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- PDB-5vsm: Crystal structure of viperin with bound [4Fe-4S] cluster, 5'-deox... -

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Basic information

Entry
Database: PDB / ID: 5vsm
TitleCrystal structure of viperin with bound [4Fe-4S] cluster, 5'-deoxyadenosine, and L-methionine
ComponentsRadical S-adenosyl methionine domain-containing protein 2
KeywordsANTIVIRAL PROTEIN / radical / S-adenosylmethionine / iron-sulfur cluster / antiviral response
Function / homology
Function and homology information


CD4-positive, alpha-beta T cell activation / Lyases; Carbon-oxygen lyases / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of T-helper 2 cell cytokine production / CD4-positive, alpha-beta T cell differentiation / negative regulation of viral genome replication / negative regulation of protein secretion / regulation of ossification / lipid droplet ...CD4-positive, alpha-beta T cell activation / Lyases; Carbon-oxygen lyases / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of T-helper 2 cell cytokine production / CD4-positive, alpha-beta T cell differentiation / negative regulation of viral genome replication / negative regulation of protein secretion / regulation of ossification / lipid droplet / ossification / response to virus / fibrillar center / : / positive regulation of immune response / 4 iron, 4 sulfur cluster binding / defense response to virus / mitochondrial inner membrane / mitochondrial outer membrane / lyase activity / innate immune response / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / 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
5'-DEOXYADENOSINE / METHIONINE / IRON/SULFUR CLUSTER / S-adenosylmethionine-dependent nucleotide dehydratase RSAD2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsFenwick, M.K. / Li, Y. / Cresswell, P. / Modis, Y. / Ealick, S.E.
Funding support United States, United Kingdom, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK067081 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102869 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Wellcome Trust101908/Z/13/Z United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural studies of viperin, an antiviral radical SAM enzyme.
Authors: Fenwick, M.K. / Li, Y. / Cresswell, P. / Modis, Y. / Ealick, S.E.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Radical S-adenosyl methionine domain-containing protein 2
B: Radical S-adenosyl methionine domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1268
Polymers73,6222
Non-polymers1,5046
Water10,269570
1
A: Radical S-adenosyl methionine domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5634
Polymers36,8111
Non-polymers7523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Radical S-adenosyl methionine domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5634
Polymers36,8111
Non-polymers7523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.364, 73.264, 141.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Radical S-adenosyl methionine domain-containing protein 2 / Viperin / Virus inhibitory protein / endoplasmic reticulum-associated / interferon-inducible


Mass: 36810.766 Da / Num. of mol.: 2 / Fragment: UNP residues 45-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rsad2, Vig1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): NiCo(DE3) / References: UniProt: Q8CBB9
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES, pH 6.8 - 7.6, 10-30% PEG MME 2000, 5 mM 5'-deoxyadenosine, and 10 mM L-methionine
PH range: 6.8 - 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 68453 / % possible obs: 99.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/av σ(I): 23.2 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6690 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: 000)refinement
HKL-2000data scaling
Cootmodel building
PHENIX(1.11.1_2575: 000)phasing
HKL-2000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Viperin with bound [4Fe-4S] cluster and S-adenosylhomocysteine

Resolution: 1.7→45.534 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.49
RfactorNum. reflection% reflection
Rfree0.1946 3332 4.88 %
Rwork0.1585 --
obs0.1603 68339 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→45.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 70 570 4782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134498
X-RAY DIFFRACTIONf_angle_d1.866087
X-RAY DIFFRACTIONf_dihedral_angle_d17.8672716
X-RAY DIFFRACTIONf_chiral_restr0.058646
X-RAY DIFFRACTIONf_plane_restr0.005787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72240.31931230.27272537X-RAY DIFFRACTION95
1.7224-1.74810.27121390.25442705X-RAY DIFFRACTION99
1.7481-1.77540.27041190.23622622X-RAY DIFFRACTION97
1.7754-1.80460.26321150.22392680X-RAY DIFFRACTION99
1.8046-1.83570.25051350.2032723X-RAY DIFFRACTION100
1.8357-1.86910.23141490.19452689X-RAY DIFFRACTION100
1.8691-1.9050.25861290.19472707X-RAY DIFFRACTION100
1.905-1.94390.22751390.18872676X-RAY DIFFRACTION100
1.9439-1.98620.24011330.18552731X-RAY DIFFRACTION100
1.9862-2.03240.2121480.17932700X-RAY DIFFRACTION100
2.0324-2.08320.18531440.17042683X-RAY DIFFRACTION99
2.0832-2.13950.21911510.16612643X-RAY DIFFRACTION98
2.1395-2.20250.18491490.15912685X-RAY DIFFRACTION99
2.2025-2.27350.21111520.15742708X-RAY DIFFRACTION100
2.2735-2.35480.20391170.15792754X-RAY DIFFRACTION100
2.3548-2.44910.19021290.15982730X-RAY DIFFRACTION100
2.4491-2.56050.19651370.16922728X-RAY DIFFRACTION100
2.5605-2.69550.1891520.16182724X-RAY DIFFRACTION99
2.6955-2.86440.2221380.15812708X-RAY DIFFRACTION99
2.8644-3.08550.1951430.15662761X-RAY DIFFRACTION100
3.0855-3.39590.1761550.14272749X-RAY DIFFRACTION100
3.3959-3.88710.18471470.1332728X-RAY DIFFRACTION98
3.8871-4.89640.16391430.1232793X-RAY DIFFRACTION99
4.8964-45.55070.17231460.15972843X-RAY DIFFRACTION96
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)
16.1652-2.17532.70622.2358-1.63064.85040.0596-0.01630.0333-0.1132-0.3011-0.42980.38140.81060.1930.27120.06630.05880.33310.10820.29621.603325.799234.7726
25.4028-0.24251.6821.3246-0.05164.9537-0.0755-0.0837-0.20480.0695-0.1125-0.16520.44670.37790.17750.2930.05420.02070.14790.03920.219515.118521.407243.6811
35.1639-4.66964.50446.6709-6.37898.08450.01960.179-0.15090.00080.11340.3174-0.1001-0.2148-0.11720.1934-0.02710.00050.16460.01490.21492.055133.024535.2812
43.6170.4384-0.70143.3774-3.36847.748-0.19960.28530.0185-0.50910.30930.41710.729-1.0864-0.10240.3122-0.09-0.03410.2489-0.02430.2873-0.660526.353640.6661
51.55240.35680.53811.4127-2.99487.4001-0.10360.08750.21980.07390.1014-0.0287-0.3162-0.4136-0.00810.24150.0264-0.01830.14580.01040.19583.243539.192537.0824
63.07773.8484-1.88237.9714-5.70479.2288-0.0726-0.29580.03740.4691-0.05640.0824-0.3737-0.38250.12120.30820.0693-0.01170.1655-0.00750.16652.481740.203743.0559
73.1953-2.3682-0.41677.51171.17228.16820.10580.25250.1449-0.5994-0.227-0.48880.08360.52520.11070.24440.0010.03310.24350.09110.25214.308139.69221.6509
82.6176-0.7674-0.05034.8899-1.03124.4568-0.1247-0.14390.31370.6330.1110.1334-0.9662-0.2034-0.00990.47620.0787-0.02370.17560.00870.27465.645649.05239.2303
95.7311-4.9787-1.1194.27321.29963.9587-0.2689-0.32510.47040.22390.0405-1.018-0.06590.79170.16640.2975-0.03440.00440.45790.11130.448824.005436.162934.6833
109.3862-3.94810.80652.6942-2.90576.5679-0.30790.64780.6233-0.4789-0.0752-0.578-0.43541.37770.31850.4283-0.058-0.02410.79820.16930.689633.488132.587934.7623
114.22161.7183-0.72694.4691-0.71831.3481-0.24420.4616-0.4471-0.11570.14990.07860.7385-0.50890.07690.403-0.13870.04370.3343-0.07030.21964.714634.5753-5.3277
123.19550.5693-0.96583.8277-0.40272.6001-0.20420.1086-0.4058-0.01670.12820.37390.8348-0.5609-0.01070.3943-0.1660.05980.3303-0.02070.2959-1.562631.98227.6825
132.8891-1.25380.02284.8328-1.72583.3681-0.1104-0.2142-0.0480.33130.15290.35060.2422-0.4786-0.06050.181-0.08280.0260.3168-0.01050.19-0.467141.413410.1372
142.24290.4225-1.42662.6609-2.03556.9902-0.10120.42710.2434-0.17520.1879-0.02690.1937-0.2928-0.1340.12960.0009-0.00430.28230.03460.236312.072949.2487-1.254
153.9321-1.2081-4.20834.20441.85856.42040.16420.41190.6555-0.16840.0718-0.0464-0.52-0.43-0.1880.11480.0298-0.01260.3080.05210.34095.229853.30973.71
164.0517-0.5511-4.03321.45580.18646.6645-0.060.03850.00810.0674-0.0027-0.18280.03890.24650.06150.08910.007-0.01970.23630.03630.174118.543448.19583.582
174.9430.46523.18271.7254-0.30228.7155-0.02170.5311-0.5899-0.26560.0721-0.02351.3411-0.0872-0.09190.4484-0.0170.08850.3489-0.08930.271217.246136.3306-13.6079
183.6351-0.1787-3.40783.4423-0.56544.4316-0.1009-0.35150.01620.21290.0071-0.40060.28141.1120.03540.16870.0543-0.03280.49190.05570.274127.657745.10593.2983
198.01766.97760.38328.87580.32273.4084-0.06130.1813-1.1557-0.3284-0.1312-0.71051.00370.14120.1330.63150.01720.10530.2537-0.01820.384412.852827.48920.0319
205.63774.031-0.07047.7675-1.84180.666-0.33880.821-1.0091-1.03220.1307-0.82881.463-0.21480.19241.1816-0.12420.1650.3754-0.12820.62017.857118.1441.4963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 74 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 173 )
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 192 )
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 215 )
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 234 )
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 250 )
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 273 )
8X-RAY DIFFRACTION8chain 'A' and (resid 274 through 294 )
9X-RAY DIFFRACTION9chain 'A' and (resid 295 through 311 )
10X-RAY DIFFRACTION10chain 'A' and (resid 312 through 335 )
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 146 )
13X-RAY DIFFRACTION13chain 'B' and (resid 147 through 173 )
14X-RAY DIFFRACTION14chain 'B' and (resid 174 through 192 )
15X-RAY DIFFRACTION15chain 'B' and (resid 193 through 215 )
16X-RAY DIFFRACTION16chain 'B' and (resid 216 through 250 )
17X-RAY DIFFRACTION17chain 'B' and (resid 251 through 273 )
18X-RAY DIFFRACTION18chain 'B' and (resid 274 through 294 )
19X-RAY DIFFRACTION19chain 'B' and (resid 295 through 311 )
20X-RAY DIFFRACTION20chain 'B' and (resid 312 through 333 )

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