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- EMDB-70200: CHIP E3 ligase CC domain dimer-Fab 2D2 epitope focused refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-70200
TitleCHIP E3 ligase CC domain dimer-Fab 2D2 epitope focused refinement
Map dataCHIP:2D2 epitope
Sample
  • Complex: Fab 2D2-CHIP E3 ligase CC domain epitope
    • Protein or peptide: E3 ubiquitin-protein ligase CHIP
    • Protein or peptide: 2D2 Fab light chain
    • Protein or peptide: 2D2 Fab heavy chain
KeywordsU-box E3 ligase / Fab / Cryo-EM / Protein degradation / LIGASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / negative regulation of peroxisome proliferator activated receptor signaling pathway / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of mitophagy / ERBB2 signaling pathway / negative regulation of cardiac muscle hypertrophy ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / negative regulation of peroxisome proliferator activated receptor signaling pathway / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of mitophagy / ERBB2 signaling pathway / negative regulation of cardiac muscle hypertrophy / nuclear inclusion body / misfolded protein binding / cellular response to misfolded protein / RIPK1-mediated regulated necrosis / ubiquitin-ubiquitin ligase activity / chaperone-mediated autophagy / TPR domain binding / SMAD binding / positive regulation of proteolysis / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / protein quality control for misfolded or incompletely synthesized proteins / protein folding chaperone complex / protein monoubiquitination / protein K63-linked ubiquitination / ubiquitin ligase complex / protein autoubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / Hsp70 protein binding / response to ischemia / positive regulation of protein ubiquitination / Downregulation of TGF-beta receptor signaling / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein stability / Regulation of TNFR1 signaling / Hsp90 protein binding / RING-type E3 ubiquitin transferase / G protein-coupled receptor binding / Regulation of necroptotic cell death / tau protein binding / Downregulation of ERBB2 signaling / kinase binding / Z disc / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / MAPK cascade / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to heat / protein-folding chaperone binding / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / protein stabilization / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / TPR repeat region circular profile. / TPR repeat profile. ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsUnnikrishnan A / Southworth D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG068125 United States
CitationJournal: To Be Published
Title: Structures of Fab-stabilized CHIP reveal a conformational switch important in E3 ligase and chaperone functions
Authors: Unnikrishnan A / Southworth D
History
DepositionApr 15, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70200.png

Downloads & links

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Map

FileDownload / File: emd_70200.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCHIP:2D2 epitope
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.3573325 - 4.2760935
Average (Standard dev.)-0.00014620183 (±0.03697572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-mapB

Fileemd_70200_half_map_1.map
Annotationhalf-mapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-mapA

Fileemd_70200_half_map_2.map
Annotationhalf-mapA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fab 2D2-CHIP E3 ligase CC domain epitope

EntireName: Fab 2D2-CHIP E3 ligase CC domain epitope
Components
  • Complex: Fab 2D2-CHIP E3 ligase CC domain epitope
    • Protein or peptide: E3 ubiquitin-protein ligase CHIP
    • Protein or peptide: 2D2 Fab light chain
    • Protein or peptide: 2D2 Fab heavy chain

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Supramolecule #1: Fab 2D2-CHIP E3 ligase CC domain epitope

SupramoleculeName: Fab 2D2-CHIP E3 ligase CC domain epitope / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase CHIP

MacromoleculeName: E3 ubiquitin-protein ligase CHIP / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.600283 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SIEERRIHQE SELHSYLSRL IAAERERELE ECQRNHEGDE DDSHVRAQQA CIEAKHDKYM ADMDELFSQV DE

UniProtKB: E3 ubiquitin-protein ligase CHIP

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Macromolecule #2: 2D2 Fab light chain

MacromoleculeName: 2D2 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.435996 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LETTLTQSPG TLSLSPGERA TLSCRASQSV SSTFLAWYQQ KPGQAPRLLI YGASRRATGI PDRFSGSGSG TDFTLTISRL EPEDFAVYY CQRYGATYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
LETTLTQSPG TLSLSPGERA TLSCRASQSV SSTFLAWYQQ KPGQAPRLLI YGASRRATGI PDRFSGSGSG TDFTLTISRL EPEDFAVYY CQRYGATYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGE

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Macromolecule #3: 2D2 Fab heavy chain

MacromoleculeName: 2D2 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.889672 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AQVQLQQSGP GLMKGGQTLS LTCAISGDSV SSNSAAWNWI RQSPSRGLEW LGRTYYRSKW YNEYAVSVKS RITINPDTSK NQFSLQLNS VTPEDTAVYY CARAVAASFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
AQVQLQQSGP GLMKGGQTLS LTCAISGDSV SSNSAAWNWI RQSPSRGLEW LGRTYYRSKW YNEYAVSVKS RITINPDTSK NQFSLQLNS VTPEDTAVYY CARAVAASFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSC

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction from cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 337834
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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