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- PDB-6q2q: Crystal structure of mouse viperin bound to uridine triphosphate ... -

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Basic information

Entry
Database: PDB / ID: 6q2q
TitleCrystal structure of mouse viperin bound to uridine triphosphate and S-adenosylhomocysteine
ComponentsRadical S-adenosyl methionine domain-containing protein 2
KeywordsIMMUNE SYSTEM / interferon stimulated gene / radical S-adenosylmethionine enzyme / iron sulfur cluster
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
S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / URIDINE 5'-TRIPHOSPHATE / S-adenosylmethionine-dependent nucleotide dehydratase RSAD2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsFenwick, M.K. / Dong, M. / Lin, H. / Ealick, S.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124165 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Basis of the Substrate Selectivity of Viperin.
Authors: Fenwick, M.K. / Su, D. / Dong, M. / Lin, H. / Ealick, S.E.
History
DepositionAug 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)76,25413
Polymers73,3892
Non-polymers2,86511
Water13,619756
1
A: Radical S-adenosyl methionine domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3048
Polymers36,6951
Non-polymers1,6097
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)37,9505
Polymers36,6951
Non-polymers1,2564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.455, 141.265, 143.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36694.699 Da / Num. of mol.: 2 / Mutation: E261A, E266A
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) / References: UniProt: Q8CBB9

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Non-polymers , 6 types, 767 molecules

#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-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#6: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 756 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-tris propane, pH 6.2-6.8, 200 mM NaCl, 19-22% (w/v) polyethylene glycol 4000 or 6000, 6 mM S-adenosylhomocysteine, and 10 mM UTP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.892→50 Å / Num. obs: 58202 / % possible obs: 96.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 8.2
Reflection shellResolution: 1.892→1.97 Å / Rmerge(I) obs: 0.566 / Num. unique obs: 5740

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vsl

5vsl


Resolution: 1.892→45.303 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.58
RfactorNum. reflection% reflection
Rfree0.1823 2904 4.99 %
Rwork0.1458 --
obs0.1477 58170 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.23 Å2 / Biso mean: 18.0147 Å2 / Biso min: 2.79 Å2
Refinement stepCycle: final / Resolution: 1.892→45.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 149 756 5594
Biso mean--15.3 31.2 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085177
X-RAY DIFFRACTIONf_angle_d0.9537011
X-RAY DIFFRACTIONf_chiral_restr0.057729
X-RAY DIFFRACTIONf_plane_restr0.005892
X-RAY DIFFRACTIONf_dihedral_angle_d15.183083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8923-1.92330.24731300.21482379X-RAY DIFFRACTION87
1.9233-1.95650.29441220.2112639X-RAY DIFFRACTION99
1.9565-1.9920.28971230.2052603X-RAY DIFFRACTION97
1.992-2.03040.23931440.19422559X-RAY DIFFRACTION94
2.0304-2.07180.24091140.18232639X-RAY DIFFRACTION99
2.0718-2.11680.19581370.16592639X-RAY DIFFRACTION98
2.1168-2.16610.21151380.16392629X-RAY DIFFRACTION97
2.1661-2.22030.19631470.14992629X-RAY DIFFRACTION99
2.2203-2.28030.17261190.15352710X-RAY DIFFRACTION97
2.2803-2.34740.18821430.1522631X-RAY DIFFRACTION99
2.3474-2.42310.18761510.14652596X-RAY DIFFRACTION95
2.4231-2.50970.18941390.15062598X-RAY DIFFRACTION97
2.5097-2.61020.17941320.14552714X-RAY DIFFRACTION97
2.6102-2.7290.15811280.13972670X-RAY DIFFRACTION98
2.729-2.87290.18221440.13692660X-RAY DIFFRACTION98
2.8729-3.05280.19431430.14252694X-RAY DIFFRACTION97
3.0528-3.28850.16471360.12982594X-RAY DIFFRACTION94
3.2885-3.61930.17121510.11642680X-RAY DIFFRACTION97
3.6193-4.14270.13111440.11062669X-RAY DIFFRACTION96
4.1427-5.21810.13021680.11082634X-RAY DIFFRACTION94
5.2181-45.3030.1851510.1512700X-RAY DIFFRACTION91
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)
11.02960.0561-0.52652.054-0.25280.5354-0.01140.1024-0.1312-0.06230.0102-0.08420.01650.0197-0.0080.06990.0043-0.00050.0678-0.02770.046515.011915.822252.4953
21.1019-0.0915-0.00691.0549-0.58741.7797-0.0237-0.03320.09480.09140.0155-0.0983-0.1690.11070.0080.0874-0.0006-0.01240.0462-0.02230.077412.994327.423659.8913
31.95510.1197-0.3052.56340.69691.3124-0.067-0.2794-0.34750.2807-0.0571-0.0940.2674-0.05480.0320.15830.0052-0.02260.0997-0.00190.03966.42628.086865.7784
40.81830.05620.06112.76540.3442.9831-0.0419-0.1617-0.13060.28850.1427-0.23220.14330.179-0.09130.11420.0014-0.0380.120.00020.09968.334413.884973.2482
51.1086-0.27960.00511.45770.4820.83110.01060.0193-0.13760.0231-0.02060.07330.0142-0.03940.02170.0912-0.01140.00560.0654-0.02350.07180.39056.014657.5413
61.8321-0.553-0.26410.3862-0.44912.4172-0.14910.6111-0.4042-0.11630.0633-0.02120.21270.0127-0.01570.1274-0.00250.01240.1076-0.05650.10419.446317.058144.0839
72.53290.6930.04152.0552-0.17291.3389-0.09220.3362-0.1541-0.2505-0.0286-0.09110.0549-0.13540.06880.08590.0215-0.00650.08390.01570.06763.850122.480445.687
80.9244-0.7157-0.08110.6209-0.37172.3459-0.0253-0.0155-0.00920.02-0.0093-0.058-0.0726-0.14120.01040.0634-0.0095-0.00320.0476-0.04880.0969-4.1787-7.570127.6591
91.1581-0.4260.04761.6085-0.11931.27260.03810.13510.0228-0.121-0.03570.09310.0139-0.0779-0.00740.0794-0.00950.00170.063-0.03370.0624-2.0856-14.97416.44
105.5468-2.2149-1.16993.2241-2.23014.1243-0.0177-0.3051-0.62330.1940.25280.60630.2362-0.3116-0.14860.2196-0.01930.04240.09960.00360.18911.4638-22.516440.3281
113.395-0.4241-2.00914.82142.72092.50190.1192-0.4841-0.3180.4379-0.2713-0.2720.3813-0.14740.05580.1467-0.0544-0.05090.18130.00280.16654.9777-29.570524.6774
121.6463-0.04190.14711.56161.07413.8259-0.021-0.1726-0.09910.01380.0575-0.09840.19270.0614-0.02450.08010.0184-0.00510.0748-0.02630.083811.7029-19.590234.2767
132.5395-0.6333-0.35080.95990.40391.5413-0.0436-0.03890.1390.04140.0104-0.0351-0.0471-0.00150.02510.1004-0.0058-0.0110.0782-0.05330.09159.6205-8.649839.7313
141.2852-0.9594-0.88422.5253-0.32361.133-0.1037-0.34180.52430.17460.0224-0.0518-0.23480.04070.09830.12220.0079-0.00440.0961-0.06130.14431.04560.561126.9326
152.6539-0.36150.69251.13930.40081.7414-0.1479-0.3220.6291-0.00870.1147-0.0393-0.3176-0.0994-0.01140.16380.0170.0040.1152-0.020.24483.52374.923623.9483
162.53-0.035-0.35820.32380.86353.39010.03120.0858-0.38660.13090.2246-0.38140.48810.3241-0.01730.14140.0147-0.01670.0799-0.03490.178615.3569-17.132117.8722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 102 )A71 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 173 )A103 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 192 )A174 - 192
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 215 )A193 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 298 )A216 - 298
6X-RAY DIFFRACTION6chain 'A' and (resid 299 through 315 )A299 - 315
7X-RAY DIFFRACTION7chain 'A' and (resid 316 through 360 )A316 - 360
8X-RAY DIFFRACTION8chain 'B' and (resid 70 through 102 )B70 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 180 )B103 - 180
10X-RAY DIFFRACTION10chain 'B' and (resid 181 through 200 )B181 - 200
11X-RAY DIFFRACTION11chain 'B' and (resid 201 through 215 )B201 - 215
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 250 )B216 - 250
13X-RAY DIFFRACTION13chain 'B' and (resid 251 through 298 )B251 - 298
14X-RAY DIFFRACTION14chain 'B' and (resid 299 through 315 )B299 - 315
15X-RAY DIFFRACTION15chain 'B' and (resid 316 through 346 )B316 - 346
16X-RAY DIFFRACTION16chain 'B' and (resid 347 through 362 )B347 - 362

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