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- PDB-8b6c: Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadi... -

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Basic information

Entry
Database: PDB / ID: 8b6c
TitleCryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative CK147
Components
  • (60S ribosomal protein ...) x 31
  • (Protein transport protein Sec61 subunit ...Protein targeting) x 2
  • (Ribosomal protein ...) x 8
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Ribosomal_L18_c domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • eL18
KeywordsMEMBRANE PROTEIN / Ribosome / Sec61 / TRAP / Translocon / Translation / RNA binding protein / eEF2 / CK147 / CADA / Translocon inhibitor / 80S / 60S / 40S / cyclotriazadisulfonamide
Function / homology
Function and homology information


protein transmembrane transporter activity / protein targeting / rough endoplasmic reticulum / cytosolic ribosome / ribosome binding / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome ...protein transmembrane transporter activity / protein targeting / rough endoplasmic reticulum / cytosolic ribosome / ribosome binding / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / endoplasmic reticulum membrane / nucleolus / cytoplasm
Similarity search - Function
Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Protein secE/sec61-gamma signature. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / Ribosomal protein L44e signature. / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L39e, conserved site ...Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Protein secE/sec61-gamma signature. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / Ribosomal protein L44e signature. / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L39e, conserved site / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L36e signature. / Ribosomal protein L39e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L18e / Ribosomal L39 protein / Ribosomal protein L31e signature. / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e signature. / Ribosomal protein L6 signature 2. / Ribosomal protein L1e signature. / Ribosomal protein L15e signature. / Ribosomal protein L21e signature. / Ribosomal protein L37e signature. / Ribosomal protein L23 signature. / Ribosomal protein L30 signature. / Ribosomal protein L5 signature. / Ribosomal protein L29 signature. / Ribosomal protein L15 signature. / Ribosomal protein L14 signature. / Ribosomal protein L22 signature. / Ribosomal protein L24 signature. / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1 family / Ribosomal protein L3 signature.
Similarity search - Domain/homology
Chem-OWI / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 ...Chem-OWI / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Protein transport protein Sec61 subunit gamma / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsPauwels, E. / Shewakramani, N.R. / De Wijngaert, B. / Vermeire, K. / Das, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
KU Leuven Belgium
CitationJournal: Sci Adv / Year: 2023
Title: Structural insights into TRAP association with ribosome-Sec61 complex and translocon inhibition by a CADA derivative.
Authors: Eva Pauwels / Neesha R Shewakramani / Brent De Wijngaert / Anita Camps / Becky Provinciael / Joren Stroobants / Kai-Uwe Kalies / Enno Hartmann / Piet Maes / Kurt Vermeire / Kalyan Das /
Abstract: During cotranslational translocation, the signal peptide of a nascent chain binds Sec61 translocon to initiate protein transport through the endoplasmic reticulum (ER) membrane. Our cryo-electron ...During cotranslational translocation, the signal peptide of a nascent chain binds Sec61 translocon to initiate protein transport through the endoplasmic reticulum (ER) membrane. Our cryo-electron microscopy structure of ribosome-Sec61 shows binding of an ordered heterotetrameric translocon-associated protein (TRAP) complex, in which TRAP-γ is anchored at two adjacent positions of 28 ribosomal RNA and interacts with ribosomal protein L38 and Sec61α/γ. Four transmembrane helices (TMHs) of TRAP-γ cluster with one C-terminal helix of each α, β, and δ subunits. The seven TMH bundle helps position a crescent-shaped trimeric TRAP-α/β/δ core in the ER lumen, facing the Sec61 channel. Further, our in vitro assay establishes the cyclotriazadisulfonamide derivative CK147 as a translocon inhibitor. A structure of ribosome-Sec61-CK147 reveals CK147 binding the channel and interacting with the plug helix from the lumenal side. The CK147 resistance mutations surround the inhibitor. These structures help in understanding the TRAP functions and provide a new Sec61 site for designing translocon inhibitors.
History
DepositionSep 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: 60S ribosomal protein L21
5: 28S rRNA
F: 60S ribosomal protein L7
D: Ribosomal_L18_c domain-containing protein
S: 60S ribosomal protein L18a
b: 60S ribosomal protein L29
B: Ribosomal protein L3
d: 60S ribosomal protein L31
8: 5.8S rRNA
G: 60S ribosomal protein L7a
J: 60S ribosomal protein L11
c: 60S ribosomal protein L30
j: Ribosomal protein L37
A: Ribosomal protein L8
I: Ribosomal protein L10
q: Protein transport protein Sec61 subunit gamma
p: 60S ribosomal protein L37a
V: 60S ribosomal protein L23
m: 60S ribosomal protein L40
l: 60S ribosomal protein L39-like
P: 60S ribosomal protein L17
E: 60S ribosomal protein L6
Q: eL18
R: 60S ribosomal protein L19
W: Ribosomal protein L24
O: 60S ribosomal protein L13a
K: Protein transport protein Sec61 subunit alpha isoform 1
C: 60S ribosomal protein L4
o: 60S ribosomal protein L36a-like
r: 60S ribosomal protein L28
f: 60S ribosomal protein L35a
e: Ribosomal protein L32
Z: 60S ribosomal protein L27
a: 60S ribosomal protein L27a
g: 60S ribosomal protein L34
k: 60S ribosomal protein L38
H: 60S ribosomal protein L9
L: 60S ribosomal protein L13
7: 5S rRNA
N: Ribosomal protein L15
i: 60S ribosomal protein L36
h: 60S ribosomal protein L35
M: 60S ribosomal protein L14
Y: Ribosomal protein L26
X: Ribosomal_L23eN domain-containing protein
U: 60S ribosomal protein L22 (Fragment)
n: 60S ribosomal protein L41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,505,606231
Polymers2,500,33647
Non-polymers5,270184
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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60S ribosomal protein ... , 31 types, 31 molecules TFSbdGJcpVmlPEROCorfZagkHLihMUn

#1: Protein 60S ribosomal protein L21 /


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#3: Protein 60S ribosomal protein L7 /


Mass: 26658.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#5: Protein 60S ribosomal protein L18a /


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#6: Protein 60S ribosomal protein L29 /


Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#8: Protein 60S ribosomal protein L31 /


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#10: Protein 60S ribosomal protein L7a /


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#11: Protein 60S ribosomal protein L11 /


Mass: 19399.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#12: Protein 60S ribosomal protein L30 /


Mass: 10914.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#17: Protein 60S ribosomal protein L37a /


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#18: Protein 60S ribosomal protein L23 /


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#19: Protein 60S ribosomal protein L40 /


Mass: 6212.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#20: Protein/peptide 60S ribosomal protein L39-like /


Mass: 6324.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#21: Protein 60S ribosomal protein L17 /


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#22: Protein 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#24: Protein 60S ribosomal protein L19 /


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein 60S ribosomal protein L13a /


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein 60S ribosomal protein L4 /


Mass: 41114.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9DCT1
#29: Protein 60S ribosomal protein L36a-like / Ribosome


Mass: 12070.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#30: Protein 60S ribosomal protein L28 /


Mass: 14220.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#31: Protein 60S ribosomal protein L35a /


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#33: Protein 60S ribosomal protein L27 /


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#34: Protein 60S ribosomal protein L27a /


Mass: 16489.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#35: Protein 60S ribosomal protein L34 /


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#36: Protein 60S ribosomal protein L38 /


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#37: Protein 60S ribosomal protein L9 /


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#38: Protein 60S ribosomal protein L13 /


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#41: Protein 60S ribosomal protein L36 /


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#42: Protein 60S ribosomal protein L35 /


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#43: Protein 60S ribosomal protein L14 /


Mass: 16217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#46: Protein 60S ribosomal protein L22 (Fragment) / Ribosome


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein/peptide 60S ribosomal protein L41 /


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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RNA chain , 3 types, 3 molecules 587

#2: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1557700.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_3
#39: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4

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Protein , 3 types, 3 molecules DQX

#4: Protein Ribosomal_L18_c domain-containing protein


Mass: 34077.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#23: Protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: F6QKI9
#45: Protein Ribosomal_L23eN domain-containing protein


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76

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Ribosomal protein ... , 8 types, 8 molecules BjAIWeNY

#7: Protein Ribosomal protein L3 /


Mass: 45119.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#13: Protein Ribosomal protein L37 /


Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#14: Protein Ribosomal protein L8 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#15: Protein Ribosomal protein L10 /


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#25: Protein Ribosomal protein L24 /


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#32: Protein Ribosomal protein L32 /


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#40: Protein Ribosomal protein L15 /


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#44: Protein Ribosomal protein L26 /


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0

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Protein transport protein Sec61 subunit ... , 2 types, 2 molecules qK

#16: Protein Protein transport protein Sec61 subunit gamma / Protein targeting


Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPE6
#27: Protein Protein transport protein Sec61 subunit alpha isoform 1 / Protein targeting


Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 3 types, 184 molecules

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


Mass: 24.305 Da / Num. of mol.: 178 / Source method: obtained synthetically / Formula: Mg
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#50: Chemical ChemComp-OWI / 4-[[9-(cyclohexylmethyl)-3-methylidene-5-(4-methylphenyl)sulfonyl-1,5,9-triazacyclododec-1-yl]sulfonyl]-~{N},~{N}-dimethyl-aniline


Mass: 616.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H48N4O4S2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: 80S ribosome complex with Sec61 and inhibitor CK147 / Type: RIBOSOME
Entity ID: #2, #39, #9, #14, #7, #28, #4, #22, #3, #10, #37, #15, #11, #27, #38, #43, #40, #26, #21, #23-#24, #5, #1, #46, #18, #25, #45, #44, #33-#34, #6, #12, #8, #32, #31, #35, #42, #41, #13, #36, ...Entity ID: #2, #39, #9, #14, #7, #28, #4, #22, #3, #10, #37, #15, #11, #27, #38, #43, #40, #26, #21, #23-#24, #5, #1, #46, #18, #25, #45, #44, #33-#34, #6, #12, #8, #32, #31, #35, #42, #41, #13, #36, #20, #19, #47, #29, #17, #16, #30
Source: NATURAL
Source (natural)Organism: Canis lupus familiaris (dog)
Buffer solutionpH: 7.5
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: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 40 sec. / Electron dose: 0.8 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1734

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPU2.9.0image acquisition
4CTFFIND4CTF correction
7Coot0.9.8.1model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.2model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 370000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132229 / Symmetry type: POINT
Atomic model buildingB value: 97.24 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient / Details: Real space refinement
Atomic model building
IDPDB-ID 3D fitting-ID
16MTE

6mte

1
23J7Q

3j7q

1

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