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- EMDB-21427: Single Particle Cryo-EM Structure of the Natively Isolated Sec61,... -

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Basic information

Entry
Database: EMDB / ID: EMD-21427
TitleSingle Particle Cryo-EM Structure of the Natively Isolated Sec61, TMCO1, Nicalin, TMEM147, and CCDC47 Containing Ribosome-Translocon Complex
Map data
Sample
  • Complex: Native complex of a translating ribosome and a novel translocon containing the Sec61 complex, TMEM147, NOMO, Nicalin, CCDC47, and TMCO1.
    • Complex: 60S SubunitEukaryotic large ribosomal subunit (60S)
      • Complex: 60S acidic ribosomal protein P0
      • Complex: 60S acidic ribosomal protein P1
      • Complex: 60S acidic ribosomal protein P2
      • Complex: 60S ribosomal protein L10
      • Complex: 60S ribosomal protein L10a
      • Complex: 60S ribosomal protein L11
      • Complex: 60S ribosomal protein L12
      • Complex: 60S ribosomal protein L13
      • Complex: 60S ribosomal protein L13a
      • Complex: 60S ribosomal protein L14
      • Complex: 60S ribosomal protein L15
      • Complex: 60S ribosomal protein L17
      • Complex: 60S ribosomal protein L18
      • Complex: 60S ribosomal protein L18a
      • Complex: 60S ribosomal protein L19
      • Complex: 60S ribosomal protein L21
      • Complex: 60S ribosomal protein L22
      • Complex: 60S ribosomal protein L23
      • Complex: 60S ribosomal protein L23a
      • Complex: 60S ribosomal protein L24
      • Complex: 60S ribosomal protein L26
      • Complex: 60S ribosomal protein L27
      • Complex: 60S ribosomal protein L27a
      • Complex: 60S ribosomal protein L28
      • Complex: 60S ribosomal protein L3
      • Complex: 60S ribosomal protein L30
      • Complex: 60S ribosomal protein L31
      • Complex: 60S ribosomal protein L32
      • Complex: 60S ribosomal protein L34
      • Complex: 60S ribosomal protein L35
      • Complex: 60S ribosomal protein L35a
      • Complex: 60S ribosomal protein L36
      • Complex: 60S ribosomal protein L36a
      • Complex: 60S ribosomal protein L37a
      • Complex: 60S ribosomal protein L38
      • Complex: 60S ribosomal protein L39
      • Complex: 60S ribosomal protein L4
      • Complex: 60S ribosomal protein L5
      • Complex: 60S ribosomal protein L6
      • Complex: 60S ribosomal protein L7
      • Complex: 60S ribosomal protein L7a
      • Complex: 60S ribosomal protein L8
      • Complex: 60S ribosomal protein L9
    • Complex: 40S Subunit
      • Complex: 40S ribosomal protein S10
      • Complex: 40S ribosomal protein S11
      • Complex: 40S ribosomal protein S12
      • Complex: 40S ribosomal protein S13
      • Complex: 40S ribosomal protein S14
      • Complex: 40S ribosomal protein S15
      • Complex: 40S ribosomal protein S15a
      • Complex: 40S ribosomal protein S16
      • Complex: 40S ribosomal protein S17
      • Complex: 40S ribosomal protein S18
      • Complex: 40S ribosomal protein S19
      • Complex: 40S ribosomal protein S2
      • Complex: 40S ribosomal protein S21
      • Complex: 40S ribosomal protein S23
      • Complex: 40S ribosomal protein S24
      • Complex: 40S ribosomal protein S25
      • Complex: 40S ribosomal protein S26
      • Complex: 40S ribosomal protein S27
      • Complex: 40S ribosomal protein S27-like
      • Complex: 40S ribosomal protein S28
      • Complex: 40S ribosomal protein S29
      • Complex: 40S ribosomal protein S3
      • Complex: 40S ribosomal protein S30
      • Complex: 40S ribosomal protein S3a
      • Complex: 40S ribosomal protein S4, X isoformRibosome
      • Complex: 40S ribosomal protein S5
      • Complex: 40S ribosomal protein S6
      • Complex: 40S ribosomal protein S7
      • Complex: 40S ribosomal protein S8
      • Complex: 40S ribosomal protein S9
      • Complex: 40S ribosomal protein SA
    • Complex: Translocon
      • Complex: Sec61 Complex
      • Complex: TMCO1
      • Complex: NOMO-Nicalin-TMEM147 Complex
      • Complex: CCDC47
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMcGilvray PT / Anghel SA / Sundaram A / Trnka MJ / Zhong F / Hu H / Burlingame AL / Keenan RJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM130051-01 United States
CitationJournal: Elife / Year: 2020
Title: An ER translocon for multi-pass membrane protein biogenesis.
Authors: Philip T McGilvray / S Andrei Anghel / Arunkumar Sundaram / Frank Zhong / Michael J Trnka / James R Fuller / Hong Hu / Alma L Burlingame / Robert J Keenan /
Abstract: Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here ...Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here we describe a ~ 360 kDa ribosome-associated complex comprising the core Sec61 channel and five accessory factors: TMCO1, CCDC47 and the Nicalin-TMEM147-NOMO complex. Cryo-electron microscopy reveals a large assembly at the ribosome exit tunnel organized around a central membrane cavity. Similar to protein-conducting channels that facilitate movement of transmembrane segments, cytosolic and luminal funnels in TMCO1 and TMEM147, respectively, suggest routes into the central membrane cavity. High-throughput mRNA sequencing shows selective translocon engagement with hundreds of different multi-pass membrane proteins. Consistent with a role in multi-pass membrane protein biogenesis, cells lacking different accessory components show reduced levels of one such client, the glutamate transporter EAAT1. These results identify a new human translocon and provide a molecular framework for understanding its role in multi-pass membrane protein biogenesis.
History
DepositionFeb 21, 2020-
Header (metadata) releaseMar 25, 2020-
Map releaseSep 2, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0073
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0073
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21427.png

Downloads & links

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Map

FileDownload / File: emd_21427.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.0073 / Movie #1: 0.0073
Minimum - Maximum-0.014456131 - 0.04746323
Average (Standard dev.)0.00015776935 (±0.0019139652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00500
Dimensions500500500
Spacing500500500
CellA=B=C: 680.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z680.000680.000680.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00500
NC/NR/NS500500500
D min/max/mean-0.0140.0470.000

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Supplemental data

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Half map: #2

Fileemd_21427_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_21427_half_map_2.map
Projections & Slices
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Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native complex of a translating ribosome and a novel translocon c...

EntireName: Native complex of a translating ribosome and a novel translocon containing the Sec61 complex, TMEM147, NOMO, Nicalin, CCDC47, and TMCO1.
Components
  • Complex: Native complex of a translating ribosome and a novel translocon containing the Sec61 complex, TMEM147, NOMO, Nicalin, CCDC47, and TMCO1.
    • Complex: 60S SubunitEukaryotic large ribosomal subunit (60S)
      • Complex: 60S acidic ribosomal protein P0
      • Complex: 60S acidic ribosomal protein P1
      • Complex: 60S acidic ribosomal protein P2
      • Complex: 60S ribosomal protein L10
      • Complex: 60S ribosomal protein L10a
      • Complex: 60S ribosomal protein L11
      • Complex: 60S ribosomal protein L12
      • Complex: 60S ribosomal protein L13
      • Complex: 60S ribosomal protein L13a
      • Complex: 60S ribosomal protein L14
      • Complex: 60S ribosomal protein L15
      • Complex: 60S ribosomal protein L17
      • Complex: 60S ribosomal protein L18
      • Complex: 60S ribosomal protein L18a
      • Complex: 60S ribosomal protein L19
      • Complex: 60S ribosomal protein L21
      • Complex: 60S ribosomal protein L22
      • Complex: 60S ribosomal protein L23
      • Complex: 60S ribosomal protein L23a
      • Complex: 60S ribosomal protein L24
      • Complex: 60S ribosomal protein L26
      • Complex: 60S ribosomal protein L27
      • Complex: 60S ribosomal protein L27a
      • Complex: 60S ribosomal protein L28
      • Complex: 60S ribosomal protein L3
      • Complex: 60S ribosomal protein L30
      • Complex: 60S ribosomal protein L31
      • Complex: 60S ribosomal protein L32
      • Complex: 60S ribosomal protein L34
      • Complex: 60S ribosomal protein L35
      • Complex: 60S ribosomal protein L35a
      • Complex: 60S ribosomal protein L36
      • Complex: 60S ribosomal protein L36a
      • Complex: 60S ribosomal protein L37a
      • Complex: 60S ribosomal protein L38
      • Complex: 60S ribosomal protein L39
      • Complex: 60S ribosomal protein L4
      • Complex: 60S ribosomal protein L5
      • Complex: 60S ribosomal protein L6
      • Complex: 60S ribosomal protein L7
      • Complex: 60S ribosomal protein L7a
      • Complex: 60S ribosomal protein L8
      • Complex: 60S ribosomal protein L9
    • Complex: 40S Subunit
      • Complex: 40S ribosomal protein S10
      • Complex: 40S ribosomal protein S11
      • Complex: 40S ribosomal protein S12
      • Complex: 40S ribosomal protein S13
      • Complex: 40S ribosomal protein S14
      • Complex: 40S ribosomal protein S15
      • Complex: 40S ribosomal protein S15a
      • Complex: 40S ribosomal protein S16
      • Complex: 40S ribosomal protein S17
      • Complex: 40S ribosomal protein S18
      • Complex: 40S ribosomal protein S19
      • Complex: 40S ribosomal protein S2
      • Complex: 40S ribosomal protein S21
      • Complex: 40S ribosomal protein S23
      • Complex: 40S ribosomal protein S24
      • Complex: 40S ribosomal protein S25
      • Complex: 40S ribosomal protein S26
      • Complex: 40S ribosomal protein S27
      • Complex: 40S ribosomal protein S27-like
      • Complex: 40S ribosomal protein S28
      • Complex: 40S ribosomal protein S29
      • Complex: 40S ribosomal protein S3
      • Complex: 40S ribosomal protein S30
      • Complex: 40S ribosomal protein S3a
      • Complex: 40S ribosomal protein S4, X isoformRibosome
      • Complex: 40S ribosomal protein S5
      • Complex: 40S ribosomal protein S6
      • Complex: 40S ribosomal protein S7
      • Complex: 40S ribosomal protein S8
      • Complex: 40S ribosomal protein S9
      • Complex: 40S ribosomal protein SA
    • Complex: Translocon
      • Complex: Sec61 Complex
      • Complex: TMCO1
      • Complex: NOMO-Nicalin-TMEM147 Complex
      • Complex: CCDC47

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Supramolecule #1: Native complex of a translating ribosome and a novel translocon c...

SupramoleculeName: Native complex of a translating ribosome and a novel translocon containing the Sec61 complex, TMEM147, NOMO, Nicalin, CCDC47, and TMCO1.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
Molecular weightTheoretical: 56 KDa

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Supramolecule #2: 60S Subunit

SupramoleculeName: 60S Subunit / type: complex / ID: 2 / Parent: 1
Details: 60S ribosomal protein L9 60S ribosomal protein L8 60S ribosomal protein L7a 60S ribosomal protein L7 60S ribosomal protein L6 60S ribosomal protein L5 60S ribosomal protein L4 60S ribosomal ...Details: 60S ribosomal protein L9 60S ribosomal protein L8 60S ribosomal protein L7a 60S ribosomal protein L7 60S ribosomal protein L6 60S ribosomal protein L5 60S ribosomal protein L4 60S ribosomal protein L39 60S ribosomal protein L38 60S ribosomal protein L37a 60S ribosomal protein L36a 60S ribosomal protein L36 60S ribosomal protein L35a 60S ribosomal protein L35 60S ribosomal protein L34 60S ribosomal protein L32 60S ribosomal protein L31 60S ribosomal protein L30 60S ribosomal protein L3 60S ribosomal protein L28 60S ribosomal protein L27a 60S ribosomal protein L27 60S ribosomal protein L26 60S ribosomal protein L24 60S ribosomal protein L23a 60S ribosomal protein L23 60S ribosomal protein L22-like 1 60S ribosomal protein L22 60S ribosomal protein L21 60S ribosomal protein L19 60S ribosomal protein L18a 60S ribosomal protein L18 60S ribosomal protein L17 60S ribosomal protein L15 60S ribosomal protein L14 60S ribosomal protein L13a 60S ribosomal protein L13 60S ribosomal protein L12 60S ribosomal protein L11 60S ribosomal protein L10a 60S ribosomal protein L10 60S ribosomal export protein NMD3 60S acidic ribosomal protein P2 60S acidic ribosomal protein P1 60S acidic ribosomal protein P0-like 60S acidic ribosomal protein P0 Ubiquitin-60S ribosomal protein L40
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
Molecular weightTheoretical: 2.42 MDa

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Supramolecule #3: 40S Subunit

SupramoleculeName: 40S Subunit / type: complex / ID: 3 / Parent: 1
Details: 40S ribosomal protein SA 40S ribosomal protein S9 40S ribosomal protein S8 40S ribosomal protein S7 40S ribosomal protein S6 40S ribosomal protein S5 40S ribosomal protein S4, X isoform 40S ...Details: 40S ribosomal protein SA 40S ribosomal protein S9 40S ribosomal protein S8 40S ribosomal protein S7 40S ribosomal protein S6 40S ribosomal protein S5 40S ribosomal protein S4, X isoform 40S ribosomal protein S3a 40S ribosomal protein S30 40S ribosomal protein S3 40S ribosomal protein S29 40S ribosomal protein S28 40S ribosomal protein S27-like 40S ribosomal protein S27 40S ribosomal protein S26 40S ribosomal protein S25 40S ribosomal protein S24 40S ribosomal protein S23 40S ribosomal protein S21 40S ribosomal protein S20 40S ribosomal protein S2 40S ribosomal protein S19 40S ribosomal protein S18 40S ribosomal protein S17 40S ribosomal protein S16 40S ribosomal protein S15a 40S ribosomal protein S15 40S ribosomal protein S14 40S ribosomal protein S13 40S ribosomal protein S12 40S ribosomal protein S11 40S ribosomal protein S10 Ubiquitin-40S ribosomal protein S27a
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
Molecular weightTheoretical: 1.12 MDa

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Supramolecule #4: Translocon

SupramoleculeName: Translocon / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #5: Sec61 Complex

SupramoleculeName: Sec61 Complex / type: complex / ID: 5 / Parent: 4 / Details: Sec61alpha, beta, and gamma
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
Molecular weightTheoretical: 70 KDa

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Supramolecule #6: TMCO1

SupramoleculeName: TMCO1 / type: complex / ID: 6 / Parent: 4
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #7: NOMO-Nicalin-TMEM147 Complex

SupramoleculeName: NOMO-Nicalin-TMEM147 Complex / type: complex / ID: 7 / Parent: 4
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #8: CCDC47

SupramoleculeName: CCDC47 / type: complex / ID: 8 / Parent: 4
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #9: 60S acidic ribosomal protein P0

SupramoleculeName: 60S acidic ribosomal protein P0 / type: complex / ID: 9 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #10: 60S acidic ribosomal protein P1

SupramoleculeName: 60S acidic ribosomal protein P1 / type: complex / ID: 10 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #11: 60S acidic ribosomal protein P2

SupramoleculeName: 60S acidic ribosomal protein P2 / type: complex / ID: 11 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #12: 60S ribosomal protein L10

SupramoleculeName: 60S ribosomal protein L10 / type: complex / ID: 12 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #13: 60S ribosomal protein L10a

SupramoleculeName: 60S ribosomal protein L10a / type: complex / ID: 13 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #14: 60S ribosomal protein L11

SupramoleculeName: 60S ribosomal protein L11 / type: complex / ID: 14 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #15: 60S ribosomal protein L12

SupramoleculeName: 60S ribosomal protein L12 / type: complex / ID: 15 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #16: 60S ribosomal protein L13

SupramoleculeName: 60S ribosomal protein L13 / type: complex / ID: 16 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #17: 60S ribosomal protein L13a

SupramoleculeName: 60S ribosomal protein L13a / type: complex / ID: 17 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #18: 60S ribosomal protein L14

SupramoleculeName: 60S ribosomal protein L14 / type: complex / ID: 18 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #19: 60S ribosomal protein L15

SupramoleculeName: 60S ribosomal protein L15 / type: complex / ID: 19 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #20: 60S ribosomal protein L17

SupramoleculeName: 60S ribosomal protein L17 / type: complex / ID: 20 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #21: 60S ribosomal protein L18

SupramoleculeName: 60S ribosomal protein L18 / type: complex / ID: 21 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #22: 60S ribosomal protein L18a

SupramoleculeName: 60S ribosomal protein L18a / type: complex / ID: 22 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #23: 60S ribosomal protein L19

SupramoleculeName: 60S ribosomal protein L19 / type: complex / ID: 23 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #24: 60S ribosomal protein L21

SupramoleculeName: 60S ribosomal protein L21 / type: complex / ID: 24 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #25: 60S ribosomal protein L22

SupramoleculeName: 60S ribosomal protein L22 / type: complex / ID: 25 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #26: 60S ribosomal protein L23

SupramoleculeName: 60S ribosomal protein L23 / type: complex / ID: 26 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #27: 60S ribosomal protein L23a

SupramoleculeName: 60S ribosomal protein L23a / type: complex / ID: 27 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #28: 60S ribosomal protein L24

SupramoleculeName: 60S ribosomal protein L24 / type: complex / ID: 28 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #29: 60S ribosomal protein L26

SupramoleculeName: 60S ribosomal protein L26 / type: complex / ID: 29 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #30: 60S ribosomal protein L27

SupramoleculeName: 60S ribosomal protein L27 / type: complex / ID: 30 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #31: 60S ribosomal protein L27a

SupramoleculeName: 60S ribosomal protein L27a / type: complex / ID: 31 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #32: 60S ribosomal protein L28

SupramoleculeName: 60S ribosomal protein L28 / type: complex / ID: 32 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #33: 60S ribosomal protein L3

SupramoleculeName: 60S ribosomal protein L3 / type: complex / ID: 33 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #34: 60S ribosomal protein L30

SupramoleculeName: 60S ribosomal protein L30 / type: complex / ID: 34 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #35: 60S ribosomal protein L31

SupramoleculeName: 60S ribosomal protein L31 / type: complex / ID: 35 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #36: 60S ribosomal protein L32

SupramoleculeName: 60S ribosomal protein L32 / type: complex / ID: 36 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #37: 60S ribosomal protein L34

SupramoleculeName: 60S ribosomal protein L34 / type: complex / ID: 37 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #38: 60S ribosomal protein L35

SupramoleculeName: 60S ribosomal protein L35 / type: complex / ID: 38 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #39: 60S ribosomal protein L35a

SupramoleculeName: 60S ribosomal protein L35a / type: complex / ID: 39 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #40: 60S ribosomal protein L36

SupramoleculeName: 60S ribosomal protein L36 / type: complex / ID: 40 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #41: 60S ribosomal protein L36a

SupramoleculeName: 60S ribosomal protein L36a / type: complex / ID: 41 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #42: 60S ribosomal protein L37a

SupramoleculeName: 60S ribosomal protein L37a / type: complex / ID: 42 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #43: 60S ribosomal protein L38

SupramoleculeName: 60S ribosomal protein L38 / type: complex / ID: 43 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #44: 60S ribosomal protein L39

SupramoleculeName: 60S ribosomal protein L39 / type: complex / ID: 44 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #45: 60S ribosomal protein L4

SupramoleculeName: 60S ribosomal protein L4 / type: complex / ID: 45 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

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Supramolecule #46: 60S ribosomal protein L5

SupramoleculeName: 60S ribosomal protein L5 / type: complex / ID: 46 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #47: 60S ribosomal protein L6

SupramoleculeName: 60S ribosomal protein L6 / type: complex / ID: 47 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #48: 60S ribosomal protein L7

SupramoleculeName: 60S ribosomal protein L7 / type: complex / ID: 48 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #49: 60S ribosomal protein L7a

SupramoleculeName: 60S ribosomal protein L7a / type: complex / ID: 49 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #50: 60S ribosomal protein L8

SupramoleculeName: 60S ribosomal protein L8 / type: complex / ID: 50 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #51: 60S ribosomal protein L9

SupramoleculeName: 60S ribosomal protein L9 / type: complex / ID: 51 / Parent: 2
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #52: 40S ribosomal protein S10

SupramoleculeName: 40S ribosomal protein S10 / type: complex / ID: 52 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #53: 40S ribosomal protein S11

SupramoleculeName: 40S ribosomal protein S11 / type: complex / ID: 53 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #54: 40S ribosomal protein S12

SupramoleculeName: 40S ribosomal protein S12 / type: complex / ID: 54 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #55: 40S ribosomal protein S13

SupramoleculeName: 40S ribosomal protein S13 / type: complex / ID: 55 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #56: 40S ribosomal protein S14

SupramoleculeName: 40S ribosomal protein S14 / type: complex / ID: 56 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #57: 40S ribosomal protein S15

SupramoleculeName: 40S ribosomal protein S15 / type: complex / ID: 57 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #58: 40S ribosomal protein S15a

SupramoleculeName: 40S ribosomal protein S15a / type: complex / ID: 58 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #59: 40S ribosomal protein S16

SupramoleculeName: 40S ribosomal protein S16 / type: complex / ID: 59 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #60: 40S ribosomal protein S17

SupramoleculeName: 40S ribosomal protein S17 / type: complex / ID: 60 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #61: 40S ribosomal protein S18

SupramoleculeName: 40S ribosomal protein S18 / type: complex / ID: 61 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #62: 40S ribosomal protein S19

SupramoleculeName: 40S ribosomal protein S19 / type: complex / ID: 62 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #63: 40S ribosomal protein S2

SupramoleculeName: 40S ribosomal protein S2 / type: complex / ID: 63 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #64: 40S ribosomal protein S21

SupramoleculeName: 40S ribosomal protein S21 / type: complex / ID: 64 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #65: 40S ribosomal protein S23

SupramoleculeName: 40S ribosomal protein S23 / type: complex / ID: 65 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #66: 40S ribosomal protein S24

SupramoleculeName: 40S ribosomal protein S24 / type: complex / ID: 66 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #67: 40S ribosomal protein S25

SupramoleculeName: 40S ribosomal protein S25 / type: complex / ID: 67 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #68: 40S ribosomal protein S26

SupramoleculeName: 40S ribosomal protein S26 / type: complex / ID: 68 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #69: 40S ribosomal protein S27

SupramoleculeName: 40S ribosomal protein S27 / type: complex / ID: 69 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #70: 40S ribosomal protein S27-like

SupramoleculeName: 40S ribosomal protein S27-like / type: complex / ID: 70 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #71: 40S ribosomal protein S28

SupramoleculeName: 40S ribosomal protein S28 / type: complex / ID: 71 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #72: 40S ribosomal protein S29

SupramoleculeName: 40S ribosomal protein S29 / type: complex / ID: 72 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #73: 40S ribosomal protein S3

SupramoleculeName: 40S ribosomal protein S3 / type: complex / ID: 73 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #74: 40S ribosomal protein S30

SupramoleculeName: 40S ribosomal protein S30 / type: complex / ID: 74 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #75: 40S ribosomal protein S3a

SupramoleculeName: 40S ribosomal protein S3a / type: complex / ID: 75 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #76: 40S ribosomal protein S4, X isoform

SupramoleculeName: 40S ribosomal protein S4, X isoform / type: complex / ID: 76 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #77: 40S ribosomal protein S5

SupramoleculeName: 40S ribosomal protein S5 / type: complex / ID: 77 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #78: 40S ribosomal protein S6

SupramoleculeName: 40S ribosomal protein S6 / type: complex / ID: 78 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #79: 40S ribosomal protein S7

SupramoleculeName: 40S ribosomal protein S7 / type: complex / ID: 79 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #80: 40S ribosomal protein S8

SupramoleculeName: 40S ribosomal protein S8 / type: complex / ID: 80 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #81: 40S ribosomal protein S9

SupramoleculeName: 40S ribosomal protein S9 / type: complex / ID: 81 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

+
Supramolecule #82: 40S ribosomal protein SA

SupramoleculeName: 40S ribosomal protein SA / type: complex / ID: 82 / Parent: 3
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMC2H3KO2potassium acetate
50.0 mMC8H18N2O4SHEPES, pH 7.4
5.0 mMMgCl2magnesium chloride
0.25 percent (w/v)C56H92O29digitonin
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: Two filter papers were added to each arm, 2.5 microliters of sample were added to grids, and 0.5 second of drain time was allowed before vitrification..
DetailsSample was well-dispersed on a thin (~2nm) carbon film.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5562 / Average exposure time: 3.8 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1049128
CTF correctionSoftware - Name: Gctf (ver. 0.5)
Startup modelType of model: EMDB MAP
EMDB ID:

5592


Details: EMD-5592, Human ribosome low pass-filtered to 50 Angstrom resolution
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 9 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 82684
FSC plot (resolution estimation)

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