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- PDB-9dgw: X-ray crystal structure of the Viperin-like enzyme from T. virens... -

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Basic information

Entry
Database: PDB / ID: 9dgw
TitleX-ray crystal structure of the Viperin-like enzyme from T. virens with bound CTP and SAM
ComponentsRadical SAM core domain-containing protein
KeywordsANTIVIRAL PROTEIN / viperin-like enzyme / CTP / SAM / 4Fe-4S cluster
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / defense response to virus / mitochondrion / metal ion binding
Similarity search - Function
: / 4Fe-4S single cluster domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Radical SAM core domain-containing protein
Similarity search - Component
Biological speciesTrichoderma virens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLachowicz, J.C. / Bonanno, J.B. / Grove, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007491 United States
CitationJournal: Structure / Year: 2025
Title: Structural insights from active site variants and beta-8 loop interactions in viperin-like enzymes.
Authors: Lachowicz, J.C. / Grudman, S. / Bonanno, J.B. / Fiser, A. / Grove, T.L.
History
DepositionSep 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Radical SAM core domain-containing protein
B: Radical SAM core domain-containing protein
C: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,27812
Polymers108,5793
Non-polymers3,7009
Water5,386299
1
A: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4264
Polymers36,1931
Non-polymers1,2333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4264
Polymers36,1931
Non-polymers1,2333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4264
Polymers36,1931
Non-polymers1,2333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.569, 80.309, 105.613
Angle α, β, γ (deg.)90.00, 96.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Radical SAM core domain-containing protein


Mass: 36192.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma virens (fungus) / Strain: Gv29-8 / Gene: TRIVIDRAFT_58105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9MQB8
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M NaCl, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.72→28.59 Å / Num. obs: 354684 / % possible obs: 99.3 % / Redundancy: 3.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.063 / Rrim(I) all: 0.095 / Net I/σ(I): 9.6
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 17788 / CC1/2: 0.87 / Rpim(I) all: 0.377 / Rrim(I) all: 0.587

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→28.59 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Chain C of the final TvVip1 with CTP structure demonstrated significant static disorder. Therefore, chain C of TvVip1 with CTP was modeled ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Chain C of the final TvVip1 with CTP structure demonstrated significant static disorder. Therefore, chain C of TvVip1 with CTP was modeled as an NCS copy of chains A and B and refinement was performed utilizing TLS restraints.
RfactorNum. reflection% reflectionSelection details
Rfree0.29231 4454 4.9 %RANDOM
Rwork0.26133 ---
obs0.26284 85544 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0 Å2-1.58 Å2
2--0.34 Å20 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.72→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6743 0 192 299 7234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0127136
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166576
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.8269674
X-RAY DIFFRACTIONr_angle_other_deg0.7721.77715156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.542536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.212101248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028288
X-RAY DIFFRACTIONr_gen_planes_other0.010.021692
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1413.7863373
X-RAY DIFFRACTIONr_mcbond_other1.143.7863373
X-RAY DIFFRACTIONr_mcangle_it1.9646.8134211
X-RAY DIFFRACTIONr_mcangle_other1.9646.8144212
X-RAY DIFFRACTIONr_scbond_it1.263.7793763
X-RAY DIFFRACTIONr_scbond_other1.2563.7763752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1016.9395416
X-RAY DIFFRACTIONr_long_range_B_refined3.05435.647842
X-RAY DIFFRACTIONr_long_range_B_other3.06135.617806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 328 -
Rwork0.375 6239 -
obs--98.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8095-0.03930.76991.6264-0.15542.6276-0.0760.16030.115-0.03390.0067-0.0594-0.19740.17540.06940.0677-0.03160.02410.02480.00120.025618.43316.45711.46
21.6867-0.27470.31261.67480.30872.48540.1180.1928-0.1056-0.0509-0.0684-0.08030.15580.0557-0.04970.04810.03680.00480.0445-0.01550.03927.82614.371-24.583
31.8102-0.40170.68813.4241-1.36343.9268-0.00960.0946-0.0685-0.1547-0.0164-0.26230.24940.23780.02610.1279-0.01280.0240.1817-0.00460.106420.35852.35-46.315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 295
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION2B17 - 298
4X-RAY DIFFRACTION2B401 - 403
5X-RAY DIFFRACTION3C18 - 297
6X-RAY DIFFRACTION3C401 - 403

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