[English] 日本語
Yorodumi
- PDB-5vsl: Crystal structure of viperin with bound [4Fe-4S] cluster and S-ad... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vsl
TitleCrystal structure of viperin with bound [4Fe-4S] cluster and S-adenosylhomocysteine (SAH)
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
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 / SAD / Resolution: 1.972 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)75,0946
Polymers73,6222
Non-polymers1,4724
Water7,242402
1
A: Radical S-adenosyl methionine domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5473
Polymers36,8111
Non-polymers7362
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)37,5473
Polymers36,8111
Non-polymers7362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.934, 73.854, 141.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(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-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES, pH 6.8 - 7.6, 10 - 30 % (w/v) PEG MME 2000, and 5 mM SAH
PH range: 6.8 - 7.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 42331 / % possible obs: 95 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.079 / Net I/av σ(I): 17.1 / Net I/σ(I): 12.6
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4223 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: 000)refinement
HKL-2000data scaling
Cootmodel building
SHELXDphasing
PHENIX(1.11.1_2575: 000)phasing
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.972→46.065 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.38
RfactorNum. reflection% reflection
Rfree0.1997 2110 4.99 %
Rwork0.1549 --
obs0.1571 42302 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.972→46.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 68 402 4645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154406
X-RAY DIFFRACTIONf_angle_d2.0085954
X-RAY DIFFRACTIONf_dihedral_angle_d16.6942675
X-RAY DIFFRACTIONf_chiral_restr0.055635
X-RAY DIFFRACTIONf_plane_restr0.005763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9716-2.01750.27091500.22932645X-RAY DIFFRACTION96
2.0175-2.06790.28851330.21272696X-RAY DIFFRACTION97
2.0679-2.12390.24131650.19612668X-RAY DIFFRACTION97
2.1239-2.18630.23851390.18052727X-RAY DIFFRACTION97
2.1863-2.25690.21331530.17282656X-RAY DIFFRACTION97
2.2569-2.33760.20571160.16232729X-RAY DIFFRACTION97
2.3376-2.43120.22151300.15982705X-RAY DIFFRACTION97
2.4312-2.54180.19621360.1622727X-RAY DIFFRACTION97
2.5418-2.67580.22751500.16042697X-RAY DIFFRACTION97
2.6758-2.84340.22841420.15742665X-RAY DIFFRACTION95
2.8434-3.06290.21121370.15762679X-RAY DIFFRACTION96
3.0629-3.37110.19341460.14862659X-RAY DIFFRACTION94
3.3711-3.85870.20821410.13872643X-RAY DIFFRACTION93
3.8587-4.86070.16671340.12582680X-RAY DIFFRACTION93
4.8607-46.07760.15031380.152616X-RAY DIFFRACTION86
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)
11.9958-0.80160.24161.3066-0.54592.61380.0189-0.0152-0.0671-0.114-0.2571-0.29580.56550.550.1560.29340.06930.04420.23350.0980.320118.008423.665840.0725
21.23890.5946-0.76112.602-2.89625.2899-0.04050.1920.0038-0.11070.05920.02360.1178-0.2732-0.02210.1950.008-0.00920.15360.00140.20844.505135.414434.967
32.8921-1.98611.67597.1472-2.84233.6853-0.0554-0.10220.3390.43620.05010.2023-0.9233-0.14-0.01230.42940.0681-0.0250.15670.00380.30725.142349.272139.1605
47.9232-3.68470.50832.61840.33470.6888-0.065-0.04720.6973-0.3391-0.2109-0.8672-0.04140.68370.20160.3350.00430.0750.59970.19140.533428.642534.980134.6497
53.72861.8872-1.3253.7035-0.25740.5576-0.34360.5593-0.4324-0.05570.27570.01440.5862-0.4030.01920.4118-0.16270.02890.3325-0.05440.24424.821635.3837-4.6101
62.83660.079-0.00253.5824-0.46881.3115-0.1697-0.0373-0.35760.15120.14350.3380.6811-0.488-0.05310.3265-0.1260.06470.3010.01450.2674-0.92536.01588.7134
73.0643-0.023-1.61561.10.18773.5491-0.06370.31820.2698-0.01870.05840.0208-0.0522-0.14070.0030.1144-0.0058-0.00950.18560.05090.227813.191150.56322.4938
83.4943-0.3696-0.36071.98140.23095.5169-0.20220.3516-0.313-0.1951-0.0223-0.13030.65410.40260.10950.240.0020.06240.31740.00780.257222.355841.1869-5.3237
96.16135.12482.19484.30771.45173.24540.20080.21-0.9718-0.1638-0.108-0.56140.83040.2417-0.25490.6833-0.02260.10360.231-0.04750.532112.859328.0292-0.1018
103.87173.80150.27895.4444-0.58120.4536-0.26950.648-0.9942-0.74580.4209-1.05340.98640.0013-0.14761.1472-0.13250.11620.3774-0.12970.75698.340518.73220.7539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 173 )
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 273 )
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 294 )
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 337 )
5X-RAY DIFFRACTION5chain 'B' and (resid 74 through 102 )
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 173 )
7X-RAY DIFFRACTION7chain 'B' and (resid 174 through 250 )
8X-RAY DIFFRACTION8chain 'B' and (resid 251 through 294 )
9X-RAY DIFFRACTION9chain 'B' and (resid 295 through 311 )
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 335 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more