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- EMDB-21121: cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) -

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Basic information

Entry
Database: EMDB / ID: EMD-21121
Titlecryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)
Map data
Samplecryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)
  • Immunoglobulin G-binding protein G,Cullin-5
  • RING-box protein 2
  • ligand
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / ERBB2 signaling pathway / Neddylation / cullin-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / Cul5-RING ubiquitin ligase complex / protein neddylation / NEDD8 ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...radial glia guided migration of Purkinje cell / cerebral cortex radially oriented cell migration / ERBB2 signaling pathway / Neddylation / cullin-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / Cul5-RING ubiquitin ligase complex / protein neddylation / NEDD8 ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / site of DNA damage / IgG binding / intrinsic apoptotic signaling pathway in response to oxidative stress / cullin family protein binding / apoptotic mitochondrial changes / intrinsic apoptotic signaling pathway / calcium channel activity / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Downregulation of ERBB2 signaling / G1/S transition of mitotic cell cycle / ubiquitin protein ligase activity / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / activation of cysteine-type endopeptidase activity involved in apoptotic process / Neddylation / cell wall / ubiquitin-dependent protein catabolic process / signaling receptor activity / protein ubiquitination / ubiquitin protein ligase binding / negative regulation of apoptotic process / zinc ion binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
RING-H2 zinc finger domain / Zinc finger, RING-H2-type / Cullin protein neddylation domain / Cullin family signature. / Cullin, conserved site / Cullin protein neddylation domain / Cullin protein, neddylation domain / Cullin repeat-like-containing domain superfamily / IgG-binding B / B domain ...RING-H2 zinc finger domain / Zinc finger, RING-H2-type / Cullin protein neddylation domain / Cullin family signature. / Cullin, conserved site / Cullin protein neddylation domain / Cullin protein, neddylation domain / Cullin repeat-like-containing domain superfamily / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Cullin / Cullin, N-terminal / Cullin family / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Winged helix DNA-binding domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / Cullin-5 / RING-box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsKomives EA / Lumpkin RJ / Baker RW / Leschziner AE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817774 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structure and dynamics of the ASB9 CUL-RING E3 Ligase.
Authors: Ryan J Lumpkin / Richard W Baker / Andres E Leschziner / Elizabeth A Komives /
Abstract: The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18- ...The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18-member ankyrin and SOCS box (ASB) family is the largest substrate receptor family. Here we report cryo-EM data for the substrate, creatine kinase (CKB) bound to ASB9-ELOB/C, and for full-length CUL5 bound to the RING protein, RBX2, which binds various E2s. To date, no full structures are available either for a substrate-bound ASB nor for CUL5. Hydrogen-deuterium exchange (HDX-MS) mapped onto a full structural model of the ligase revealed long-range allostery extending from the substrate through CUL5. We propose a revised allosteric mechanism for how CUL-E3 ligases function. ASB9 and CUL5 behave as rigid rods, connected through a hinge provided by ELOB/C transmitting long-range allosteric crosstalk from the substrate through CUL5 to the RBX2 flexible linker.
History
DepositionDec 13, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v9i
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21121.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 200 pix.
= 232. Å
1.16 Å/pix.
x 200 pix.
= 232. Å
1.16 Å/pix.
x 200 pix.
= 232. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-0.4154094 - 1.7585512
Average (Standard dev.)0.0060616485 (±0.07242459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 232.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z232.000232.000232.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.4151.7590.006

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Supplemental data

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Additional map: unfiltered map

Fileemd_21121_additional.map
Annotationunfiltered map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: half map 1

Fileemd_21121_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: unfiltered map

Fileemd_21121_half_map_2.map
Annotationunfiltered map
Projections & Slices
AxesZYX

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Density Histograms

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Sample components

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Entire cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)

EntireName: cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)
Number of Components: 4

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Component #1: protein, cryo-EM structure of Cullin5 bound to RING-box protein 2...

ProteinName: cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)
Recombinant expression: No
MassTheoretical: 100 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: BL21

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Component #2: protein, Immunoglobulin G-binding protein G,Cullin-5

ProteinName: Immunoglobulin G-binding protein G,Cullin-5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.4565 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #3: protein, RING-box protein 2

ProteinName: RING-box protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.7215 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: 4 second blot time, blot force 20.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 59 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 36000 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1200.0 - 2000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 46877
3D reconstructionSoftware: cryoSPARC / Resolution: 5.2 Å / Resolution Method: FSC 0.143 CUT-OFF / Details: Non-uniform refinement in cryoSPARC v2 / Euler angles: Non-uniform refinement in cryoSPARC v2.

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 4JGH, 3DPL
Output model

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