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- PDB-9zfn: Tulane virus protease without added ligands -

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Basic information

Entry
Database: PDB / ID: 9zfn
TitleTulane virus protease without added ligands
Components3C-like protease
KeywordsVIRAL PROTEIN / Tulane virus protease
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / host cell / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / Reverse transcriptase/Diguanylate cyclase domain ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesTulane virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPham, S.H. / Sankaran, B. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI057788 United States
CitationJournal: J.Virol. / Year: 2026
Title: Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases.
Authors: Pham, S. / Sharma, N. / Sankaran, B. / Nguyen, J. / Estes, M.K. / Hyser, J.M. / Prasad, B.V.V.
History
DepositionDec 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like protease
B: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)36,9812
Polymers36,9812
Non-polymers00
Water2,414134
1
A: 3C-like protease

A: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)36,9812
Polymers36,9812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
2
B: 3C-like protease

B: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)36,9812
Polymers36,9812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)56.280, 78.160, 86.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 3C-like protease


Mass: 18490.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tulane virus / Production host: Escherichia coli B (bacteria) / References: UniProt: B2Y6C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M amino acids mix, 1.2% cholic acid derivative mix, 0.1M Buffer system 1 pH 6.5, 37.5% Precipitant Mix 4 (Morpheus Fusion E5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0002 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0002 Å / Relative weight: 1
ReflectionResolution: 2.1→45.67 Å / Num. obs: 19959 / % possible obs: 86.8 % / Redundancy: 11 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.085 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1490 / CC1/2: 0.889 / CC star: 0.97 / Rrim(I) all: 0.734 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.67 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 998 5 %
Rwork0.2039 18950 -
obs0.2054 19948 86.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 0 134 2687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052602
X-RAY DIFFRACTIONf_angle_d0.71513525
X-RAY DIFFRACTIONf_chiral_restr0.0548415
X-RAY DIFFRACTIONf_plane_restr0.0094453
X-RAY DIFFRACTIONf_dihedral_angle_d14.2054944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.26911600.23443045X-RAY DIFFRACTION99.38
2.21-2.350.3434870.25371670X-RAY DIFFRACTION54.09
2.35-2.530.26031620.22483058X-RAY DIFFRACTION99.94
2.53-2.790.29481240.24132346X-RAY DIFFRACTION76.02
2.79-3.190.22961620.21463095X-RAY DIFFRACTION99.57
3.19-4.020.23061300.19492468X-RAY DIFFRACTION78.18
4.02-45.670.2031730.17983268X-RAY DIFFRACTION99.57

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