, B.M. / Rorbach, J.
History
DepositionOct 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: mitochondrial tRNAVal
D: 39S ribosomal protein L2, mitochondrial
E: 39S ribosomal protein L3, mitochondrial
F: 39S ribosomal protein L4, mitochondrial
H: 39S ribosomal protein L9, mitochondrial
I: 39S ribosomal protein L10, mitochondrial
J: 39S ribosomal protein L11, mitochondrial
K: 39S ribosomal protein L13, mitochondrial
L: 39S ribosomal protein L14, mitochondrial
M: 39S ribosomal protein L15, mitochondrial
N: 39S ribosomal protein L16, mitochondrial
O: 39S ribosomal protein L17, mitochondrial
P: 39S ribosomal protein L18, mitochondrial
Q: 39S ribosomal protein L19, mitochondrial
R: 39S ribosomal protein L20, mitochondrial
S: 39S ribosomal protein L21, mitochondrial
T: 39S ribosomal protein L22, mitochondrial
U: 39S ribosomal protein L23, mitochondrial
V: 39S ribosomal protein L24, mitochondrial
W: 39S ribosomal protein L27, mitochondrial
X: 39S ribosomal protein L28, mitochondrial
Y: 39S ribosomal protein L47, mitochondrial
Z: 39S ribosomal protein L30, mitochondrial
0: 39S ribosomal protein L32, mitochondrial
1: 39S ribosomal protein L33, mitochondrial
2: 39S ribosomal protein L34, mitochondrial
3: 39S ribosomal protein L35, mitochondrial
5: 39S ribosomal protein L37, mitochondrial
6: 39S ribosomal protein L38, mitochondrial


Theoretical massNumber of molelcules
Total (without water)1,237,16330
Polymers1,237,16330
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area128390 Å2
ΔGint-951 kcal/mol
Surface area356710 Å2
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 16S ribosomal RNA


Mass: 500019.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1025814679
#2: RNA chain mitochondrial tRNAVal


Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021

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39S ribosomal protein ... , 28 types, 28 molecules DEFHIJKLMNOPQRSTUVWXYZ012356

#3: Protein 39S ribosomal protein L2, mitochondrial / L2mt / MRP-L2 / Mitochondrial large ribosomal subunit protein uL2m


Mass: 33355.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653
#4: Protein 39S ribosomal protein L3, mitochondrial / L3mt / MRP-L3 / Mitochondrial large ribosomal subunit protein uL3m


Mass: 38689.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09001
#5: Protein 39S ribosomal protein L4, mitochondrial / L4mt / MRP-L4 / Mitochondrial large ribosomal subunit protein uL4m


Mass: 34970.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#6: Protein 39S ribosomal protein L9, mitochondrial / L9mt / MRP-L9 / Mitochondrial large ribosomal subunit protein bL9m


Mass: 30296.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#7: Protein 39S ribosomal protein L10, mitochondrial / L10mt / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / L8mt / MRP-L8 / Mitochondrial large ...L10mt / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / L8mt / MRP-L8 / Mitochondrial large ribosomal subunit protein uL10m


Mass: 29322.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7H8
#8: Protein 39S ribosomal protein L11, mitochondrial / L11mt / MRP-L11 / Mitochondrial large ribosomal subunit protein uL11m


Mass: 20716.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B7
#9: Protein 39S ribosomal protein L13, mitochondrial / MRP-L13 / Mitochondrial large ribosomal subunit protein uL13m


Mass: 20722.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#10: Protein 39S ribosomal protein L14, mitochondrial / L14mt / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32 / Mitochondrial large ...L14mt / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32 / Mitochondrial large ribosomal subunit protein uL14m


Mass: 15973.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1L8
#11: Protein 39S ribosomal protein L15, mitochondrial / L15mt / MRP-L15 / Mitochondrial large ribosomal subunit protein uL15m


Mass: 33473.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P015
#12: Protein 39S ribosomal protein L16, mitochondrial / L16mt / MRP-L16 / Mitochondrial large ribosomal subunit protein uL16m


Mass: 28496.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#13: Protein 39S ribosomal protein L17, mitochondrial / L17mt / MRP-L17 / LYST-interacting protein 2 / Mitochondrial large ribosomal subunit protein bL17m


Mass: 20083.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2
#14: Protein 39S ribosomal protein L18, mitochondrial / L18mt / MRP-L18 / Mitochondrial large ribosomal subunit protein uL18m


Mass: 20607.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H0U6
#15: Protein 39S ribosomal protein L19, mitochondrial / L19mt / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15 / Mitochondrial large ...L19mt / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15 / Mitochondrial large ribosomal subunit protein bL19m


Mass: 33584.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49406
#16: Protein 39S ribosomal protein L20, mitochondrial / L20mt / MRP-L20 / Mitochondrial large ribosomal subunit protein bL20m


Mass: 17479.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC9
#17: Protein 39S ribosomal protein L21, mitochondrial / L21mt / MRP-L21 / Mitochondrial large ribosomal subunit protein bL21m


Mass: 22847.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z2W9
#18: Protein 39S ribosomal protein L22, mitochondrial / L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ...L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ribosomal subunit protein uL22m


Mass: 23683.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWU5
#19: Protein 39S ribosomal protein L23, mitochondrial / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / ...MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / Ribosomal protein L23-like


Mass: 17807.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16540
#20: Protein 39S ribosomal protein L24, mitochondrial / L24mt / MRP-L24 / Mitochondrial large ribosomal subunit protein uL24m


Mass: 24953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35
#21: Protein 39S ribosomal protein L27, mitochondrial / L27mt / MRP-L27 / Mitochondrial large ribosomal subunit protein bL27m


Mass: 16102.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#22: Protein 39S ribosomal protein L28, mitochondrial / L28mt / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / ...L28mt / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / Mitochondrial large ribosomal subunit protein bL28m


Mass: 30202.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#23: Protein 39S ribosomal protein L47, mitochondrial / L47mt / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma ...L47mt / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis-related protein 1


Mass: 29508.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HD33
#24: Protein 39S ribosomal protein L30, mitochondrial / L30mt / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / Mitochondrial large ...L30mt / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / Mitochondrial large ribosomal subunit protein uL30m


Mass: 18582.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TCC3
#25: Protein 39S ribosomal protein L32, mitochondrial / L32mt / MRP-L32 / Mitochondrial large ribosomal subunit protein bL32m


Mass: 21437.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC8
#26: Protein 39S ribosomal protein L33, mitochondrial / L33mt / MRP-L33 / Mitochondrial large ribosomal subunit protein bL33m


Mass: 7635.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75394
#27: Protein 39S ribosomal protein L34, mitochondrial / L34mt / MRP-L34 / Mitochondrial large ribosomal subunit protein bL34m


Mass: 10183.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQ48
#28: Protein 39S ribosomal protein L35, mitochondrial / L35mt / MRP-L35 / Mitochondrial large ribosomal subunit protein bL35m


Mass: 21558.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZE8
#29: Protein 39S ribosomal protein L37, mitochondrial / L37mt / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2 / Mitochondrial large ...L37mt / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2 / Mitochondrial large ribosomal subunit protein mL37


Mass: 48183.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE1
#30: Protein 39S ribosomal protein L38, mitochondrial / L38mt / MRP-L38 / Mitochondrial large ribosomal subunit protein mL38


Mass: 44659.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DV4

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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

ComponentName: mtLSU assembly intermediate (State 1) / Type: ORGANELLE OR CELLULAR COMPONENT
Entity ID: #25-#28, #9-#10, #13-#17, #21-#24, #3, #29-#30, #2, #4-#6, #11-#12, #18-#20, #1, #7-#8
Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: Ice
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
Image scansMovie frames/image: 25 / Used frames/image: 1-25

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 404181
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41197 / Symmetry type: POINT

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