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- EMDB-44203: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44203
TitleUbiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 4
Map dataFull map from the gold-standard refinement, globally sharpened using an B-factor of -40 A^2, used for model building and refinement.
Sample
  • Complex: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
    • Protein or peptide: E3 ubiquitin-protein ligase pub2
  • Protein or peptide: Ubiquitin
  • Ligand: 4-aminobutanenitrile
KeywordsUBIQUITIN / E2 / E3 / HECT / NEDD4 / RSP5 / PUB2 / UBC4 / TRANSTHIOESTERIFICATION / THIOESTER / TRANSTHIOLATION / TETRAHEDRAL INTERMEDIATE / ADENYLATION / INHIBITOR / LIGASE / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / UBL / ATP ATP-BINDING / AMP / NUCLEOTIDE-BINDING / ISOPEPTIDE BOND
Function / homology
Function and homology information


RHOQ GTPase cycle / RHOU GTPase cycle / Regulation of PTEN localization / Regulation of PTEN stability and activity / cytoplasm to vacuole targeting by the NVT pathway / cell cortex of cell tip / Peroxisomal protein import / E3 ubiquitin ligases ubiquitinate target proteins / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation ...RHOQ GTPase cycle / RHOU GTPase cycle / Regulation of PTEN localization / Regulation of PTEN stability and activity / cytoplasm to vacuole targeting by the NVT pathway / cell cortex of cell tip / Peroxisomal protein import / E3 ubiquitin ligases ubiquitinate target proteins / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / HECT-type E3 ubiquitin transferase / E2 ubiquitin-conjugating enzyme / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cell division site / ubiquitin conjugating enzyme activity / modification-dependent protein catabolic process / protein tag activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleolus / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / WW domain ...E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / C2 domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40B fusion protein / Ubiquitin-conjugating enzyme E2 4 / E3 ubiquitin-protein ligase pub2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsKochanczyk T / Lima CD
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118080 United States
CitationJournal: Nature / Year: 2024
Title: Structural basis for transthiolation intermediates in the ubiquitin pathway.
Authors: Tomasz Kochańczyk / Zachary S Hann / Michaelyn C Lux / Avelyn Mae V Delos Reyes / Cheng Ji / Derek S Tan / Christopher D Lima /
Abstract: Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin ...Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3 complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next.
History
DepositionMar 22, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44203.png

Downloads & links

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Map

FileDownload / File: emd_44203.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map from the gold-standard refinement, globally sharpened using an B-factor of -40 A^2, used for model building and refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.525
Minimum - Maximum-1.9062346 - 4.1638594
Average (Standard dev.)0.00021270118 (±0.04095714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map from the gold-standard refinement (unsharpened).

Fileemd_44203_additional_1.map
AnnotationFull map from the gold-standard refinement (unsharpened).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from the gold-standard refinement.

Fileemd_44203_half_map_1.map
AnnotationHalf map 1 from the gold-standard refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from the gold-standard refinement.

Fileemd_44203_half_map_2.map
AnnotationHalf map 2 from the gold-standard refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex

EntireName: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex
Components
  • Complex: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
    • Protein or peptide: E3 ubiquitin-protein ligase pub2
  • Protein or peptide: Ubiquitin
  • Ligand: 4-aminobutanenitrile

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Supramolecule #1: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex

SupramoleculeName: Covalent E2-Ub-E3 HECT transthiolation intermediate mimic complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843

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Macromolecule #1: Ubiquitin-conjugating enzyme E2 4

MacromoleculeName: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 1
Details: C-terminal GGLVPR is a residual artifact after thrombin cleavage of affinity tag
Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 17.043336 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MALKRINREL ADLGKDPPSS SSAGPVGDDL FHWQATIMGP ADSPYAGGVF FLSIHFPTDY PFKPPKVNFT TRIYHPNINS NGSICLDIL RDQWSPALTI SKVLLSISSL LTDPNPDDPL VPEIAHVYKT DRSRYELSAR EWTRKYAIGG LVPR

UniProtKB: Ubiquitin-conjugating enzyme E2 4

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Macromolecule #2: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 2
Details: N-terminal GSGG is a residual artifact after TEV protease cleavage of affinity tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 8.769948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSGGMQIFVK TLTGKTITLE VESSDTIDNV KSKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRG

UniProtKB: Ubiquitin-ribosomal protein eL40B fusion protein

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Macromolecule #3: E3 ubiquitin-protein ligase pub2

MacromoleculeName: E3 ubiquitin-protein ligase pub2 / type: protein_or_peptide / ID: 3
Details: N-terminal SHM is a residual artifact after cleaving the affinity tag
Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 44.231828 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SHMDEYQRKI AYMYDRPEMA VNDAQLQLKV SRATTFEDAY DIISKLSVSD MKKKLLIRFR NEDGLDYGGV SREFFYILSH AIFNPGYSL FEYATDDNYG LQISPLSSVN PDFRSYFRFV GRVMGLAIYH RRYLDVQFVL PFYKRILQKP LCLEDVKDVD E VYYESLKW ...String:
SHMDEYQRKI AYMYDRPEMA VNDAQLQLKV SRATTFEDAY DIISKLSVSD MKKKLLIRFR NEDGLDYGGV SREFFYILSH AIFNPGYSL FEYATDDNYG LQISPLSSVN PDFRSYFRFV GRVMGLAIYH RRYLDVQFVL PFYKRILQKP LCLEDVKDVD E VYYESLKW IKNNDVDESL CLNFSVEENR FGESVTVDLI PNGRNIAVNN QNKMNYLKAL TEHKLVTSTE EQFNALKGGL NE LIPDSVL QIFNENELDT LLNGKRDIDV QDWKRFTDYR SYTETDDIVI WFWELLSEWS PEKKAKLLQF ATGTSRLPLS GFK DMHGSD GPRKFTIEKV GHISQLPKAH TCFNRLDIPP YNSKEELEQK LTIAIQETAG FGTE

UniProtKB: E3 ubiquitin-protein ligase pub2

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Macromolecule #4: 4-aminobutanenitrile

MacromoleculeName: 4-aminobutanenitrile / type: ligand / ID: 4 / Number of copies: 1 / Formula: A1AIV
Molecular weightTheoretical: 84.12 Da

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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

Concentration4.5 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
20.0 mMC4H12NO3Tris HCl buffer
100.0 mMNaClSodium chloride
1.0 mg/mlC32H59N2O8SCHAPSO

Details: 20 mM Tris-HCl, 100 mM NaCl, 0.1% CHAPSO
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 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) / Detector mode: SUPER-RESOLUTION / Average exposure time: 4.0 sec. / Average electron dose: 72.0 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: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model from cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 103055
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9b58:
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 4

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