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- EMDB-44589: human ZYG11B ElonginB/C complex binding to SARS-CoV2 Orf10 protein -

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Basic information

Entry
Database: EMDB / ID: EMD-44589
Titlehuman ZYG11B ElonginB/C complex binding to SARS-CoV2 Orf10 protein
Map data
Sample
  • Complex: Ternary complex of ZYG11B and Elon/C
    • Protein or peptide: Protein zyg-11 homolog B
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Putative ORF10 protein
KeywordsGly/N degron / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery ...target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / 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 / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Orf10 protein, SARS-CoV-2 / : / : / Protein zer-1 homolog-like, C-terminal domain / Zer-1-like, Leucine-rich repeats / : / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain ...Orf10 protein, SARS-CoV-2 / : / : / Protein zer-1 homolog-like, C-terminal domain / Zer-1-like, Leucine-rich repeats / : / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Leucine-rich repeat profile. / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Putative ORF10 protein / Elongin-C / Elongin-B / Protein zyg-11 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu X / Gross JD
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 23, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44589.png

Downloads & links

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Map

FileDownload / File: emd_44589.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 256 pix.
= 213.76 Å		0.84 Å/pix.
x 256 pix.
= 213.76 Å		0.84 Å/pix.
x 256 pix.
= 213.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-29.623707 - 38.113154999999999
Average (Standard dev.)0.000000000000081 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44589_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44589_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of ZYG11B and Elon/C

EntireName: Ternary complex of ZYG11B and Elon/C
Components
  • Complex: Ternary complex of ZYG11B and Elon/C
    • Protein or peptide: Protein zyg-11 homolog B
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Putative ORF10 protein

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Supramolecule #1: Ternary complex of ZYG11B and Elon/C

SupramoleculeName: Ternary complex of ZYG11B and Elon/C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 kDa/nm

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Macromolecule #1: Protein zyg-11 homolog B

MacromoleculeName: Protein zyg-11 homolog B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.463344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SHMVDPEDQA GAAMEEASPY SLLDICLNFL TTHLEKFCSA RQDGTLCLQE PGVFPQEVAD RLLRTMAFHG LLNDGTVGIF RGNQMRLKR ACIRKAKISA VAFRKAFCHH KLVELDATGV NADITITDII SGLGSNKWIQ QNLQCLVLNS LTLSLEDPYE R CFSRLSGL ...String:
SHMVDPEDQA GAAMEEASPY SLLDICLNFL TTHLEKFCSA RQDGTLCLQE PGVFPQEVAD RLLRTMAFHG LLNDGTVGIF RGNQMRLKR ACIRKAKISA VAFRKAFCHH KLVELDATGV NADITITDII SGLGSNKWIQ QNLQCLVLNS LTLSLEDPYE R CFSRLSGL RALSITNVLF YNEDLAEVAS LPRLESLDIS NTSITDITAL LACKDRLKSL TMHHLKCLKM TTTQILDVVR EL KHLNHLD ISDDKQFTSD IALRLLEQKD ILPNLVSLDV SGRKHVTDKA VEAFIQQRPS MQFVGLLATD AGYSEFLTGE GHL KVSGEA NETQIAEALK RYSERAFFVR EALFHLFSLT HVMEKTKPEI LKLVVTGMRN HPMNLPVQLA ASACVFNLTK QDLA AGMPV RLLADVTHLL LKAMEHFPNH QQLQKNCLLS LCSDRILQDV PFNRFEAAKL VMQWLCNHED QNMQRMAVAI ISILA AKLS TEQTAQLGTE LFIVRQLLQI VKQKTNQNSV DTTLKFTLSA LWNLTDESPT TCRHFIENQG LELFMRVLES FPTESS IQQ KVLGLLNNIA EVQELHSELM WKDFIDHISS LLHSVEVEVS YFAAGIIAHL ISRGEQAWTL SRSQRNSLLD DLHSAIL KW PTPECEMVAY RSFNPFFPLL GCFTTPGVQL WAVWAMQHVC SKNPSRYCSM LIEEGGLQHL YNIKDHEHTD PHVQQIAV A ILDSLEKHIV RHGRPPPCKK QPQARLN

UniProtKB: Protein zyg-11 homolog B

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Macromolecule #2: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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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: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

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Macromolecule #4: Putative ORF10 protein

MacromoleculeName: Putative ORF10 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 4.451198 KDa
SequenceString:
MGYINVFAFP FTIYSLLLCR MNSRNYIAQV DVVNFNLT

UniProtKB: Putative ORF10 protein

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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

Concentration0.25 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 75 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 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

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325264
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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