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- PDB-8fwx: Apo crystal structure of beluga whale Gammacoronavirus SW1 Mpro -

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Basic information

Entry
Database: PDB / ID: 8fwx
TitleApo crystal structure of beluga whale Gammacoronavirus SW1 Mpro
ComponentsMain Protease
KeywordsVIRAL PROTEIN / Hydrolase
Function / homology
Function and homology information


host cell membrane / viral genome replication / transferase activity / omega peptidase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / proteolysis ...host cell membrane / viral genome replication / transferase activity / omega peptidase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Papain-like viral protease, palm and finger domains, coronavirus / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto 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. ...Papain-like viral protease, palm and finger domains, coronavirus / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto 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. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / ORF 1a polyprotein
Similarity search - Component
Biological speciesBeluga whale coronavirus SW1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsOrnelas, E. / Knapp, M.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Viruses / Year: 2023
Title: Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses.
Authors: Zvornicanin, S.N. / Shaqra, A.M. / Huang, Q.J. / Ornelas, E. / Moghe, M. / Knapp, M. / Moquin, S. / Dovala, D. / Schiffer, C.A. / Kurt Yilmaz, N.
History
DepositionJan 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Main Protease
B: Main Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4186
Polymers67,0242
Non-polymers3944
Water3,045169
1
A: Main Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7043
Polymers33,5121
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Main Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7143
Polymers33,5121
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.864, 136.062, 49.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21B-549-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 22 or resid 24...
d_2ens_1(chain "B" and (resid 1 through 20 or (resid 21...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAHISHISAA1 - 221 - 22
d_12ASNASNALAALAAA24 - 10324 - 103
d_13ILEILEGLUGLUAA105 - 291105 - 291
d_14ILEILELEULEUAA293 - 302293 - 302
d_21ALAALAHISHISBB1 - 221 - 22
d_22ASNASNALAALABB24 - 10324 - 103
d_23ILEILEGLUGLUBB105 - 291105 - 291
d_24ILEILELEULEUBB293 - 302293 - 302

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Components

#1: Protein Main Protease / ORF 1a polyprotein


Mass: 33512.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beluga whale coronavirus SW1 / Production host: Escherichia coli (E. coli) / References: UniProt: B2BW32
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Oct 13, 2021 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.97→70.59 Å / Num. obs: 32590 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.46 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.059 / Rrim(I) all: 0.147 / Χ2: 1.08 / Net I/σ(I): 11.3
Reflection shellResolution: 2.57→2.71 Å / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 1.028 / Num. measured all: 16496 / Num. unique obs: 2667 / CC1/2: 0.821 / Rpim(I) all: 0.448 / Rrim(I) all: 1.124 / Χ2: 1.15 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→68.03 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.54
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1628 5 %RANDOM
Rwork0.1986 30903 --
obs0.2006 32531 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.97 Å2
Refinement stepCycle: LAST / Resolution: 2.12→68.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4571 0 22 169 4762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324746
X-RAY DIFFRACTIONf_angle_d0.60056470
X-RAY DIFFRACTIONf_chiral_restr0.0452701
X-RAY DIFFRACTIONf_plane_restr0.0042836
X-RAY DIFFRACTIONf_dihedral_angle_d13.46311604
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.734287177133 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.180.35051610.29772473X-RAY DIFFRACTION98.21
2.18-2.250.34451160.31212517X-RAY DIFFRACTION99.7
2.25-2.330.32411330.27682538X-RAY DIFFRACTION99.9
2.33-2.420.32791160.26182554X-RAY DIFFRACTION100
2.42-2.530.31791360.24572562X-RAY DIFFRACTION100
2.53-2.670.26011480.23222541X-RAY DIFFRACTION100
2.67-2.840.27071380.22952556X-RAY DIFFRACTION100
2.84-3.050.25741360.22182560X-RAY DIFFRACTION100
3.05-3.360.24461420.20312584X-RAY DIFFRACTION100
3.36-3.850.2131210.1782621X-RAY DIFFRACTION100
3.85-4.850.19121470.14952618X-RAY DIFFRACTION100
4.85-68.030.19691340.16932779X-RAY DIFFRACTION100
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)
12.35765891924-1.09901558248-1.626416558911.12470243835-0.5589412508793.692926078110.2384467020190.2063218037561.19119058216-0.2285888033250.151531708523-0.5875624572430.02258838971680.07878479013-0.4171576220970.4067929039570.01945753620830.0956423997120.3281338006250.004572736257250.73675912449233.753588956820.89940695515.82497233281
23.24967388762-1.6264639291-0.8758459286722.278538595070.7535621803081.917028196910.4563312752710.4307585875341.25806136595-0.6485726206920.0845670441643-0.747712836751-0.3382661110480.230413827582-0.3409011510050.4767179732560.03205041692520.2543238283480.4901129700990.05266850410140.77327878064345.485168107917.095449747-4.53967505848
33.76307431806-1.34922956311-1.723880364042.503706896790.9480967942722.07924960710.04375070331870.126461619570.356495469344-0.1374701717160.138251469204-0.2204746399190.0658056328516-0.0821816364578-0.1989725124850.2982327404240.02852459659040.02771143586620.306026101754-0.002865017867370.23534000402233.159158952811.58273744892.71206539536
42.23407288486-1.30273503030.0247751669541.925832316260.6613299048090.728416800393-0.488642243873-0.113826713463-0.4842009552350.3192902369920.1282482224070.3198812526080.917602341211-0.1116669491080.2061637433950.540442279339-0.01993290966810.07890509722910.2874370122080.003607601862970.31636666960822.0201415512-0.58302037269115.4202485687
52.31066430394-0.941014201327-0.6792542568120.8494094490170.3273351486181.91695677711-0.42373281602-0.339960021538-0.7692602843180.6386469164730.159546883492-0.04543124857310.7894298809190.1641469301450.3030815563990.7315097215420.1091858963480.156388156470.366713939980.06524012974060.42891791446124.5484038391-6.1366723131722.0737886171
61.52575347354-0.95699253772-1.08966143241.52085448104-0.1587283093922.44889568594-0.239886705544-0.145091312972-0.228918317880.108522148241-0.02306813696490.1145578656260.442530088425-0.1989825134150.1938363559590.444000082710.04048180895120.0503682326920.3463012031050.01451753593180.23435986436719.62072386035.2993286887320.3528881203
71.68422399172-0.3687198978980.04105297580922.151336530791.65022678514.135631988130.089383100467-0.2389564845560.5947023746140.02843241648680.188114256743-0.781800350337-0.157836920106-0.320984189885-0.2950245094550.2882773048360.0371014604914-0.08091824880970.35217763326-0.1089392928570.55170198711127.96688523226.73700442116.6753693781
81.865945428080.598068307437-0.1211523190731.214726265760.01957893298311.715488790840.171787741834-1.095920663041.305637791880.4881017096970.508624727457-0.803509993870.1587169075830.110057079941-0.1449084321750.4312856977220.0202404777609-0.08678195229190.524888288835-0.4827666433610.93733505319126.337315096637.953649771932.2029022894
90.9643012675150.681680267804-0.5893455340151.322400903790.5398166405051.513045020620.107295888960.09525851091990.942690332903-0.3955126240660.353616153859-0.633417114321-0.495288112423-0.0386405694085-0.07920736311530.3496558710.09242890321460.06114156823070.153666477322-0.2323154742031.0571850439523.952372400740.200342438921.1506933642
103.6932550401-0.924574486438-0.2194883571362.255440509870.9118905213361.52236273005-0.0276055229119-0.1820796081620.3585094927070.1325547410970.109650698335-0.2566844749950.03018883058770.0338064475493-0.07732070575380.3125026279870.0100821386792-0.03035842780330.25829070124-0.04614929502880.31393448705818.700821577726.966464595719.7571328932
110.0640967371435-0.09538155724250.007094917779380.124296875014-0.03776160003460.2368618593-0.0793747347257-0.5127574886370.08686061916470.3015899395210.241407897623-0.1711808725480.034319200551-0.767146006177-0.1574035928060.4601087442210.0541631235083-0.03007783428890.677652203038-0.07636926160740.3391804768916.2253203190424.417869317827.2433699405
121.20217819532-0.4709846869250.7635202460393.658844279720.4027955645762.657495020480.1392602162960.230368415738-0.212236187883-0.128215088343-0.2311727514510.703503118563-0.158611781414-0.0125585432090.1442675212580.2731202075310.0589912964605-0.02881266472040.372600812139-0.08604026335840.3776308860662.4447274981516.10979244-0.479798861604
131.38692546778-1.179249886630.637074505832.132583124660.5646127999621.27628938378-0.02455032447750.172080178862-0.0471563832337-0.0526582886205-0.04033636952730.3355555004340.07855027120450.103639766480.1087580014710.3022136191220.03998995123650.007477999696040.385400354437-0.03385968911450.24404923647111.729197429913.65246019972.25332096505
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 24 )AA1 - 241 - 24
22chain 'A' and (resid 25 through 107 )AA25 - 10725 - 107
33chain 'A' and (resid 108 through 182 )AA108 - 182108 - 182
44chain 'A' and (resid 183 through 226 )AA183 - 226183 - 226
55chain 'A' and (resid 227 through 269 )AA227 - 269227 - 269
66chain 'A' and (resid 270 through 302 )AA270 - 302270 - 302
77chain 'B' and (resid 1 through 24 )BB1 - 241 - 24
88chain 'B' and (resid 25 through 73 )BB25 - 7325 - 73
99chain 'B' and (resid 74 through 107 )BB74 - 10774 - 107
1010chain 'B' and (resid 108 through 182 )BB108 - 182108 - 182
1111chain 'B' and (resid 183 through 197 )BB183 - 197183 - 197
1212chain 'B' and (resid 198 through 269 )BB198 - 269198 - 269
1313chain 'B' and (resid 270 through 302 )BB270 - 302270 - 302

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