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- EMDB-24822: 20S proteasome from red blood cell lysate -

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Basic information

Entry
Database: EMDB / ID: EMD-24822
Title20S proteasome from red blood cell lysate
Map data20S proteasome from red blood cell lysate
Sample
  • Complex: 20S proteasome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsVerbeke EJ / Taylor DW
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122480, R35GM138348 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160088 United States
National Science Foundation (NSF, United States)2019238253 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)HD085901, DK110520 United States
Welch FoundationW911NF-15-1-0120, F-1515, F-1938 United States
CitationJournal: Cell Rep / Year: 2022
Title: The protein organization of a red blood cell.
Authors: Wisath Sae-Lee / Caitlyn L McCafferty / Eric J Verbeke / Pierre C Havugimana / Ophelia Papoulas / Claire D McWhite / John R Houser / Kim Vanuytsel / George J Murphy / Kevin Drew / Andrew ...Authors: Wisath Sae-Lee / Caitlyn L McCafferty / Eric J Verbeke / Pierre C Havugimana / Ophelia Papoulas / Claire D McWhite / John R Houser / Kim Vanuytsel / George J Murphy / Kevin Drew / Andrew Emili / David W Taylor / Edward M Marcotte /
Abstract: Red blood cells (RBCs) (erythrocytes) are the simplest primary human cells, lacking nuclei and major organelles and instead employing about a thousand proteins to dynamically control cellular ...Red blood cells (RBCs) (erythrocytes) are the simplest primary human cells, lacking nuclei and major organelles and instead employing about a thousand proteins to dynamically control cellular function and morphology in response to physiological cues. In this study, we define a canonical RBC proteome and interactome using quantitative mass spectrometry and machine learning. Our data reveal an RBC interactome dominated by protein homeostasis, redox biology, cytoskeletal dynamics, and carbon metabolism. We validate protein complexes through electron microscopy and chemical crosslinking and, with these data, build 3D structural models of the ankyrin/Band 3/Band 4.2 complex that bridges the spectrin cytoskeleton to the RBC membrane. The model suggests spring-like compression of ankyrin may contribute to the characteristic RBC cell shape and flexibility. Taken together, our study provides an in-depth view of the global protein organization of human RBCs and serves as a comprehensive resource for future research.
History
DepositionSep 6, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateAug 24, 2022-
Current statusAug 24, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24822.png

Downloads & links

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Map

FileDownload / File: emd_24822.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation20S proteasome from red blood cell lysate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.857
Minimum - Maximum-2.0422788 - 3.7398577
Average (Standard dev.)0.0044141104 (±0.12163241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 376.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24822_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_24822_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_24822_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 20S proteasome

EntireName: 20S proteasome
Components
  • Complex: 20S proteasome

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Supramolecule #1: 20S proteasome

SupramoleculeName: 20S proteasome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Details: 20S proteasome from red blood cell lysate
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.09 µm / Nominal magnification: 22500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1016378
CTF correctionSoftware - Name: Warp
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 59972
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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