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- EMDB-65849: Cryo-EM structure of the human UBR2 N-domain in complex with tryp... -

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Basic information

Entry
Database: EMDB / ID: EMD-65849
TitleCryo-EM structure of the human UBR2 N-domain in complex with tryptophan
Map data
Sample
  • Complex: Cryo-EM structure of the human UBR2 N-domain in complex with tryptophan
    • Protein or peptide: E3 ubiquitin-protein ligase UBR2
  • Ligand: TRYPTOPHAN
KeywordsUbiquitinalytion / METAL BINDING PROTEIN
Function / homology
Function and homology information


histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / positive regulation of T cell receptor signaling pathway / negative regulation of TOR signaling / reciprocal meiotic recombination / ubiquitin ligase complex ...histone H2A ubiquitin ligase activity / L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / male meiotic nuclear division / transposable element silencing / cellular response to L-leucine / positive regulation of T cell receptor signaling pathway / negative regulation of TOR signaling / reciprocal meiotic recombination / ubiquitin ligase complex / protein K63-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin formation / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin / zinc ion binding / nucleus / 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 UBR2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 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 UBR2 N-domain 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_65849.png

Downloads & links

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Map

FileDownload / File: emd_65849.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 267.2 Å		0.67 Å/pix.
x 400 pix.
= 267.2 Å		0.67 Å/pix.
x 400 pix.
= 267.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-1.3014119 - 2.0170279
Average (Standard dev.)-0.00014183974 (±0.034998514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 267.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65849_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_65849_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 UBR2 N-domain in complex with tryp...

EntireName: Cryo-EM structure of the human UBR2 N-domain in complex with tryptophan
Components
  • Complex: Cryo-EM structure of the human UBR2 N-domain in complex with tryptophan
    • Protein or peptide: E3 ubiquitin-protein ligase UBR2
  • Ligand: TRYPTOPHAN

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Supramolecule #1: Cryo-EM structure of the human UBR2 N-domain in complex with tryp...

SupramoleculeName: Cryo-EM structure of the human UBR2 N-domain 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 UBR2

MacromoleculeName: E3 ubiquitin-protein ligase UBR2 / 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: 200.781016 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: MASELEPEVQ AIDRSLLECS AEEIAGKWLQ ATDLTREVYQ HLAHYVPKIY CRGPNPFPQK EDMLAQHVLL GPMEWYLCGE DPAFGFPKL EQANKPSHLC GRVFKVGEPT YSCRDCAVDP TCVLCMECFL GSIHRDHRYR MTTSGGGGFC DCGDTEAWKE G PYCQKHEL ...String:
MASELEPEVQ AIDRSLLECS AEEIAGKWLQ ATDLTREVYQ HLAHYVPKIY CRGPNPFPQK EDMLAQHVLL GPMEWYLCGE DPAFGFPKL EQANKPSHLC GRVFKVGEPT YSCRDCAVDP TCVLCMECFL GSIHRDHRYR MTTSGGGGFC DCGDTEAWKE G PYCQKHEL NTSEIEEEED PLVHLSEDVI ARTYNIFAIT FRYAVEILTW EKESELPADL EMVEKSDTYY CMLFNDEVHT YE QVIYTLQ KAVNCTQKEA IGFATTVDRD GRRSVRYGDF QYCEQAKSVI VRNTSRQTKP LKVQVMHSSI VAHQNFGLKL LSW LGSIIG YSDGLRRILC QVGLQEGPDG ENSSLVDRLM LSDSKLWKGA RSVYHQLFMS SLLMDLKYKK LFAVRFAKNY QQLQ RDFME DDHERAVSVT ALSVQFFTAP TLARMLITEE NLMSIIIKTF MDHLRHRDAQ GRFQFERYTA LQAFKFRRVQ SLILD LKYV LISKPTEWSD ELRQKFLEGF DAFLELLKCM QGMDPITRQV GQHIEMEPEW EAAFTLQMKL THVISMMQDW CASDEK VLI EAYKKCLAVL MQCHGGYTDG EQPITLSICG HSVETIRYCV SQEKVSIHLP VSRLLAGLHV LLSKSEVAYK FPELLPL SE LSPPMLIEHP LRCLVLCAQV HAGMWRRNGF SLVNQIYYYH NVKCRREMFD KDVVMLQTGV SMMDPNHFLM IMLSRFEL Y QIFSTPDYGK RFSSEITHKD VVQQNNTLIE EMLYLIIMLV GERFSPGVGQ VNATDEIKRE IIHQLSIKPM AHSELVKSL PEDENKETGM ESVIEAVAHF KKPGLTGRGM YELKPECAKE FNLYFYHFSR AEQSKAEEAQ RKLKRQNRED TALPPPVLPP FCPLFASLV NILQSDVMLC IMGTILQWAV EHNGYAWSES MLQRVLHLIG MALQEEKQHL ENVTEEHVVT FTFTQKISKP G EAPKNSPS ILAMLETLQN APYLEVHKDM IRWILKTFNA VKKMRESSPT SPVAETEGTI MEESSRDKDK AERKRKAEIA RL RREKIMA QMSEMQRHFI DENKELFQQT LELDASTSAV LDHSPVASDM TLTALGPAQT QVPEQRQFVT CILCQEEQEV KVE SRAMVL AAFVQRSTVL SKNRSKFIQD PEKYDPLFMH PDLSCGTHTS SCGHIMHAHC WQRYFDSVQA KEQRRQQRLR LHTS YDVEN GEFLCPLCEC LSNTVIPLLL PPRNIFNNRL NFSDQPNLTQ WIRTISQQIK ALQFLRKEES TPNNASTKNS ENVDE LQLP EGFRPDFRPK IPYSESIKEM LTTFGTATYK VGLKVHPNEE DPRVPIMCWG SCAYTIQSIE RILSDEDKPL FGPLPC RLD DCLRSLTRFA AAHWTVASVS VVQGHFCKLF ASLVPNDSHE ELPCILDIDM FHLLVGLVLA FPALQCQDFS GISLGTG DL HIFHLVTMAH IIQILLTSCT EENGMDQENP PCEEESAVLA LYKTLHQYTG SALKEIPSGW HLWRSVRAGI MPFLKCSA L FFHYLNGVPS PPDIQVPGTS HFEHLCSYLS LPNNLICLFQ ENSEIMNSLI ESWCRNSEVK RYLEGERDAI RYPRESNKL INLPEDYSSL INQASNFSCP KSGGDKSRAP TLCLVCGSLL CSQSYCCQTE LEGEDVGACT AHTYSCGSGV GIFLRVRECQ VLFLAGKTK GCFYSPPYLD DYGETDQGLR RGNPLHLCKE RFKKIQKLWH QHSVTEEIGH AQEANQTLVG IDWQHL

UniProtKB: E3 ubiquitin-protein ligase UBR2

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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: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 416289
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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