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- EMDB-12319: Nematocida Huwe1 in open conformation -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-12319
TitleNematocida Huwe1 in open conformation
Map data
Sample
  • Complex: Huwe1
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1
KeywordsHuwe1 / Nematocida / E3 Ligase / HECT / LIGASE
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / membrane
Similarity search - Function
E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Armadillo-type fold
Similarity search - Domain/homology
HECT-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesNematocida sp. ERTm5 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.37 Å
AuthorsPetrova O / Grishkovskaya I
CitationJournal: To Be Published
Title: Crystal structure of HUWE1: One ring to ubiquitinate them all
Authors: Grabarrczyk DB / Petrova OA / Haselbach D / Kessler D / Clausen T
History
DepositionFeb 9, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00778
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00778
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nh3
  • Surface level: 0.00778
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12319.png

Downloads & links

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Map

FileDownload / File: emd_12319.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.00778 / Movie #1: 0.00778
Minimum - Maximum-0.013752628 - 0.035457514
Average (Standard dev.)0.000018617466 (±0.0010490206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z344.000344.000344.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0140.0350.000

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Supplemental data

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Mask #1

Fileemd_12319_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12319_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_12319_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 : Huwe1

EntireName: Huwe1
Components
  • Complex: Huwe1
    • Protein or peptide: E3 ubiquitin-protein ligase HUWE1

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Supramolecule #1: Huwe1

SupramoleculeName: Huwe1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nematocida sp. ERTm5 (fungus)
Molecular weightTheoretical: 287 KDa

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Macromolecule #1: E3 ubiquitin-protein ligase HUWE1

MacromoleculeName: E3 ubiquitin-protein ligase HUWE1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nematocida sp. ERTm5 (fungus)
Molecular weightTheoretical: 287.751281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKIERPMERR FSQPGKQISN TIKQLSNLPE EELPTYLNNI YEWRCAKTDL LYWVDVLDRF DEILKAVVTE YGLGQFQNKP MKESDKEMV YAILKFQKLL VENSSNKSMF SSFDVVEPFI YSFELDLAIE ALYLVSFFAS KIHIQRSIKT SMALMKMETL K TLIERVKE ...String:
MKIERPMERR FSQPGKQISN TIKQLSNLPE EELPTYLNNI YEWRCAKTDL LYWVDVLDRF DEILKAVVTE YGLGQFQNKP MKESDKEMV YAILKFQKLL VENSSNKSMF SSFDVVEPFI YSFELDLAIE ALYLVSFFAS KIHIQRSIKT SMALMKMETL K TLIERVKE KPQSMYTYYD ETTNNCKRVS IKKAVKKGIY SISDKMLPSQ EIRRFIHAIR LHEMAEQHEK LKIIRMLAFS AL VYYNYTD LPIDSEFISR DLPETLAIIN TESYQMREAA VTMIDAIFRM RIRHSAVIAA MNAQSHEGMI MNLLKKVVNE DVP EHFAIV FFNFLSSCFA SGPCVSALFS AGIVQYVCNT LRDQPDISYR KRMRLVMGAN TFLFTLPAPF TWFISENGIR ILSK ELLLA VDVALGNIKD HDLLMYINSI MKIISQLFKN AGTAEAMRGF LEGEFPRAIS LILFHSEEFT PSILAYLFSA VGDYI HNEP SNLPFIIEAG IFDGFVMCMK KELPESPDFL LELPNLIEAF FLNSELIKKI DEENILDRIF ESFEIVNLSN IILMYD IGR AYGIFLENLV RHYPIISLTV KEKIYNTMKN LESMIPNTDP ELMRLLLGNL FRMMHRAVYR KTTNNQLITD KGLLNNR II SMLMLIEIPT ETELYTDVMN ILMEVFDEDQ TYVISYIAKV IDRVMKNKVT LENIEKIKRI LLIVNYLIFK NEETCEEF I KHCTSKGFLQ IVKRISQYFD NLKKDTALVS VAKNESLTNL YYSFTMGILK TVYRYSKTNA KEYLKIFGLL VEDLLSKTE QIDHLYYTQR MHGLKNYIMV DKSPQQYPQK NEFVVTQEYL MGINLSETLM EHAKNSVSML KDEKITMDAH KKVVSSILEV LSIYVRGIK NLFVPVKEPK KKVCEIEEHV LIIVELLMDY IDKSSIEHLL NIVKTAFFVT LRKQITKEMD RENEGSAEYK R RNILGSFF ISVFLNLPKE ETEAVLKSDI FTILVKNKKT FKQVYNKNCF GLLQYAAIKE SRVFSHLVSF IPKMTKQVGA ST DPAFLKL YAVGLVFVAM RDTLKKTTVL SRFIGNIVFA ESTCPAVVEA QGIVILAIVK LKIEYNLAIT IEDPIIHLNR IYA IVETAE QKEGLVILAN LLIRRVIESK EAAKEAVDTI IKNKHLGKSR MYTVHTVCSN LRNALFYSIS SFLEYLSSNF ECIS AGWEE IRHKLPDESA NPTESGQISE AVLETLSDGL FTKQIKIYSG LNAELFRTLF VHRATGKMEQ IVRIHSLCLL VVSFP QLIS TLVPEDYSFF MYFLENHAAY SKSLKPSAFQ QEDKTLAYWS GHFIMLIFNH TTYVEVKKYI LEKVLELLPT SINATV IFS ELIQEILTMR FSKNTFDENT ALVKEMNCLE VMIRSTMQID NRRKDYGSIM EILTKPMEYI TRILAVDEKE AFYEEVT QS EEEVYFEDID EGYMEDFDTD ETMDSDQVVY DDTEENSQEV GELCSEDSLT VYTAESNNYG EYLMSDEESS SEEEGMDE E QSSSEQSEKN EFLKSLCILP ISKLIGKEME IFNADERMPF VQKILEGSII SNLQEKEPSS TDEETFDSEE GSYRRHQYL MRREEENDDE ELNDYAIDPT DPDAHLDDEG PEEIDEGVDE YDDESQYDYD GNGSDDEEYD DEESFATGEE IAIGDENGEI PELDVEVLN NLPSSILEDT VENFYQDRIS SSTEYRAISL HFLNRLREEV RSVFEEHEAR YMETFAGEIV PRREEKKKKP Q EMPFIAER EAAASVPIDI VFGLIHMVLQ CGNRRNLYRI IHNISANKEV RIFSVETLVN SIYQAVVEGA SSSAGAGSST VN ASAGSSG NNEVIAPEVI TKRGFEALTY LCTKSSDFTT VFSYNTELIN KILQATNKRT ISESVKLLST VGDCFNNDKV AEP ENIEVR KYIGFLEYDM TDDTFKHFCE FIKKTDRFYR PMYLLYLMGG SKKSLEECLD KKAEFNSHTH HKGIIKLVRM LSLV NIMGI TETYLDSLME LREMPFWEYY FNIILPKEKE SLYASSILPL FKAFVIVHTI QMYIGRNENI NEFSEIPNSD SSIYY SVVE KEKDLINTFI QADPDLLFHA FAGLQKKILD FDNKRIYFYK KIREDVQLRP TISLMVQRGA VFEDTFHQLM RLNGEQ VRN AKFNIKFAGE EGVDAGGLTR EWYSELSKEM FNANYALFTP IGSSYQPNHI SHINPEHLVY FKFIGRIIGK AVYDEMT VD CHFTRAFYKR VLSIPVDLTD VEALDPEFHR SLVWILENDI ENVLDMTFSI EQDRFGITEI IDLKENGRNI AVTNENKR E YVELVCRFKL VRVIERQLSA FAEGFFEILD VDMLKMFNEK ELELLISGLP EIDVDDWRNN TIYFGYTSDS QVIRWYWRA VRNFSMEERA KLLQFATGTS KLPLEGFAGL RCQNGNQKFQ IHKASGGSSR LPTAHTCFNQ LDLPEYDSYE QLVKALLFSL EECTSGFGF A

UniProtKB: HECT-type E3 ubiquitin transferase

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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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMsodium chlorideNaClSodium chloride
5.0 mMmagnesium chlorideMgCl2
0.05 mMTECEP
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 4 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 57866
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7bii

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7nh3:
Nematocida Huwe1 in open conformation.

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