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- PDB-3phx: OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3phx
TitleOTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15
Components
  • RNA-directed RNA polymerase L
  • Ubiquitin-like protein ISG15
KeywordsHydrolase/Protein Binding / OTU domain / De-ubiquitinase / De-ISGylase / Hydrolase-Protein Binding complex
Function / homology
Function and homology information


ISG15-protein conjugation / positive regulation of protein oligomerization / RNA-templated viral transcription / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative stranded viral RNA replication / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway ...ISG15-protein conjugation / positive regulation of protein oligomerization / RNA-templated viral transcription / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative stranded viral RNA replication / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / positive regulation of interleukin-10 production / protein deubiquitination / positive regulation of bone mineralization / endoplasmic reticulum unfolded protein response / ERAD pathway / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / modification-dependent protein catabolic process / ISG15 antiviral mechanism / positive regulation of type II interferon production / protein tag activity / Interferon alpha/beta signaling / integrin binding / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / defense response to virus / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on ester bonds / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / defense response to bacterium / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / innate immune response / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / nucleotide binding / DNA-templated transcription / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ETHANAMINE / Ubiquitin-like protein ISG15 / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.3Mar 26, 2025Group: 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_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,94717
Polymers29,9972
Non-polymers95015
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA-directed RNA polymerase L
hetero molecules

B: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,94717
Polymers29,9972
Non-polymers95015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1520 Å2
ΔGint-336 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.520, 37.100, 84.350
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#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: 21011.580 Da / Num. of mol.: 1 / Fragment: UNP residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Strain: Nigeria/IbAr10200/1970 / Gene: L / Production host: Escherichia coli (E. coli)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
#2: Protein Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein / hUCRP


Mass: 8985.266 Da / Num. of mol.: 1 / Fragment: UNP residues 79-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: P05161

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Non-polymers , 4 types, 207 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-NEH / ETHANAMINE


Mass: 45.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG8K, 0.2M zinc acetate, 0.1M MES sodium salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2010
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 33549

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.4_122)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 1607 4.94 %
Rwork0.1395 --
obs0.1421 32537 95.15 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.659 Å2 / ksol: 0.438 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7409 Å2-0 Å2-1.5703 Å2
2---2.2719 Å20 Å2
3----1.3003 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 23 192 2136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161980
X-RAY DIFFRACTIONf_angle_d1.3952679
X-RAY DIFFRACTIONf_dihedral_angle_d13.955728
X-RAY DIFFRACTIONf_chiral_restr0.104291
X-RAY DIFFRACTIONf_plane_restr0.007347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.25581720.17782837X-RAY DIFFRACTION89
1.6572-1.72350.24861700.15752937X-RAY DIFFRACTION91
1.7235-1.8020.21471440.12652988X-RAY DIFFRACTION93
1.802-1.8970.18481320.10783063X-RAY DIFFRACTION94
1.897-2.01580.16941530.1053097X-RAY DIFFRACTION96
2.0158-2.17140.20721850.11543143X-RAY DIFFRACTION97
2.1714-2.38980.17951610.11693165X-RAY DIFFRACTION98
2.3898-2.73540.15931660.12763206X-RAY DIFFRACTION98
2.7354-3.44560.18181570.13493211X-RAY DIFFRACTION98
3.4456-300.19591670.17623283X-RAY DIFFRACTION97

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