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- PDB-5v5h: OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ub... -

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Basic information

Entry
Database: PDB / ID: 5v5h
TitleOTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.2
Components
  • RNA-directed RNA polymerase L
  • Ubiquitin variant CC.2
Keywordshydrolase / transferase / Ovarian Tumor Domain protease / deubiquitinase / ubiquitin variant
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / Hydrolases; Acting on ester bonds / ubiquitinyl hydrolase 1 ...RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / Hydrolases; Acting on ester bonds / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
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 / Bunyavirus RNA dependent RNA polymerase ...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 / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKhare, B. / Mark, B.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-05310 Canada
Research Manitoba Canada
CitationJournal: PLoS Pathog. / Year: 2017
Title: Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants.
Authors: Zhang, W. / Bailey-Elkin, B.A. / Knaap, R.C.M. / Khare, B. / Dalebout, T.J. / Johnson, G.G. / van Kasteren, P.B. / McLeish, N.J. / Gu, J. / He, W. / Kikkert, M. / Mark, B.L. / Sidhu, S.S.
History
DepositionMar 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 13, 2017Group: Advisory / Category: database_PDB_caveat
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 variant CC.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2815
Polymers31,9542
Non-polymers3273
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-47 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.398, 33.599, 71.248
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

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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


Mass: 19770.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)
Strain: Nigeria/IbAr10200/1970 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
#2: Protein Ubiquitin variant CC.2


Mass: 12183.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 226 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (w/v) PEG 4000, 0.2 M CaCl2 and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→43.434 Å / Num. obs: 38017 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1876 / CC1/2: 0.79 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PT2

3pt2


Resolution: 1.5→43.434 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1781 1999 5.26 %
Rwork0.1563 --
obs0.1575 38005 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→43.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 17 223 2145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081987
X-RAY DIFFRACTIONf_angle_d0.9712701
X-RAY DIFFRACTIONf_dihedral_angle_d13.5651193
X-RAY DIFFRACTIONf_chiral_restr0.055298
X-RAY DIFFRACTIONf_plane_restr0.007344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.53780.32491390.27812523X-RAY DIFFRACTION96
1.5378-1.57930.2631410.23562547X-RAY DIFFRACTION98
1.5793-1.62580.2241410.2122533X-RAY DIFFRACTION98
1.6258-1.67830.22941420.19682560X-RAY DIFFRACTION98
1.6783-1.73830.21141410.1772525X-RAY DIFFRACTION98
1.7383-1.80790.23591420.17562565X-RAY DIFFRACTION99
1.8079-1.89020.16621430.15672582X-RAY DIFFRACTION99
1.8902-1.98980.19681440.14252579X-RAY DIFFRACTION99
1.9898-2.11450.15781430.13972564X-RAY DIFFRACTION98
2.1145-2.27770.15621410.14172562X-RAY DIFFRACTION98
2.2777-2.50690.16541430.14442575X-RAY DIFFRACTION99
2.5069-2.86960.1621450.14912615X-RAY DIFFRACTION99
2.8696-3.61520.17021460.15042612X-RAY DIFFRACTION98
3.6152-43.45210.16991480.15032664X-RAY DIFFRACTION97
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)
12.53350.6181-0.44951.1436-0.03222.6962-0.021-0.0531-0.06070.029-0.079-0.00020.04930.01980.08540.11750.0157-0.00750.08830.01050.1224-16.858515.231411.5222
22.1220.4357-0.83161.8663-0.3363.03030.0058-0.44760.1060.2515-0.11070.00240.10440.28440.08510.1996-0.00920.00290.3103-0.02140.1813-19.292913.099835.5832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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