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1 advances.sciencemag.org/cgi/content/full/3/9/eaao2182/dc1 Supplementary Materials for Potyvirus virion structure shows conserved protein fold and RNA binding site in ssrna viruses Miguel Zamora, Eduardo Méndez-López, Xabier Agirrezabala, Rebeca Cuesta, José L. Lavín, M. Amelia Sánchez-Pina, Miguel A. Aranda, Mikel Valle This PDF file includes: Published 20 September 2017, Sci. Adv. 3, eaao2182 (2017) DOI: /sciadv.aao2182 fig. S1. CryoEM and atomic model for WMV. fig. S2. Structural comparison between potyvirus and potexvirus. fig. S3. Representation of the structural alignment between regions of CPs and NPs from several ssrna viruses. fig. S4. Output from the 3D library search using the WMV CP core region as target. fig. S5. Morphological universe of ssrna viruses with structural homology between their CPs/NPs.
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3 fig. S1. CryoEM and atomic model for WMV. (A) Iso-surface rendering of the cryoem map calculated for WMV virions. Colors of the map show estimates of local resolution (color-scale included). (B) Rendering of the density map attributed to one WMV CP subunit after segmentation. Signal for a segment of ssrna is also included. The colorcode indicates local resolution as in (A). The inset shows a cartoon with an schematic depiction of WMV CP and ssrna. (C) Local features of the cryoem map together with modeled atomic coordinates. The density depicts accurately the side chain of bulky amino acids. (D) Fourier Shell Correlation (FSC) calculated between fully independent half data sets (gold standard), and between the final cryoem map and a simulated density derived from the atomic model. The FSC thresholds of 0.14 for the cryoem data, and of 0.5 for the comparison between cryoem and the atomic model, estimate the global resolution at 4.0 Å. (E) Table summary of the figures of merit calculated in Molprobity for the validation of the atomic model of WMV CP.
4 fig. S2. Structural comparison between potyvirus and potexvirus. (A) CryoEM map rendering of potyvirus WMV together with the derived atomic model for WMV CP and the ssrna. (B) Iso-surface rendering for the cryoem map for PepMV together with the atomic model for PepMV CP and corresponding ssrna (4). In both panels A and B, the densities are colored: CP core region (light blue); N-terminal arm (dark blue); C-terminal arm (yellow); density for the ssrna (red). The ribbons are colored in rainbow mode from N- to C-terminal ends. (C) Superimposition of the two atomic models for WMV CP (Rainbow colors) and PepMV CP (gray). The structural alignment was generated by Matras (13).
5 WMV CP vs PepMV CP (5FN1) Aligned length= 135, RMSD= 2.85, Seq_ID=n_identical/n_aligned= TM-score= NTRATKTQFESWYSAVKVEYDLNDEQMGVIMNGFMVWCIDNGTSPDVNGVWVMMDGEE-QVEYPLK--PIVENAKPTLRQIMHHFSDAAEAYIEMRNSESPYMPRYGLLRNLRDRELARYAFDFY-EVTS KTPNRAREAIAQMKAAAL :::::::::::::::::: :::::::::::::::::::::::::::::.:::::....:::: ::::::::::::::::::::::::::::: ::::::::::::: :::::::::: :.:..::::::::::::::::: TSVATPAEIEALGKIFTA-MGLAANETGPAMWDLARAYADVQSSKSAQLIGATPS---NPALSRRALAAQFDRINITPRQFCMYFAKVVWNILLDSN----IPPANWAKLGYQE-DTKFAAFDFFDGVTNPASLQPADGLIRQPNEKELAAHSVAKYGALARQKIS WMV CP vs RVFV NP (4H5O) Aligned length= 125, RMSD= 4.04, Seq_ID=n_identical/n_aligned= TM-score= NTRATKTQFESWYSAVKVEYDLNDEQMGVIMNGFMVWCIDNGTSPDVNGVWVMMDGEEQVE--YP-LK---PIVEN--AKP-T-L-RQIMHHFSDAAEAYIEMRNSESPYM-PRYGLLRNLR---DRELARYAFDFY-E-VTS-K---TPNRAREAIAQMKAAAL.::.::.:::::: ::.:::::::::::::::::::...:::....::: ::.: :::..::. : ::.::::::::::::: : :: :::::..::: :::::::::::: : :::....:::::::::::::: -GFDARRVIELLKQ-YG------GADWEKDAKKMIVLALTRGN-KPRRMMMKMS---KEGKATVEALINKYKLKE-GNPSRDELTLSRVAAALAGRTCQALV-V-----LSEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFS WMV CP vs TSWV NP (5IP2) Aligned length= 110, RMSD= 4.68, Seq_ID=n_identical/n_aligned= TM-score= NTRATKTQ--FESW--YSAVKVEYDLNDEQMGVIMN-GFMVWCIDNGTSPDVNGVWVMMDGEEQVEYP--LKPIVE---NAK-----P-----TLRQIMHHFSDAAEAYIE-M-RNSESPYMP--R-YGLLRNLRDRE--LARYAF--DFY---EV-TSKTPNRAREAIAQMKAAAL :.: ::.::::::::::...::...:.. :::. :::::::::::::::::: : :::..::.: : ::::::::.:: :::::: ::. :: :.::.:..:::::::... FNFKTF--CLEN--LDQ IKK-MSIISCLTFLKNRQSIMKVI KQSDFTF-GKITIKKTSDRIGATDMTFRRLDSLIRVRLVEETGNSENLNTIKSKIASHPLIQAYGLPLDDAKSVRLAIMLGGSLPLIASVDSFEMISVVLAIYQDAKY- WMV CP vs La Crosse virus NP (4BHH) Aligned length= 103, RMSD= 4.36, Seq_ID=n_identical/n_aligned= TM-score= NTRATKTQFESWYSAVKVEYDLNDEQMGVIMN-GFMVWCIDNGT-SPDVNG VWVMMDGEEQVEYPLKPIVENA------K-P----TLRQIM-HHFSDAAEAYIE---M-RNSES-PY--MPRYGLLRNLR-DRE--LARYAFDFY-EVTSKTPNRAREAIAQMKAAAL ::...::::::::::.:::...::....:.:... :.::.:: ::::::::::.....::. :: ::::::::::..:: ::::::::: ::::.::...:::::: ES-LNLAAVRIFFLNAAKAKAAL-SRKPERKANPKFG EWQV-EVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLETFKFYPLTIGIHR-V--- WMV CP vs Influenza A virus NP (3ZDP) Aligned length= 121, RMSD= 4.51, Seq_ID=n_identical/n_aligned= TM-score= NTRATKTQFESWYSAVKVEYDLNDEQM-G-VIMNGFMVW--C IDNGTSPD------VNGVWVMMDGE EQVEYPLK--PIVENAK-----PTLRQIMHHF-SDAAEAYIEMRNSESPYMPRYGLLRNL--RD-R----E--L-ARYAF-DFY-EVTSKTPNRARE-AIA-QMKAAAL ::::::::::::::::::::::: : :::::::... :::..::::::....:::::: ::::::: ::.::::::: ::::::::::::..:..:....::::... ::...:::.:.. :... SVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEH----PSAGKDPKKTGGPIY--RRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQR-TRA LVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMEL-IRM-----IKRG
6 fig. S3. Representation of the structural alignment between regions of CPs and NPs from several ssrna viruses. The structure of current atomic model for WMV CP was compared with several viral proteins using TM-align (14). TM-score and RMSD between Cα atoms after the 3D alignment are shown. The output includes the alignment of protein sequences where ":" denotes aligned residue pairs of Cα atoms where the distance between them is below 5.0 Å, and "." denotes other aligned residues. The compared structures are as in Fig. 4: WMV CP and ssrna from the current work; PepMV CP, PDB code 5FN1 (4); Influenza virus A NP, PDB code 3ZDP (20); RVFV NP, PDB code 4H5O (21); La Crosse virus NP, PDB code 4BHH (22); and TSWV NP, PDB code 5IP2 (23).
7 PDB entry Naa Ncmp SqID rms Ssse Rsse Sdis Rdis Zsc RelS RelO 5fn PepMV CP : H1 H2 E1 E2 H3 --- H4 H5 H H7 WMV : S HHHHHHHHHHHHHHHT STTHHHHHHHHHHHHHHS S SEEE STT EEE HHHHHT ---SS SHHHHTS SHHHHHHHHHHHHHS HHHHTT GGGGGG SS SSS TTHHHHHHHHHHHT 97 :NTRATKTQFESWYSAVKVEYDLNDEQMGVIMNGFMVWCIDNGTSPDVNGVWVMMDGEEQVEYPLKPIVENA---KPTLRQIMHHFSDAAEAYIEMRNSESPYMPRYGLLRNLRDRELARYAFDFYE--VT SKTPNRAREAIAQMKAAAL: 240 ** * * * * * * * ** * * * **** * * ** 50:TSVATPAEIEALGKIFTAMG-LAANETGPAMWDLARAYADVQSSKSAQLIGATPSN---PALSRRALAAQFDRINITPRQFCMYFAKVVWNILLDSN----IPPANWAKLGY-QEDTKFAAFDFFDGVTNPASLQPADGLIRQPNEKELAAHSVAKYGAL:200 PepMV:TTS HHHHHHHHHHHHHHT- SSS HHHHHHHHHHHHHS TT B TT ---SS BHHHHHHHGGGGT HHHHHGGGHHHHHHHHHTSS---- S TTTT - GGGSTT SS TTSSSTTS TT SS HHHHHHHHHHHHHHH : H2 - H3 --- H4 H5 H H7 pdb entry Naa Ncmp SqID rms Ssse Rsse Sdis Rdis Zsc RelS RelO 3ov RVFV NP : H1 H2 E1 E2-- H H4 H5 H H7 WMV : S HHHHHHHHHHHHHHHT STTHHHHHHHHHHHHHHS S SEEE STT EE--E H---HHH---HT SS S-HHHHTS SHHHHHHHHHHHHHS HHHHTT ---GGGGGG SS - SSS----- TTHHHHHHHHHHHT 97 :NTRATKTQFESWYSAVKVEYDLNDEQMGVIMNGFMVWCIDNGTSPDVNGVWVMMDGEEQVEY--PLK---PIV---ENAKPTL-RQIMHHFSDAAEAYIEMRNSESPYMPRYGLLRNLRD---RELARYAFDFY-EVTSKT-----PNRAREAIAQMKAAAL: 240 * * * * * * * 31:QGFDARRVIELLKQYGG ADWEKDAKKMIVLALTRGN---KPRRMMMKMSKEGKATVEALINKYKLKEGNPSRDELTLSRVAAALAGWTCQALVVL-----SEWLPVTGTTMDGLSPAYPRHMMHPSFAGMVDPSLPGDYLRAILDAHSLYLLQFS:177 RVFV : S HHHHHHHHHHHHG GGHHHHHHHHHHHHHHT S--- HHHHGGGS HHHH HHHHHHHHHHT SSS TT HHHHHHHTHHHHHHHHHHH-----GGGSSS HHHHHH HSTT GGGSSGGGGGG TTS HHHHHHHHHHHHHHHHHHH : H H4 --- H5 H6 H7 H H9 H10 PDB entry Naa Ncmp SqID rms Ssse Rsse Sdis Rdis Zsc RelS RelO 4dyn Influenza A virus NP : H1 H--2 E E2 H H4 H5 H H7 WMV : S HHHHHHHHHHHHHHHT STTH--HHHHHHHHHHHHHS S SEEE S TT EEE HHHHHT S-----S SHHHHTS SHHHHHHHHHHHHHS HHHHTT G GGGGG S-S --- SSS TTHHHHHHHH 97 :NTRATKTQFESWYSAVKVEYDLNDEQM--GVIMNGFMVWCIDNGTSPDVNGVWVMMD GEEQVEYPLKPIVENAK-----PTLRQIMHHFSDAAEAYIEMRNSESPYMPRYGLLRNLRDR ELARYAFD-FY---EVTSKTPNRAREAIAQM: 235 * * * * * * * * * * 28:SVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFD----PKKTGGPIYRRVDGKWRRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTR ALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGV-GTMVMELIR:195 Flu :HHHHHHHHHHHHHHHHHHHTT HHHHTBHHHHHHHHHHHHHHH ---- EEEEEEEEEETTEEEEEEEEEEHHHHHHHHHHHTTTS HHHHHHHHHHHHHHHHHH HH HHHHTT GGGGGG TTTTS SS HHHHHHS H-HHHHHHHHH H1 H2 H E1 E2 H4 H5 H H7 H-8 PDB entry Naa Ncmp SqID rms Ssse Rsse Sdis Rdis Zsc RelS RelO 4bgp La Crosse virus NP :H E1 E2 H H4 H H6 --- H7 WMV :HHHHHHHHHHHHHS -- S SEEE STT EEE HHHHH--T SS S---HHHHTS SHHHHHHHHHHHHH S HHHHTT GG---GGGG S S SSS TTHHHHHHHHHHHT 124 :GVIMNGFMVWCIDNGT--SPDVN------GVWVMMDGEEQVEYPLKPIVE--NAKPTL---RQIMHHFSDAAEAYIEMRNSE SPYMPRYGLLRNLRDRE---LARYAFDFYEVTSKTPNRAREAIAQMKAAAL: 240 * * * * * * * * 32:ESLNLAAVRIFFLNAAKAKAALSRKPERKANPKFGE----WQVEVINNHFPGNRNNPIGNNDLTIHRLSGYLARWVLDQYNENDDESQHELIRTTIINPIAESNGVGWDSGPEIYLSFFPGTEMFLET---FKFYPLTIGIHRV:168 LaCr :TT HHHHHHHHHHHHHHHHHHTT SEE EETT----EE EE SGGGTTS TT HHHHHHHHHHHHHHHHHH HHHHHHHHHH HHHHHTT GGG HHHHHTTSTTGGGGTTT---TTTHHHHHHHHHH : H2 E1 E2 ----E3 E4 H3 H4 H5 H6 --- H7
8 fig. S4. Output from the 3D library search using the WMV CP core region as target. The core region of the atomic model for WMV CP was used as the input to search for structural homologues within a library of representatives structures from the PDB in Matras (13). The representation of primary sequences shows the alignment of secondary structure elements. The detected structural homologues have Z-score above meaningful threshold (Zsc>5). The picked atomic models within the database are: PepMV CP, PDB code 5FN1 (4); RVFV NP, PDB code 3OV9 (43); Influenza virus A NP, PDB code 4DYN (44); and La Crosse virus NP, PDB code 4BGP (22). The figures of merit provided for the structural alignment and similarity measurements are: Naa, number of compared amino acids; Ncmp, Number of compared secondary structure elements; SqID, sequence identity (%) defined as number of identical amino acids divided by Naa; rms, root mean square deviation (Å) of aligned Cα atoms; Ssse, score of secondary structure elements; Rsse, normalized Ssse score (%); Sdis, Distance score; Rdis, normalized distance score (%); Zsc, Z score; RelS, Reliability (%) that a pair with this Zsc belongs to the same SCOP superfamily; RelO, Reliability (%) that a pair with this Zsc belongs to the same SCOP fold.
9 fig. S5. Morphological universe of ssrna viruses with structural homology between their CPs/NPs. (A) Fraction of a negatively stained WMV particle. Superimposed there is a rendering of the cryoem density map calculated for the virions. (B) Rendering of the cryoem map for RVFV (EMD-5124, (45)). (C) Segmented cryoelectron tomogram for influenza A virus (18). Ribonucleoprotein complexes are depicted in purple (image courtesy of J. Martín-Benito). The relative sizes of the depicted structures are proportional to their real dimensions.
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