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- EMDB-53547: Norovirus NS3 hexamer in complex with ATP-gamma-S -

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Basic information

Entry
Database: EMDB / ID: EMD-53547
TitleNorovirus NS3 hexamer in complex with ATP-gamma-S
Map dataLocal resolution filtered map
Sample
  • Complex: Norovirus NS3 hexamer in complex with ATP-gamma-S
    • Protein or peptide: NTPase
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsHelicase / NTPase / AAA+ ATPase / VIRAL PROTEIN
Function / homology
Function and homology information


calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / RNA-directed RNA polymerase, C-terminal domain ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesNorwalk virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHaas M / Drulyte I / Hurdiss DL
Funding support Netherlands, European Union, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)VI.Veni.212.102 Netherlands
European Research Council (ERC)101164550European Union
CitationJournal: Biorxiv / Year: 2025
Title: Integrative Structure of Norovirus NS3 Suggests a Role in RNA Transport
Authors: Haas M / Mills JT / Kelley C / Das A / Hof H / Niemel C / Donselaar T / Drulyte I / van Kuppeveld FJ / Dulin D / Snijder J / Herod MR / Hurdiss DL
History
DepositionMay 2, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53547.png

Downloads & links

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Map

FileDownload / File: emd_53547.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.1367081 - 2.0592694
Average (Standard dev.)0.0005524155 (±0.032272052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53547_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_53547_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_53547_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_53547_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_53547_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Norovirus NS3 hexamer in complex with ATP-gamma-S

EntireName: Norovirus NS3 hexamer in complex with ATP-gamma-S
Components
  • Complex: Norovirus NS3 hexamer in complex with ATP-gamma-S
    • Protein or peptide: NTPase
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Norovirus NS3 hexamer in complex with ATP-gamma-S

SupramoleculeName: Norovirus NS3 hexamer in complex with ATP-gamma-S / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Norwalk virus
Molecular weightTheoretical: 229 KDa

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Macromolecule #1: NTPase

MacromoleculeName: NTPase / type: protein_or_peptide / ID: 1
Details: A soluble hexamerization domain, cc-hex, and a linker region are included before the N-terminally truncated (61 amino acids) NS3 construct.
Number of copies: 6 / Enantiomer: LEVO / EC number: nucleoside-triphosphate phosphatase
Source (natural)Organism: Norwalk virus
Molecular weightTheoretical: 38.269594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGGGGSGGG GSGELKAIAQ ELKAIAKELK AIAWELKAIA QGAGGSGSYF QSNAGGDQTE KTLKDIESAV IDMEVLSSTS VTQLVRDKQ SARAYMAILD NEEEKARKLS VRNADPHVVS STNALISRIS MARAALAKAQ AEMTSRMRPV VIMMCGPPGI G KTKAAEHL ...String:
GPGGGGSGGG GSGELKAIAQ ELKAIAKELK AIAWELKAIA QGAGGSGSYF QSNAGGDQTE KTLKDIESAV IDMEVLSSTS VTQLVRDKQ SARAYMAILD NEEEKARKLS VRNADPHVVS STNALISRIS MARAALAKAQ AEMTSRMRPV VIMMCGPPGI G KTKAAEHL AKRLANEIRP GGKVGLVPRE AVDHWDGYHG EEVMLWDDYG MTKIQEDCNK LQAIADSAPL TLNCDRIENK GM QFVSDAI VITTNAPGPA PVDFVNLGPV CRRVDFLVYC TAPEVEHTRK VSPGDTTALK DCFKPDFSHL KMELAPQGGF DNQ GNTPFG KGVMKPTTIN RLLIQAVALT MERQDEFQLQ

UniProtKB: Genome polyprotein

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Macromolecule #2: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 6 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 204 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.35 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1010 / Average electron dose: 50.5 e/Å2 / Details: Falcon 4i direct electron detector
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1229229
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123643
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9r34:
Norovirus NS3 hexamer in complex with ATP-gamma-S

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