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- PDB-6q2p: Crystal structure of mouse viperin bound to cytidine triphosphate... -

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Basic information

Entry
Database: PDB / ID: 6q2p
TitleCrystal structure of mouse viperin bound to cytidine 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


Lyases; Carbon-oxygen lyases / CD4-positive, alpha-beta T cell activation / 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 / lipid droplet / response to virus ...Lyases; Carbon-oxygen lyases / CD4-positive, alpha-beta T cell activation / 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 / lipid droplet / response to virus / fibrillar center / 4 iron, 4 sulfur cluster binding / defense response to virus / mitochondrial outer membrane / mitochondrial inner membrane / lyase activity / innate immune response / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / 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-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / S-adenosylmethionine-dependent nucleotide dehydratase RSAD2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.452 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_auth_seq_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_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)76,21712
Polymers73,3892
Non-polymers2,82710
Water17,276959
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A: Radical S-adenosyl methionine domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9856
Polymers36,6951
Non-polymers1,2905
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)38,2326
Polymers36,6951
Non-polymers1,5375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.483, 142.588, 143.732
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, 969 molecules

#2: Chemical ChemComp-SF4 / 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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


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


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
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 CTP

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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: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 131974 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.6
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.563 / Num. unique obs: 13005

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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: 1.452→39.766 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.04
RfactorNum. reflection% reflection
Rfree0.1595 6699 5.08 %
Rwork0.1405 --
obs0.1415 131887 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.2 Å2 / Biso mean: 14.3472 Å2 / Biso min: 2.89 Å2
Refinement stepCycle: final / Resolution: 1.452→39.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4707 0 148 959 5814
Biso mean--9.66 27.7 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135276
X-RAY DIFFRACTIONf_angle_d1.7727164
X-RAY DIFFRACTIONf_chiral_restr0.081747
X-RAY DIFFRACTIONf_plane_restr0.005920
X-RAY DIFFRACTIONf_dihedral_angle_d16.7311992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.452-1.46830.21681770.21663834X-RAY DIFFRACTION91
1.4683-1.48560.22432400.21174095X-RAY DIFFRACTION100
1.4856-1.50370.23052070.2084148X-RAY DIFFRACTION100
1.5037-1.52270.23532130.20014149X-RAY DIFFRACTION97
1.5227-1.54270.21972160.18714090X-RAY DIFFRACTION100
1.5427-1.56390.21432050.18414138X-RAY DIFFRACTION99
1.5639-1.58620.19961920.18154127X-RAY DIFFRACTION96
1.5862-1.60990.19712050.17994090X-RAY DIFFRACTION99
1.6099-1.63510.17492280.16154188X-RAY DIFFRACTION100
1.6351-1.66190.18472520.1634156X-RAY DIFFRACTION99
1.6619-1.69050.1791940.15454151X-RAY DIFFRACTION100
1.6905-1.72130.1612340.14854192X-RAY DIFFRACTION100
1.7213-1.75440.16962500.14534139X-RAY DIFFRACTION99
1.7544-1.79020.16912220.14084159X-RAY DIFFRACTION100
1.7902-1.82910.17952010.13964251X-RAY DIFFRACTION99
1.8291-1.87160.16962050.13714054X-RAY DIFFRACTION97
1.8716-1.91850.16072320.13944168X-RAY DIFFRACTION98
1.9185-1.97030.16862660.14024096X-RAY DIFFRACTION100
1.9703-2.02830.15372380.13144253X-RAY DIFFRACTION100
2.0283-2.09380.14322460.12894124X-RAY DIFFRACTION100
2.0938-2.16860.12482340.134234X-RAY DIFFRACTION100
2.1686-2.25540.14972300.12414195X-RAY DIFFRACTION99
2.2554-2.3580.14482250.1274130X-RAY DIFFRACTION98
2.358-2.48230.14072190.13074168X-RAY DIFFRACTION98
2.4823-2.63780.14262200.13384274X-RAY DIFFRACTION100
2.6378-2.84150.14822130.13264293X-RAY DIFFRACTION100
2.8415-3.12730.16562330.13214239X-RAY DIFFRACTION99
3.1273-3.57960.12752400.11784194X-RAY DIFFRACTION97
3.5796-4.50890.1242220.1084382X-RAY DIFFRACTION100
4.5089-39.7660.1712400.144477X-RAY DIFFRACTION98
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)
11.2335-0.3903-0.20671.8608-0.28710.46820.0030.0751-0.0435-0.02750.0031-0.01750.00070.0098-0.00890.0409-0.0029-0.00360.0384-0.01930.024114.648717.008451.6548
21.9877-0.75560.40792.3023-0.80991.5536-0.01430.10460.2077-0.08440.0082-0.1178-0.10450.07520.00290.0648-0.00010.00540.0339-0.01740.049512.348530.275550.8585
32.9083-0.232-0.30253.8926-0.06162.314-0.0566-0.05390.12320.22160.0439-0.2316-0.0850.14560.02070.0547-0.006-0.02280.0571-0.02580.039316.408328.294960.8838
40.962-0.48380.46862.0867-0.80052.136-0.0423-0.04940.06230.1690.0291-0.0741-0.15660.12480.0260.05130.0003-0.00440.0498-0.01610.046211.200326.813564.9618
50.33430.1944-0.13960.80720.27941.011-0.014-0.122-0.09450.17860.0239-0.13740.17470.0765-0.00840.1120.0149-0.02520.08470.010.08897.547711.346569.2643
60.98250.1660.08911.55070.71131.05550.0006-0.0692-0.08460.1379-0.06010.07570.0656-0.10260.06590.0767-0.00760.01030.0567-0.00430.0414-1.057910.365863.6527
72.56180.03340.17932.42820.46261.21760.0430.1288-0.0478-0.09670.054-0.118-0.03170.0621-0.05450.0640.00280.00110.0519-0.04130.05810.93962.396647.7498
81.73660.7633-0.81520.7325-0.54950.6112-0.02750.0512-0.0473-0.03620.02680.01360.047-0.0403-0.00360.0526-0.001-0.00390.0524-0.02110.0406-0.035211.711750.8137
92.33861.3093-0.5512.1715-0.1241.33890.00640.23760.1238-0.18970.0405-0.0179-0.05950.0042-0.05110.08670.0079-0.00150.08870.00780.03347.129222.426739.2782
102.8653-0.12660.64455.71751.50591.0806-0.0546-0.37810.07930.2198-0.1640.2628-0.0617-0.36810.19820.05510.01150.00960.1007-0.00580.0648-4.297526.791158.7152
110.628-0.1913-0.00280.63860.15660.9088-0.00820.0381-0.0054-0.0243-0.0210.02820.0056-0.03620.02060.0446-0.01420.00470.0418-0.01980.0577-1.8742-13.201620.82
120.573-0.6373-0.00712.131.24514.14430.0367-0.0816-0.20980.2818-0.03770.07920.4686-0.17950.0470.1231-0.0557-0.00230.09490.00270.14591.6393-27.388529.9723
130.7524-0.03910.05270.46770.19820.9017-0.0086-0.0483-0.00870.02860.0071-0.02450.05430.0438-0.00650.0675-0-0.00590.0451-0.02250.068210.5553-12.703236.636
141.71970.0325-0.10320.83070.60821.4368-0.05060.01230.1325-0.0080.0573-0.0379-0.07470.05830.00790.0547-0.01410.00330.03130.00620.06216.0163-1.743821.5818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 102 )A70 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 127 )A103 - 127
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 146 )A128 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 173 )A147 - 173
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 214 )A174 - 214
6X-RAY DIFFRACTION6chain 'A' and (resid 215 through 250 )A215 - 250
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 273 )A251 - 273
8X-RAY DIFFRACTION8chain 'A' and (resid 274 through 315 )A274 - 315
9X-RAY DIFFRACTION9chain 'A' and (resid 316 through 346 )A316 - 346
10X-RAY DIFFRACTION10chain 'A' and (resid 347 through 360 )A347 - 360
11X-RAY DIFFRACTION11chain 'B' and (resid 70 through 192 )B70 - 192
12X-RAY DIFFRACTION12chain 'B' and (resid 193 through 215 )B193 - 215
13X-RAY DIFFRACTION13chain 'B' and (resid 216 through 298 )B216 - 298
14X-RAY DIFFRACTION14chain 'B' and (resid 299 through 362 )B299 - 362

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