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- EMDB-65850: Cryo-EM structure of the human UBR1 in complex with tryptophan -

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Basic information

Entry
Database: EMDB / ID: EMD-65850
TitleCryo-EM structure of the human UBR1 in complex with tryptophan
Map data
Sample
  • Complex: Cryo-EM structure of the human UBR1 in complex with tryptophan
    • Protein or peptide: E3 ubiquitin-protein ligase UBR1
  • Ligand: TRYPTOPHAN
KeywordsUbiquitination / LIGASE
Function / homology
Function and homology information


L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process ...L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) ...: / E3 ubiquitin-protein ligase ELL-like / E3 ubiquitin-protein ligase UBR-like, C-terminal / : / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsYan R / Hu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of the human UBR1 in complex with tryptophan
Authors: Yan R / Hu Z
History
DepositionAug 15, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65850.png

Downloads & links

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Map

FileDownload / File: emd_65850.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 450 pix.
= 301.5 Å		0.67 Å/pix.
x 450 pix.
= 301.5 Å		0.67 Å/pix.
x 450 pix.
= 301.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.0045217 - 1.5831249
Average (Standard dev.)-0.00040330473 (±0.027387101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 301.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65850_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_65850_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 the human UBR1 in complex with tryptophan

EntireName: Cryo-EM structure of the human UBR1 in complex with tryptophan
Components
  • Complex: Cryo-EM structure of the human UBR1 in complex with tryptophan
    • Protein or peptide: E3 ubiquitin-protein ligase UBR1
  • Ligand: TRYPTOPHAN

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Supramolecule #1: Cryo-EM structure of the human UBR1 in complex with tryptophan

SupramoleculeName: Cryo-EM structure of the human UBR1 in complex with tryptophan
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase UBR1

MacromoleculeName: E3 ubiquitin-protein ligase UBR1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200.446344 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: MADEEAGGTE RMEISAELPQ TPQRLASWWD QQVDFYTAFL HHLAQLVPEI YFAEMDPDLE KQEESVQMSI FTPLEWYLFG EDPDICLEK LKHSGAFQLC GRVFKSGETT YSCRDCAIDP TCVLCMDCFQ DSVHKNHRYK MHTSTGGGFC DCGDTEAWKT G PFCVNHEP ...String:
MADEEAGGTE RMEISAELPQ TPQRLASWWD QQVDFYTAFL HHLAQLVPEI YFAEMDPDLE KQEESVQMSI FTPLEWYLFG EDPDICLEK LKHSGAFQLC GRVFKSGETT YSCRDCAIDP TCVLCMDCFQ DSVHKNHRYK MHTSTGGGFC DCGDTEAWKT G PFCVNHEP GRAGTIKENS RCPLNEEVIV QARKIFPSVI KYVVEMTIWE EEKELPPELQ IREKNERYYC VLFNDEHHSY DH VIYSLQR ALDCELAEAQ LHTTAIDKEG RRAVKAGAYA ACQEAKEDIK SHSENVSQHP LHVEVLHSEI MAHQKFALRL GSW MNKIMS YSSDFRQIFC QACLREEPDS ENPCLISRLM LWDAKLYKGA RKILHELIFS SFFMEMEYKK LFAMEFVKYY KQLQ KEYIS DDHDRSISIT ALSVQMFTVP TLARHLIEEQ NVISVITETL LEVLPEYLDR NNKFNFQGYS QDKLGRVYAV ICDLK YILI SKPTIWTERL RMQFLEGFRS FLKILTCMQG MEEIRRQVGQ HIEVDPDWEA AIAIQMQLKN ILLMFQEWCA CDEELL LVA YKECHKAVMR CSTSFISSSK TVVQSCGHSL ETKSYRVSED LVSIHLPLSR TLAGLHVRLS RLGAVSRLHE FVSFEDF QV EVLVEYPLRC LVLVAQVVAE MWRRNGLSLI SQVFYYQDVK CREEMYDKDI IMLQIGASLM DPNKFLLLVL QRYELAEA F NKTISTKDQD LIKQYNTLIE EMLQVLIYIV GERYVPGVGN VTKEEVTMRE IIHLLCIEPM PHSAIAKNLP ENENNETGL ENVINKVATF KKPGVSGHGV YELKDESLKD FNMYFYHYSK TQHSKAEHMQ KKRRKQENKD EALPPPPPPE FCPAFSKVIN LLNCDIMMY ILRTVFERAI DTDSNLWTEG MLQMAFHILA LGLLEEKQQL QKAPEEEVTF DFYHKASRLG SSAMNIQMLL E KLKGIPQL EGQKDMITWI LQMFDTVKRL REKSCLIVAT TSGSESIKND EITHDKEKAE RKRKAEAARL HRQKIMAQMS AL QKNFIET HKLMYDNTSE MPGKEDSIME EESTPAVSDY SRIALGPKRG PSVTEKEVLT CILCQEEQEV KIENNAMVLS ACV QKSTAL TQHRGKPIEL SGEALDPLFM DPDLAYGTYT GSCGHVMHAV CWQKYFEAVQ LSSQQRIHVD LFDLESGEYL CPLC KSLCN TVIPIIPLQP QKINSENADA LAQLLTLARW IQTVLARISG YNIRHAKGEN PIPIFFNQGM GDSTLEFHSI LSFGV ESSI KYSNSIKEMV ILFATTIYRI GLKVPPDERD PRVPMLTWST CAFTIQAIEN LLGDEGKPLF GALQNRQHNG LKALMQ FAV AQRITCPQVL IQKHLVRLLS VVLPNIKSED TPCLLSIDLF HVLVGAVLAF PSLYWDDPVD LQPSSVSSSY NHLYLFH LI TMAHMLQILL TVDTGLPLAQ VQEDSEEAHS ASSFFAEISQ YTSGSIGCDI PGWYLWVSLK NGITPYLRCA ALFFHYLL G VTPPEELHTN SAEGEYSALC SYLSLPTNLF LLFQEYWDTV RPLLQRWCAD PALLNCLKQK NTVVRYPRKR NSLIELPDD YSCLLNQASH FRCPRSADDE RKHPVLCLFC GAILCSQNIC CQEIVNGEEV GACIFHALHC GAGVCIFLKI RECRVVLVEG KARGCAYPA PYLDEYGETD PGLKRGNPLH LSRERYRKLH LVWQQHCIIE EIARSQETNQ MLFGFNWQLL

UniProtKB: E3 ubiquitin-protein ligase UBR1

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Macromolecule #2: TRYPTOPHAN

MacromoleculeName: TRYPTOPHAN / type: ligand / ID: 2 / Number of copies: 1 / Formula: TRP
Molecular weightTheoretical: 204.225 Da
Chemical component information

ChemComp-TRP:
TRYPTOPHAN

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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: NITROGEN

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Average electron dose: 1.5625 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: 1.4000000000000001 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 151423
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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