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- EMDB-37167: Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37167
TitleCryo-EM structure of HRD1-SEL1LFL-XTP3B complex
Map data
Sample
  • Complex: Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex
    • Protein or peptide: E3 ubiquitin-protein ligase synoviolin
    • Protein or peptide: Endoplasmic reticulum lectin 1
    • Protein or peptide: ANA
    • Protein or peptide: Protein sel-1 homolog 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsERAD / protein degradation / ALLERGEN
Function / homology
Function and homology information


negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / endoplasmic reticulum mannose trimming / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / Pre-NOTCH Processing in Golgi / immature B cell differentiation / XBP1(S) activates chaperone genes / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol ...negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / endoplasmic reticulum mannose trimming / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / Pre-NOTCH Processing in Golgi / immature B cell differentiation / XBP1(S) activates chaperone genes / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol / triglyceride metabolic process / ubiquitin-specific protease binding / protein secretion / smooth endoplasmic reticulum / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / ERAD pathway / Notch signaling pathway / ER Quality Control Compartment (ERQC) / endomembrane system / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / RING-type E3 ubiquitin transferase / ABC-family proteins mediated transport / ubiquitin protein ligase activity / unfolded protein binding / protein-folding chaperone binding / ATPase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding / nucleoplasm / membrane
Similarity search - Function
Protein OS9-like domain / Protein OS-9-like / Glucosidase II beta subunit-like protein / : / : / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Mannose-6-phosphate receptor binding domain superfamily / MRH domain ...Protein OS9-like domain / Protein OS-9-like / Glucosidase II beta subunit-like protein / : / : / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Ring finger domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase synoviolin / Endoplasmic reticulum lectin 1 / Protein sel-1 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsQian HW / He JJ
Funding support1 items
OrganizationGrant numberCountry
Other privateKY9100000034
CitationJournal: To Be Published
Title: Cryo-EM structure of human complex A
Authors: Qian HW / He JJ
History
DepositionAug 13, 2023-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37167.png

Downloads & links

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Map

FileDownload / File: emd_37167.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0439
Minimum - Maximum-1.0006 - 1.1288905
Average (Standard dev.)0.00045841307 (±0.0172719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37167_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_37167_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 : Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex

EntireName: Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex
Components
  • Complex: Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex
    • Protein or peptide: E3 ubiquitin-protein ligase synoviolin
    • Protein or peptide: Endoplasmic reticulum lectin 1
    • Protein or peptide: ANA
    • Protein or peptide: Protein sel-1 homolog 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex

SupramoleculeName: Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase synoviolin

MacromoleculeName: E3 ubiquitin-protein ligase synoviolin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.744586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFRTAVMMAA SLALTGAVVA HAYYLKHQFY PTVVYLTKSS PSMAVLYIQA FVLVFLLGKV MGKVFFGQLR AAEMEHLLER SWYAVTETC LAFTVFRDDF SPRFVALFTL LLFLKCFHWL AEDRVDFMER SPNISWLFHC RIVSLMFLLG ILDFLFVSHA Y HSILTRGA ...String:
MFRTAVMMAA SLALTGAVVA HAYYLKHQFY PTVVYLTKSS PSMAVLYIQA FVLVFLLGKV MGKVFFGQLR AAEMEHLLER SWYAVTETC LAFTVFRDDF SPRFVALFTL LLFLKCFHWL AEDRVDFMER SPNISWLFHC RIVSLMFLLG ILDFLFVSHA Y HSILTRGA SVQLVFGFEY AILMTMVLTI FIKYVLHSVD LQSENPWDNK AVYMLYTELF TGFIKVLLYM AFMTIMIKVH TF PLFAIRP MYLAMRQFKK AVTDAIMSRR AIRNMNTLYP DATPEELQAM DNVCIICREE MVTGAKRLPC NHIFHTSCLR SWF QRQQTC PTCRMDVLRA SLPAQSPPPP EPADQGPPPA PHPPPLLPQP PNFPQGLLPP FPPGMFPLWP PMGPFPPVPP PPSS GEAVA PPSTSAAALS RPSGAATTTA AGTSATAASA TASGPGSGSA PEAGPAPGFP FPPPWMGMPL PPPFAFPPMP VPPAG FAGL TPEELRALEG HERQHLEARL QSLRNIHTLL DAAMLQINQY LTVLASLGPP RPATSVNSTE ETATTVVAAA SSTSIP SSE ATTPTPGASP PAPEMERPPA PESVGTEEMP EDGEPDAAEL RRRRLQKLES PVAH

UniProtKB: E3 ubiquitin-protein ligase synoviolin

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Macromolecule #2: Endoplasmic reticulum lectin 1

MacromoleculeName: Endoplasmic reticulum lectin 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.931109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGGGGVRS LVPGGPVLLV LCGLLEASGG GRALPQLSDD IPFRVNWPGT EFSLPTTGVL YKEDNYVIMT TAHKEKYKCI LPLVTSGDE EEEKDYKGPN PRELLEPLFK QSSCSYRIES YWTYEVCHGK HIRQYHEEKE TGQKINIHEY YLGNMLAKNL L FEKEREAE ...String:
MEEGGGGVRS LVPGGPVLLV LCGLLEASGG GRALPQLSDD IPFRVNWPGT EFSLPTTGVL YKEDNYVIMT TAHKEKYKCI LPLVTSGDE EEEKDYKGPN PRELLEPLFK QSSCSYRIES YWTYEVCHGK HIRQYHEEKE TGQKINIHEY YLGNMLAKNL L FEKEREAE EKEKSNEIPT KNIEGQMTPY YPVGMGNGTP CSLKQNRPRS STVMYICHPE SKHEILSVAE VTTCEYEVVI LT PLLCSHP KYRFRASPVN DIFCQSLPGS PFKPLTLRQL EQQEEILRVP FRRNKEEDLQ STKEERFPAI HKSIAIGSQP VLT VGTTHI SKLTDDQLIK EFLSGSYCFR GGVGWWKYEF CYGKHVHQYH EDKDSGKTSV VVGTWNQEEH IEWAKKNTAR AYHL QDDGT QTVRMVSHFY GNGDICDITD KPRQVTVKLK CKESDSPHAV TVYMLEPHSC QYILGVESPV ICKILDTADE NGLLS LPN

UniProtKB: Endoplasmic reticulum lectin 1

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Macromolecule #3: ANA

MacromoleculeName: ANA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 274.274 Da
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ANA

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Macromolecule #4: Protein sel-1 homolog 1

MacromoleculeName: Protein sel-1 homolog 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.170957 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RRQMQEAEMM YQTGMKILNG SNKKSQKREA YRYLQKAASM NHTKALERVS YALLFGDYLP QNIQAAREMF EKLTEEGSPK GQTALGFLY ASGLGVNSSQ AKALVYYTFG ALGGNLIAHM VLGYRYWAGI GVLQSCESAL THYRLVANHV ASDISLTGGS V VQRIRLPD ...String:
RRQMQEAEMM YQTGMKILNG SNKKSQKREA YRYLQKAASM NHTKALERVS YALLFGDYLP QNIQAAREMF EKLTEEGSPK GQTALGFLY ASGLGVNSSQ AKALVYYTFG ALGGNLIAHM VLGYRYWAGI GVLQSCESAL THYRLVANHV ASDISLTGGS V VQRIRLPD EVENPGMNSG MLEEDLIQYY QFLAEKGDVQ AQVGLGQLHL HGGRGVEQNH QRAFDYFNLA ANAGNSHAMA FL GKMYSEG SDIVPQSNET ALHYFKKAAD MGNPVGQSGL GMAYLYGRGV QVNYDLALKY FQKAAEQGWV DGQLQLGSMY YNG IGVKRD YKQALKYFNL ASQGGHILAF YNLAQMHASG TGVMRSCHTA VELFKNVCER GRWSERLMTA YNSYKDGDYN AAVI QYLLL AEQGYEVAQS NAAFILDQRE ASIVGENETY PRALLHWNRA ASQGYTVARI KLGDYHFYGF GTDVDYETAF IHYRL ASEQ QHSAQAMFNL GYMHEKGLGI KQDIHLAKRF YDMAAEASPD AQVPVFLALC KLGVVYFLQY IRE

UniProtKB: Protein sel-1 homolog 1

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration12 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215524
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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