♦Non-structural polyprotein (Polyprotein nsP1234) (P1234) [Cleaved into: P123
♦ P123'
♦ mRNA-capping enzyme nsP1 (EC 2.1.1.-) (EC 2.7.7.-) (Non-structural protein 1)
♦ Protease nsP2 (EC 3.1.3.33) (EC 3.4.22.-) (EC 3.6.1.15) (EC 3.6.4.13) (Non-structural protein 2) (nsP2)
♦ Non-structural protein 3 (nsP3)
♦ Non-structural protein 3' (nsP3')
♦ RNA-directed RNA polymerase nsP4 (EC 2.7.7.48) (Non-structural protein 4) (nsP4)]

NC_001786.1 ;  U73745.1 

MAKPVVKIDVEPESHFAKQVQSCFPQFEIEAVQTTPNDHAHARAFSHLATKLIEMETAKDQIILDIGSAPARRLYSEHKYHCVCPMKCTEDPERMLGYAR
KLIAGSAKGKAEKLRDLRDVLATPDIETQSLCLHTDASCRYRGDVAVYQDVYAIDAPTTLYHQALKGVRTAYWIGFDTTPFMYDALAGAYPLYSTNWADE
QVLESRNIGLCSDKVSEGGKKGRSILRKKFLKQSDRVMFSVGSTLYTESRKLLQSWHLPSTFHLKGKSSFTCRCDTIVSCEGYVLKKITMCPGVTGKPIG
YAVTHHKEGFVVGKVTDTIRGERVSFAVCTYVPTTLCDQMTGILATEVTADDAQKLLVGLNQRIVVNGRTQRNTNTMKNYLLPLVAQALAKWAKEAKQDM
EDERPLNERQRTLTCLCCWAFKRNKRHAIYKRPDTQSIVKVPCEFTSFPLVSLWSAGMSISLRQKLKMMLQARQPTQIAAVTEELIQEAAAVEQEAVDTA
NAELDHAAWPSIVDTTERHVEVEVEELDQRAGEGVVETPRNSIKVSTQIGDALIGSYLILSPQAVLRSEKLACIHDLAEQVKLVTHSGRSGRYAVDKYXG
RVLVPTGVAIDIQSFQALSESATLVYNEREFVNRKLWHIAVYGAALNTDEEGYEKVPVERAESDYVFDVDQKMCLKKEQASGWVLCGELVNPPFHEFAYE
GLRTRPSAPYKVHTVGVYGVPGSGKSAIIKNTVTMSDLVLSGKKENCLEIMNDVLKHRALRITAKTVDSVLLNGVKHTPNILYIDEAFSCHAGTLLATIA
IVRPKQKVVLCGDPKQCGFFNMMQLKVNYNHDICSEVFHKSISRRCTQDITAIVSKLHYQDRMRTTNPRKGDIIIDTTGTTKPAKTDLILTCFRGWVKQL
QQDYRGNEVMTAAASQGLTRASVYAVRTKVNENPLYAQTSEHVNVLLTRTENKLVWKTLSTDPWIKTLTNPPRGHYTATIAEWEAEHQGIMKAIQGYAPP
VNTFMNKVNVCWAKTLTPVLETAGISLSAEDWSELLPPFAQDVAYSPEVALNIICTKMYGFDLDTGLFSRPSVPMTYTKDHWDNRVGGKMYGFSQQAYDQ
LARRHPYLRGREKSGMQIVVTEMRIQRPRSDANIIPINRRLPHSLVATHEYRRAARAEEFFTTTRGYTMLLVSEYNMNLPNKKITWLAPIGTQGAHHTAN
LNLGIPPLLGSFDAVVVNMPTPFRNHHYQQCEDHAMKLQMLAGDALRHIKPGGSLWVKAYGYADRHSEHVVLALARKFKSFRVTQPSCVTSNTEVFLHFS
IFDNGKRAIALHSANRKANSIFQNTFLPAGSAPAYRVKRGDISNAPEDAVVNAANQQGVKGAGVCGAIYRKWPDAFGDVATPTGTAVSKSVQDKLVIHAV
GPNFSKCSEEEGDRDLASAYRAAAEIVMDKKITTVAVPLLSTGIYAGGKNRVEQSLNHLFTAFDNTDADVTIYCMDKTWEKKIKEAIDHRTSVEMVQDDV
QLEEELVRVHPLSSLAGRKGYSTDSGRVFSYLEGTKFHQTAVDIAEMQVLWPALKESNEQIVAYTLGESMDQIRGKCPTEDTDASTPPRTVPCLCRYAMT
PERVYRLKCTNTTQFTVCSSFELPKYHIQGVQRVKCERIIILDPTVPPTYKRPCIRRYPSTISCNSSEDSRSLSTFSVSSDSSIGSLPVGDTRPIPAPRT
IFRPVPAPRAPVLRTTPPPKPPRTFTVRAEVHQAPPTPVPPPRPKRAAKLAREMHPGFTFGDFGEHEVEELTASPLTFGDFAEGEIQGMGVEFELGRAGG
YIFSSDTGPGHLQQRSVLQNCTAECIYEPAKLEKIHAPKLDKTKEDILRSKYQMKPSEANKSRYQSRKVENMKAEIVGRLLDGLGEYLGTEHPVECYRIT
YPVPIYSTSDLRGLSSAKTAVRACNAFLEANFPSVTSYKITDEYDAYLDMVDGSESCLDRSSFSPSRLRSFPKTHSYLDPQINSAVPSPFQNTLQNVLAA
ATKRNCNVTQMRELPTYDSAVLNVEAFRKYACKPDVWDEYRDNPICITTENVTTYVAKLKGPKAAALFAKTHNLIPLHQVPMDKFTVDMKRDVKVTPGTK
HTEERPKVQVIQAAEPLATAYLCGIHRELVRRLNNALFPNIHTLFDMSAEDFDAIIAEHFKHGDHVLETDIASFDKSQDDSMALTALMILEDLGVDQNLM
NLIEAAFGEIVSTHLPTGTRFKFGAMMKSGMFLTLFVNTILNVVIACRVLEDQLAQSPWPAFIGDDNIIHGIISDKLMADRCATWMNMEVKILDSIVGIR
PPYFCGGFIVCDDVTGTACRVADPLKRLFKLGKPLPLDDGQDEDRRRALHDEVKTWSRVGLRHRVCEAIEDRYAVHSSELVLLALTTLSKNLKSFRNIRG
KPIHLYGGPK

♦P123 and P123' are short-lived polyproteins, accumulating during early stage of infection. P123 is directly translated from the genome, whereas P123' is a product of the cleavage of P1234. They localize the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, they start viral genome replication into antigenome. After these early events, P123 and P123' are cleaved sequentially into nsP1, nsP2 and nsP3/nsP3'. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex (By similarity).
♦ nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity).
♦ nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins. Also inhibits cellular transcription by inducing rapid degradation of POLR2A, a catalytic subunit of the RNAPII complex. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (By similarity).
♦ nsP3 and nsP3' are essential for minus strand and subgenomic 26S mRNA synthesis.
♦ nsP4 is an RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA codes for structural proteins. nsP4 is a short-lived protein regulated by several ways: the opal codon readthrough and degradation by ubiquitin pathway (By similarity).

♦ Non-structural polyprotein: Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Note=Located on the cytoplasmic surface of modified endosomes and lysosomes, also called cytopathic vacuoles type I (CPVI). These vacuoles contain numerous small circular invaginations (spherules) which may be the sites of RNA synthesis.
♦ P123: Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side .
♦ P123': Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side .
♦ mRNA-capping enzyme nsP1: Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host cell membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host cell projection, host filopodium . Note=In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then a fraction of nsP1 localizes to the inner surface of the plasma membrane and its filopodial extensions (By similarity). .
♦ Protease nsP2: Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host nucleus . Note=In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then approximately half of nsP2 is found in the nucleus (By similarity). .
♦ Non-structural protein 3: Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host cytoplasm . Note=In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then nsP3 and nsP3' seems to aggregate in cytoplasm (By similarity). .
♦ Non-structural protein 3': Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host cytoplasm . Note=In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then nsP3 and nsP3' seems to aggregate in cytoplasm (By similarity). .
♦ RNA-directed RNA polymerase nsP4: Host endosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side . Host lysosome membrane
♦ Peripheral membrane protein
♦ Cytoplasmic side .

♦DOMAIN 30 257 Alphavirus-like MT.
♦ DOMAIN 688 840 (+)RNA virus helicase ATP-binding.
♦ DOMAIN 841 989 (+)RNA virus helicase C-terminal.
♦ DOMAIN 1002 1325 Peptidase C9.
♦ DOMAIN 1332 1491 Macro.
♦ DOMAIN 2164 2279 RdRp catalytic.

♦ACT_SITE 1011 1011 For cysteine protease nsP2 activity.
♦ ACT_SITE 1081 1081 For cysteine protease nsP2 activity.