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- EMDB-63169: dimeric ZYG11B-EloB-EloC + substrate peptide GYIND -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63169
Titledimeric ZYG11B-EloB-EloC + substrate peptide GYIND
Map data
Sample
  • Complex: dimeric ZYG11B-EloB-EloC + susbstrate peptide GYIND
    • Protein or peptide: Protein zyg-11 homolog B,Green fluorescent protein
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: GLY-TYR-ILE-ASN-ASP
Keywordsdimeric ZYG11B-EloB-EloC + substrate peptide GYIND / LIGASE
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 / bioluminescence / transcription corepressor binding / generation of precursor metabolites and energy / 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
: / : / 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 ...: / : / 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 / Green fluorescent protein, GFP / Leucine-rich repeat profile. / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Green fluorescent 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: 3.27 Å
AuthorsLin N / Wang Y / Gao P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of dimeric ZYG11B-EloB-EloC with substrate peptide GYIND at 3.27 Angstroms resolution.
Authors: Lin N / Wang Y / Gao P
History
DepositionJan 16, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63169.png

Downloads & links

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Map

FileDownload / File: emd_63169.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 320 pix.
= 256. Å		0.8 Å/pix.
x 320 pix.
= 256. Å		0.8 Å/pix.
x 320 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0661
Minimum - Maximum-0.49278352 - 0.9448291
Average (Standard dev.)0.00053260423 (±0.020891313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63169_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63169_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 : dimeric ZYG11B-EloB-EloC + susbstrate peptide GYIND

EntireName: dimeric ZYG11B-EloB-EloC + susbstrate peptide GYIND
Components
  • Complex: dimeric ZYG11B-EloB-EloC + susbstrate peptide GYIND
    • Protein or peptide: Protein zyg-11 homolog B,Green fluorescent protein
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: GLY-TYR-ILE-ASN-ASP

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Supramolecule #1: dimeric ZYG11B-EloB-EloC + susbstrate peptide GYIND

SupramoleculeName: dimeric ZYG11B-EloB-EloC + susbstrate peptide GYIND / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein zyg-11 homolog B,Green fluorescent protein

MacromoleculeName: Protein zyg-11 homolog B,Green fluorescent protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.848242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPEDQAGAAM EEASPYSLLD ICLNFLTTHL EKFCSARQDG TLCLQEPGVF PQEVADRLLR TMAFHGLLND GTVGIFRGNQ MRLKRACIR KAKISAVAFR KAFCHHKLVE LDATGVNADI TITDIISGLG SNKWIQQNLQ CLVLNSLTLS LEDPYERCFS R LSGLRALS ...String:
MPEDQAGAAM EEASPYSLLD ICLNFLTTHL EKFCSARQDG TLCLQEPGVF PQEVADRLLR TMAFHGLLND GTVGIFRGNQ MRLKRACIR KAKISAVAFR KAFCHHKLVE LDATGVNADI TITDIISGLG SNKWIQQNLQ CLVLNSLTLS LEDPYERCFS R LSGLRALS ITNVLFYNED LAEVASLPRL ESLDISNTSI TDITALLACK DRLKSLTMHH LKCLKMTTTQ ILDVVRELKH LN HLDISDD KQFTSDIALR LLEQKDILPN LVSLDVSGRK HVTDKAVEAF IQQRPSMQFV GLLATDAGYS EFLTGEGHLK VSG EANETQ IAEALKRYSE RAFFVREALF HLFSLTHVME KTKPEILKLV VTGMRNHPMN LPVQLAASAC VFNLTKQDLA AGMP VRLLA DVTHLLLKAM EHFPNHQQLQ KNCLLSLCSD RILQDVPFNR FEAAKLVMQW LCNHEDQNMQ RMAVAIISIL AAKLS TEQT AQLGTELFIV RQLLQIVKQK TNQNSVDTTL KFTLSALWNL TDESPTTCRH FIENQGLELF MRVLESFPTE SSIQQK VLG LLNNIAEVQE LHSELMWKDF IDHISSLLHS VEVEVSYFAA GIIAHLISRG EQAWTLSRSQ RNSLLDDLHS AILKWPT PE CEMVAYRSFN PFFPLLGCFT TPGVQLWAVW AMQHVCSKNP SRYCSMLIEE GGLQHLYNIK DHEHTDPHVQ QIAVAILD S LEKHIVRHGR PPPCKKQPQA RLNKLGSENL YFQGGSGSKG EELFTGVVPI LVELDGDVNG HKFSVSGEGE GDATYGKLT LKFICTTGKL PVPWPTLVTT LTYGVQCFSR YPDHMKRHDF FKSAMPEGYV QERTISFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKE DGNILGHKLE YNYNSHNVYI TADKQKNGIK ANFKIRHNIE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS T QSALSKDP NEKRDHMVLL EFVTAAGITH GMDELYKGSG HHHHHHHHHH H

UniProtKB: Protein zyg-11 homolog B, Green fluorescent protein

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Macromolecule #2: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.393124 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
HHHHHHHHGS ENLYFQGGSM DVFLMIRRHK TTIFTDAKES STVFELKRIV EGILKRPPDE QRLYKDDQLL DDGKTLGECG FTSQTARPQ APATVGLAFR ADDTFEALCI EPFSSPPELP DVMKPQDSGS SANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.485135 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC

UniProtKB: Elongin-C

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Macromolecule #4: GLY-TYR-ILE-ASN-ASP

MacromoleculeName: GLY-TYR-ILE-ASN-ASP / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 580.589 Da
SequenceString:
GYIND

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 186147
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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