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- EMDB-21120: Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), an... -

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Entry
Database: EMDB / ID: EMD-21120
TitleAnkyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), and ElonginC (ELOC) bound to its substrate Brain-type Creatine Kinase (CKB)
Map datasharpened map
Sample
  • Complex: Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), and ElonginC (ELOC) bound to its substrate Brain-type Creatine Kinase (CKB)
    • Protein or peptide: Creatine kinase B-type
    • Protein or peptide: Ankyrin repeat and SOCS box protein 9
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
Function / homology
Function and homology information


futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / RND3 GTPase cycle ...futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / RND3 GTPase cycle / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / substantia nigra development / transcription corepressor binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / positive regulation of protein catabolic process / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / protein ubiquitination / intracellular signal transduction / phosphorylation / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular exosome / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. ...Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Elongin B / Elongin-C / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Creatine kinase B-type / Elongin-C / Elongin-B / Ankyrin repeat and SOCS box protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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) releaseJan 15, 2020-
Map releaseApr 29, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.8
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  • Surface view with fitted model
  • Atomic models: PDB-6v9h
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21120.png

Downloads & links

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Map

FileDownload / File: emd_21120.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-2.6433063 - 4.3953366
Average (Standard dev.)-0.002291272 (±0.075924374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z348.000348.000348.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-2.6434.395-0.002

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Supplemental data

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Additional map: unfiltered map

Fileemd_21120_additional.map
Annotationunfiltered map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_21120_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_21120_half_map_2.map
Annotationhalf map 2
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), an...

EntireName: Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), and ElonginC (ELOC) bound to its substrate Brain-type Creatine Kinase (CKB)
Components
  • Complex: Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), and ElonginC (ELOC) bound to its substrate Brain-type Creatine Kinase (CKB)
    • Protein or peptide: Creatine kinase B-type
    • Protein or peptide: Ankyrin repeat and SOCS box protein 9
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B

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Supramolecule #1: Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), an...

SupramoleculeName: Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), and ElonginC (ELOC) bound to its substrate Brain-type Creatine Kinase (CKB)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Creatine kinase B-type

MacromoleculeName: Creatine kinase B-type / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: creatine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.699207 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MPFSNSHNAL KLRFPAEDEF PDLSAHNNHM AKVLTPELYA ELRAKSTPSG FTLDDVIQTG VDNPGHPYIM TVGCVAGDEE SYEVFKDLF DPIIEDRHGG YKPSDEHKTD LNPDNLQGGD DLDPNYVLSS RVRTGRSIRG FCLPPHCSRG ERRAIEKLAV E ALSSLDGD ...String:
MPFSNSHNAL KLRFPAEDEF PDLSAHNNHM AKVLTPELYA ELRAKSTPSG FTLDDVIQTG VDNPGHPYIM TVGCVAGDEE SYEVFKDLF DPIIEDRHGG YKPSDEHKTD LNPDNLQGGD DLDPNYVLSS RVRTGRSIRG FCLPPHCSRG ERRAIEKLAV E ALSSLDGD LAGRYYALKS MTEAEQQQLI DDHFLFDKPV SPLLLASGMA RDWPDARGIW HNDNKTFLVW VNEEDHLRVI SM QKGGNMK EVFTRFCTGL TQIETLFKSK DYEFMWNPHL GYILTCPSNL GTGLRAGVHI KLPNLGKHEK FSEVLKRLRL QKR GTGGVD TAAVGGVFDV SNADRLGFSE VELVQMVVDG VKLLIEMEQR LEQGQAIDDL MPAQK

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Macromolecule #2: Ankyrin repeat and SOCS box protein 9

MacromoleculeName: Ankyrin repeat and SOCS box protein 9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.186141 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKHHHHHHHH GGLVPRGSHG MDGKQGGMDG SKPAGPRDFP GIRLLSNPLM GDAVSDWSPM HEAAIHGHQL SLRNLISQGW AVNIITADH VSPLHEACLG GHLSCVKILL KHGAQVNGVT ADWHTPLFNA CVSGSWDCVN LLLQHGASVQ PESDLASPIH E AARRGHVE ...String:
MKHHHHHHHH GGLVPRGSHG MDGKQGGMDG SKPAGPRDFP GIRLLSNPLM GDAVSDWSPM HEAAIHGHQL SLRNLISQGW AVNIITADH VSPLHEACLG GHLSCVKILL KHGAQVNGVT ADWHTPLFNA CVSGSWDCVN LLLQHGASVQ PESDLASPIH E AARRGHVE CVNSLIAYGG NIDHKISHLG TPLYLACENQ QRACVKKLLE SGADVNQGKG QDSPLHAVAR TASEELACLL MD FGADTQA KNAEGKRPVE LVPPESPLAQ LFLEREGPPS LMQLCRLRIR KCFGIQQHHK ITKLVLPEDL KQFLLHL

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.974616 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MMYVKLISSD GHEFIVKREH ALTSGTIKAM LSGPGQFAEN ETNEVNFREI PSHVLSKVCM YFTYKVRYTN SSTEIPEFPI APEIALELL MAANFLDC

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Macromolecule #4: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot, blot force 20.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1309964
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: AB INITIO MODEL GENERATION IN CRYOSPARC v2
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Details: Non-uniform refinement in cryoSPARC v2 / Number images used: 285105

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Atomic model buiding 1

Initial model(PDB ID:

3zng

,

3drb

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6v9h:
Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), and ElonginC (ELOC) bound to its substrate Brain-type Creatine Kinase (CKB)

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