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- PDB-3phu: OTU Domain of Crimean Congo Hemorrhagic Fever Virus -

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Basic information

Entry
Database: PDB / ID: 3phu
TitleOTU Domain of Crimean Congo Hemorrhagic Fever Virus
ComponentsRNA-directed RNA polymerase L
KeywordsHYDROLASE / OTU DOMAIN / De-ubiquitinase / De-ISGylase
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / protein deubiquitination / endoplasmic reticulum unfolded protein response / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Hydrolases; Acting on ester bonds ...RNA-templated viral transcription / negative stranded viral RNA replication / protein deubiquitination / endoplasmic reticulum unfolded protein response / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Hydrolases; Acting on ester bonds / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / nucleotide binding / DNA-templated transcription / metal ion binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1100 / RNA-directed RNA polymerase, nairovirus / : / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1100 / RNA-directed RNA polymerase, nairovirus / : / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Cathepsin B; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Papain-like cysteine peptidase superfamily / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsAkutsu, M. / Ye, Y. / Virdee, S. / Komander, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains.
Authors: Akutsu, M. / Ye, Y. / Virdee, S. / Chin, J.W. / Komander, D.
History
DepositionNov 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6113
Polymers49,5192
Non-polymers921
Water2,576143
1
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8522
Polymers24,7591
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)24,7591
Polymers24,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.990, 115.990, 94.171
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thiolesterase / RNA- ...Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thiolesterase / RNA-directed RNA polymerase


Mass: 24759.447 Da / Num. of mol.: 2 / Fragment: UNP residues 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: Nigeria/IbAr10200/1970 / Gene: L / Production host: Escherichia coli (E. coli)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3.9M NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50.22 Å / Num. obs: 37465

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.4_122) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.382 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1823 4.98 %
Rwork0.1936 --
obs0.1955 36605 97.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.496 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7468 Å20 Å20 Å2
2---4.7468 Å2-0 Å2
3---9.4937 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 6 143 3091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133008
X-RAY DIFFRACTIONf_angle_d1.4884077
X-RAY DIFFRACTIONf_dihedral_angle_d16.0621086
X-RAY DIFFRACTIONf_chiral_restr0.096455
X-RAY DIFFRACTIONf_plane_restr0.007524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.29991560.25293296X-RAY DIFFRACTION93
2.2786-2.36990.26131640.23053331X-RAY DIFFRACTION94
2.3699-2.47770.28671710.22633371X-RAY DIFFRACTION96
2.4777-2.60830.28321940.23283437X-RAY DIFFRACTION97
2.6083-2.77180.28581810.23623491X-RAY DIFFRACTION99
2.7718-2.98570.33371850.233502X-RAY DIFFRACTION99
2.9857-3.28610.26542020.21523508X-RAY DIFFRACTION100
3.2861-3.76150.20761810.17433592X-RAY DIFFRACTION100
3.7615-4.73850.17262080.14793579X-RAY DIFFRACTION100
4.7385-49.39410.20611810.18623675X-RAY DIFFRACTION98

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