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- EMDB-38156: Structure of enterovirus protease in complex host factor -

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Basic information

Entry
Database: EMDB / ID: EMD-38156
TitleStructure of enterovirus protease in complex host factor
Map data
Sample
  • Complex: enterovirus protease in complex host factor
    • Protein or peptide: Actin-histidine N-methyltransferase
    • Protein or peptide: 2A protein (Fragment)
  • Ligand: ZINC ION
Keywordshost protein / VIRAL PROTEIN / CELL INVASION / CELL CYCLE
Function / homology
Function and homology information


protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / positive regulation of muscle cell differentiation / cysteine-type peptidase activity / viral process ...protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / positive regulation of muscle cell differentiation / cysteine-type peptidase activity / viral process / PKMTs methylate histone lysines / actin binding / RNA polymerase II-specific DNA-binding transcription factor binding / host cell cytoplasm / transcription coactivator activity / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / metal ion binding / cytoplasm
Similarity search - Function
Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / Rubisco LSMT substrate-binding / SET domain superfamily / SET domain / SET domain profile. / SET domain ...Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / Rubisco LSMT substrate-binding / SET domain superfamily / SET domain / SET domain profile. / SET domain / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Actin-histidine N-methyltransferase / 2A protein
Similarity search - Component
Biological speciesEnterovirus A71 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsGao X / Cui S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: The EV71 2A protease occupies the central cleft of SETD3 and disrupts SETD3-actin interaction.
Authors: Xiaopan Gao / Bei Wang / Kaixiang Zhu / Linyue Wang / Bo Qin / Kun Shang / Wei Ding / Jianwei Wang / Sheng Cui /
Abstract: SETD3 is an essential host factor for the replication of a variety of enteroviruses that specifically interacts with viral protease 2A. However, the interaction between SETD3 and the 2A protease has ...SETD3 is an essential host factor for the replication of a variety of enteroviruses that specifically interacts with viral protease 2A. However, the interaction between SETD3 and the 2A protease has not been fully characterized. Here, we use X-ray crystallography and cryo-electron microscopy to determine the structures of SETD3 complexed with the 2A protease of EV71 to 3.5 Å and 3.1 Å resolution, respectively. We find that the 2A protease occupies the V-shaped central cleft of SETD3 through two discrete sites. The relative positions of the two proteins vary in the crystal and cryo-EM structures, showing dynamic binding. A biolayer interferometry assay shows that the EV71 2A protease outcompetes actin for SETD3 binding. We identify key 2A residues involved in SETD3 binding and demonstrate that 2A's ability to bind SETD3 correlates with EV71 production in cells. Coimmunoprecipitation experiments in EV71 infected and 2A expressing cells indicate that 2A interferes with the SETD3-actin complex, and the disruption of this complex reduces enterovirus replication. Together, these results reveal the molecular mechanism underlying the interplay between SETD3, actin, and viral 2A during virus replication.
History
DepositionNov 28, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38156.png

Downloads & links

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Map

FileDownload / File: emd_38156.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.18975064 - 0.44429517
Average (Standard dev.)-0.00022512588 (±0.011113325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38156_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_38156_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 : enterovirus protease in complex host factor

EntireName: enterovirus protease in complex host factor
Components
  • Complex: enterovirus protease in complex host factor
    • Protein or peptide: Actin-histidine N-methyltransferase
    • Protein or peptide: 2A protein (Fragment)
  • Ligand: ZINC ION

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Supramolecule #1: enterovirus protease in complex host factor

SupramoleculeName: enterovirus protease in complex host factor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Enterovirus A71

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Macromolecule #1: Actin-histidine N-methyltransferase

MacromoleculeName: Actin-histidine N-methyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.342047 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MGKKSRVKTQ KSGTGATATV SPKEILNLTS ELLQKCSSPA PGPGKEWEEY VQIRTLVEKI RKKQKGLSVT FDGKREDYFP DLMKWASEN GASVEGFEMV NFKEEGFGLR ATRDIKAEEL FLWVPRKLLM TVESAKNSVL GPLYSQDRIL QAMGNIALAF H LLCERASP ...String:
MGKKSRVKTQ KSGTGATATV SPKEILNLTS ELLQKCSSPA PGPGKEWEEY VQIRTLVEKI RKKQKGLSVT FDGKREDYFP DLMKWASEN GASVEGFEMV NFKEEGFGLR ATRDIKAEEL FLWVPRKLLM TVESAKNSVL GPLYSQDRIL QAMGNIALAF H LLCERASP NSFWQPYIQT LPSEYDTPLY FEEDEVRYLQ STQAIHDVFS QYKNTARQYA YFYKVIQTHP HANKLPLKDS FT YEDYRWA VSSVMTRQNQ IPTEDGSRVT LALIPLWDMC NHTNGLITTG YNLEDDRCEC VALQDFRAGE QIYIFYGTRS NAE FVIHSG FFFDNNSHDR VKIKLGVSKS DRLYAMKAEV LARAGIPTSS VFALHFTEPP ISAQLLAFLR VFCMTEEELK EHLL GDSAI DRIFTLGNSE FPVSWDNEVK LWTFLEDRAS LLLKTYKTTI EEDKSVLKNH DLSVRAKMAI KLRLGEKEIL EKAVK SAAV NREYYRQQME EKAPLPKYEE SNLGLLESSV GDSRLPLVLR NLEEEAGVQD ALNIREAISK AKATENGLVN GENSIP NGT RSENESLNQE SKRAVEDAKG SSSDSTAGVK E

UniProtKB: Actin-histidine N-methyltransferase

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Macromolecule #2: 2A protein (Fragment)

MacromoleculeName: 2A protein (Fragment) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 16.562418 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
GKFGQQSGAI YVGNFRVVNR HLATHNDWAN LVWEDSSRDL LVSSTTAQGC DTIARCNCQT GVYYCNSRRK HYPVSFSKPS LIYVEASEY YPARYQSHLM LAQGHSEPGD AGGILRCQHG VVGIVSTGGN GLVGFADVRD LLWLDEEAME Q

UniProtKB: 2A protein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 80.0 K
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 opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2211651
Startup modelType of model: NONE
Final reconstructionNumber classes used: 66 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 603524
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelPDB ID:

3w95


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 103 / Target criteria: Correlation coefficient
Output model

PDB-8x8q:
Structure of enterovirus protease in complex host factor

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