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- EMDB-44224: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic... -

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Basic information

Entry
Database: EMDB / ID: EMD-44224
TitleUbiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg)
Map dataFull map from the gold-standard refinement, globally sharpened using an B-factor of -60 A^2, used for model building and refinement.
Sample
  • Complex: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (singly Ub-loaded E1-Ub-E2 complex)
    • Protein or peptide: Ubiquitin-activating enzyme E1 1
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
    • Protein or peptide: Ubiquitin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 4-aminobutanenitrile
Keywordsubiquitin / E1 / E2 / UBA1 / 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


E3 ubiquitin ligases ubiquitinate target proteins / Peroxisomal protein import / nuclear SCF ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / E2 ubiquitin-conjugating enzyme ...E3 ubiquitin ligases ubiquitinate target proteins / Peroxisomal protein import / nuclear SCF ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / SREBP signaling pathway / positive regulation of mitotic metaphase/anaphase transition / E2 ubiquitin-conjugating enzyme / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / ubiquitin ligase complex / modification-dependent protein catabolic process / protein polyubiquitination / protein tag activity / ubiquitin-protein transferase activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA damage response / nucleolus / magnesium ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle ...Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e 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-activating enzyme E1 1 / Ubiquitin-ribosomal protein eL40B fusion protein / Ubiquitin-conjugating enzyme E2 4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 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: To be published
Title: Structural basis for transthiolation intermediates in the ubiquitin pathway
Authors: Kochanczyk T / Hann ZS / Lux MC / Reyes AMVD / Ji C / Tan DS / Lima CD
History
DepositionMar 22, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44224.png

Downloads & links

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Map

FileDownload / File: emd_44224.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map from the gold-standard refinement, globally sharpened using an B-factor of -60 A^2, used for model building and refinement.
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.69
Minimum - Maximum-2.6710658 - 4.7714
Average (Standard dev.)0.0003045789 (±0.07227047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 408.576 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_44224_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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Additional map: Full map of Ub(T) 3D class 10 reconstructed...

Fileemd_44224_additional_10.map
AnnotationFull map of Ub(T) 3D class 10 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 8 reconstructed...

Fileemd_44224_additional_11.map
AnnotationFull map of Ub(T) 3D class 8 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 7 reconstructed...

Fileemd_44224_additional_2.map
AnnotationFull map of Ub(T) 3D class 7 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 5 reconstructed...

Fileemd_44224_additional_3.map
AnnotationFull map of Ub(T) 3D class 5 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 1 reconstructed...

Fileemd_44224_additional_4.map
AnnotationFull map of Ub(T) 3D class 1 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 9 reconstructed...

Fileemd_44224_additional_5.map
AnnotationFull map of Ub(T) 3D class 9 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 4 reconstructed...

Fileemd_44224_additional_6.map
AnnotationFull map of Ub(T) 3D class 4 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 6 reconstructed...

Fileemd_44224_additional_7.map
AnnotationFull map of Ub(T) 3D class 6 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 3 reconstructed...

Fileemd_44224_additional_8.map
AnnotationFull map of Ub(T) 3D class 3 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map of Ub(T) 3D class 2 reconstructed...

Fileemd_44224_additional_9.map
AnnotationFull map of Ub(T) 3D class 2 reconstructed using particle alignment information and a half-set split from the gold-standard refinement of the parental set (singly Ub-loaded - cluster 5).
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_44224_half_map_1.map
AnnotationHalf map 1 from the gold-standard refinement.
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 from the gold-standard refinement.

Fileemd_44224_half_map_2.map
AnnotationHalf map 2 from the gold-standard refinement.
Projections & Slices
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Sample components

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Entire : Covalent E1-Ub-E2 transthiolation intermediate mimic complex (sin...

EntireName: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (singly Ub-loaded E1-Ub-E2 complex)
Components
  • Complex: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (singly Ub-loaded E1-Ub-E2 complex)
    • Protein or peptide: Ubiquitin-activating enzyme E1 1
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 4
    • Protein or peptide: Ubiquitin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 4-aminobutanenitrile

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Supramolecule #1: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (sin...

SupramoleculeName: Covalent E1-Ub-E2 transthiolation intermediate mimic complex (singly Ub-loaded E1-Ub-E2 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-activating enzyme E1 1

MacromoleculeName: Ubiquitin-activating enzyme E1 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 111.764047 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SNTIDEGLYS RQLYVLGHEA MKQMSQSNVL IIGCKGLGVE IAKNVCLAGV KSVTLYDPQP TRIEDLSSQY FLTEDDIGVP RAKVTVSKL AELNQYVPVS VVDELSTEYL KNFKCVVVTE TSLTKQLEIN DFTHKNHIAY IAADSRGLFG SIFCDFGENF I CTDTDGNE ...String:
SNTIDEGLYS RQLYVLGHEA MKQMSQSNVL IIGCKGLGVE IAKNVCLAGV KSVTLYDPQP TRIEDLSSQY FLTEDDIGVP RAKVTVSKL AELNQYVPVS VVDELSTEYL KNFKCVVVTE TSLTKQLEIN DFTHKNHIAY IAADSRGLFG SIFCDFGENF I CTDTDGNE PLTGMIASIT DDGVVTMLEE TRHGLENGDF VKFTEVKGMP GLNDGTPRKV EVKGPYTFSI GSVKDLGSAG YN GVFTQVK VPTKISFKSL RESLKDPEYV YPDFGKMMRP PQYHIAFQAL SAFADAHEGS LPRPRNDIDA AEFFEFCKKI AST LQFDVE LDEKLIKEIS YQARGDLVAM SAFLGGAVAQ EVLKATTSKF YPLKQYFYFD SLESLPSSVT ISEETCKPRG CRYD GQIAV FGSEFQEKIA SLSTFLVGAG AIGCEMLKNW AMMGVATGES GHISVTDMDS IEKSNLNRQF LFRPRDVGKL KSECA STAV SIMNPSLTGK ITSYQERVGP ESEGIFGDEF FEKLSLVTNA LDNVEARMYV DRRCVFFEKP LLESGTLGTK GNTQVV VPH LTESYGSSQD PPEKSFPICT LKNFPNRIEH TIAWARDLFE GLFKQPIDNV NMYLSSPNFL ETSLKTSSNP REVLENI RD YLVTEKPLSF EECIMWARLQ FDKFFNNNIQ QLLFNFPKDS VTSTGQPFWS GPKRAPTPLS FDIHNREHFD FIVAAASL Y AFNYGLKSET DPAIYERVLA GYNPPPFAPK SGIKIQVNEN EEAPETAANK DKQELKSIAD SLPPPSSLVG FRLTPAEFE KDDDSNHHID FITAASNLRA MNYDITPADR FKTKFVAGKI VPAMCTSTAV VSGLVCLELV KLVDGKKKIE EYKNGFFNLA IGLFTFSDP IASPKMKVNG KEIDKIWDRY NLPDCTLQEL IDYFQKEEGL EVTMLSSGVS LLYANFQPPK KLAERLPLKI S ELVEQITK KKLEPFRKHL VLEICCDDAN GEDVEVPFIC IKL

UniProtKB: Ubiquitin-activating enzyme E1 1

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Macromolecule #2: Ubiquitin-conjugating enzyme E2 4

MacromoleculeName: Ubiquitin-conjugating enzyme E2 4 / type: protein_or_peptide / ID: 2 / 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 #3: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: 4-aminobutanenitrile

MacromoleculeName: 4-aminobutanenitrile / type: ligand / ID: 6 / 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

Concentration3 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
20.0 mMC4H12NO3Tris HCl buffer
100.0 mMNaClSodium chloride
5.0 mMMgCl2Magnesium chloride
1.0 mMC10H16N5O13P3Adenosine triphosphate
0.5 mg/mlC32H59N2O8SCHAPSO

Details: 20 mM Tris-HCl, 100 mM NaCl, 5 mM MgCl2, 1 mM ATP, 0.05% 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: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24668
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-9b5t:
Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg)

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