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- PDB-5wwp: Crystal structure of Middle East respiratory syndrome coronavirus... -

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Basic information

Entry
Database: PDB / ID: 5wwp
TitleCrystal structure of Middle East respiratory syndrome coronavirus helicase (MERS-CoV nsp13)
ComponentsORF1ab
KeywordsHYDROLASE / Middle East respiratory syndrome coronavirus / Nidovirales / Coronavirus / MERS / nsp13 / helicase / SF1 superfamily / ATP hydrolysis / ATPase / RNA 5'-Triphosphatase / Unwinding / Upf1 helicase / Arterivirus nsp10 / Zinc binding domain / CH domain / 1B beta-barrel domain / viral RNA synthesis / RecA-like domain / CoV replication and transcription
Function / homology
Function and homology information


mRNA capping enzyme complex / 7-methylguanosine mRNA capping / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding ...mRNA capping enzyme complex / 7-methylguanosine mRNA capping / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Nonstructural protein 14, betacoronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain ...RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Nonstructural protein 14, betacoronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus
Similarity search - Domain/homology
Biological speciesHuman betacoronavirus 2c EMC/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHao, W. / Wojdyla, J.A. / Zhao, R. / Han, R. / Das, R. / Zlatev, I. / Manoharan, M. / Wang, M. / Cui, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81501759 China
CitationJournal: PLoS Pathog. / Year: 2017
Title: Crystal structure of Middle East respiratory syndrome coronavirus helicase
Authors: Hao, W. / Wojdyla, J.A. / Zhao, R. / Han, R. / Das, R. / Zlatev, I. / Manoharan, M. / Wang, M. / Cui, S.
History
DepositionJan 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ORF1ab
A: ORF1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,54913
Polymers132,6762
Non-polymers87311
Water0
1
B: ORF1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6305
Polymers66,3381
Non-polymers2924
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ORF1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9188
Polymers66,3381
Non-polymers5807
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.675, 185.675, 185.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ORF1ab /


Mass: 66337.883 Da / Num. of mol.: 2 / Fragment: NSP13 helicase, UNP residues 5311-5908
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Gene: orf1ab / Plasmid: pFast-bac 1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: K0BWD0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 1M ammonium sulfate, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3→48.95 Å / Num. obs: 71189 / % possible obs: 99.58 % / Observed criterion σ(I): -3 / Redundancy: 3.38 % / Biso Wilson estimate: 74.366 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Net I/av σ(I): 13.17 / Net I/σ(I): 11.21
Reflection shellResolution: 3→3.18 Å / Redundancy: 3.94 % / Rmerge(I) obs: 0.786 / CC1/2: 0.606 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Cootdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.95 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.57
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 3423 4.81 %Random
Rwork0.2318 ---
obs0.234 71189 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 68.13 Å2
Refinement stepCycle: LAST / Resolution: 3→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8540 0 31 0 8571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158745
X-RAY DIFFRACTIONf_angle_d0.9511898
X-RAY DIFFRACTIONf_dihedral_angle_d11.3875247
X-RAY DIFFRACTIONf_chiral_restr0.0551386
X-RAY DIFFRACTIONf_plane_restr0.0051505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9995-3.04240.41421200.37592793X-RAY DIFFRACTION97
3.0424-3.08780.37771620.38282799X-RAY DIFFRACTION99
3.0878-3.1360.43191430.34392797X-RAY DIFFRACTION99
3.136-3.18740.411380.33262844X-RAY DIFFRACTION100
3.1874-3.24240.38151680.3182799X-RAY DIFFRACTION100
3.2424-3.30130.33261170.31752797X-RAY DIFFRACTION99
3.3013-3.36480.34971270.30952889X-RAY DIFFRACTION99
3.3648-3.43350.33971580.28822799X-RAY DIFFRACTION100
3.4335-3.50810.3651280.28442829X-RAY DIFFRACTION100
3.5081-3.58970.29831430.28322812X-RAY DIFFRACTION100
3.5897-3.67940.40151470.26892826X-RAY DIFFRACTION100
3.6794-3.77890.31711440.26072845X-RAY DIFFRACTION100
3.7789-3.890.2881270.24032827X-RAY DIFFRACTION100
3.89-4.01550.28241510.23042834X-RAY DIFFRACTION100
4.0155-4.1590.27631400.22512837X-RAY DIFFRACTION100
4.159-4.32540.26871450.2182809X-RAY DIFFRACTION100
4.3254-4.52210.25961570.20872841X-RAY DIFFRACTION100
4.5221-4.76040.24651290.19072848X-RAY DIFFRACTION100
4.7604-5.05830.23841250.19052830X-RAY DIFFRACTION100
5.0583-5.44840.27331660.20372825X-RAY DIFFRACTION100
5.4484-5.99590.26031510.20642807X-RAY DIFFRACTION100
5.9959-6.86140.21531300.21492848X-RAY DIFFRACTION100
6.8614-8.63690.21241340.18912836X-RAY DIFFRACTION100
8.6369-48.95210.21661730.19152795X-RAY DIFFRACTION99

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