The Crystallographic Structure of Panicum Mosaic Virus

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report

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The crystallographic structure of Panicum Mosaic Virus (PMV).

Makino, D.L.Larson, S.B.McPherson, A.

(2013) J Struct Biol 181: 37-52

  • DOI: 10.1016/j.jsb.2012.10.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89 ...

    The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ∼20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca(++) ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1-53, 1-49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent "arm" that intertwines with symmetry equivalent "arms" at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A-B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses.

    Related Citations: 
    • Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy.
      Makino, D.L., Larson, S.B., McPherson, A.
      (2005) Acta Crystallogr D Biol Crystallogr 61: 173

    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA.


Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein
QA [auth A1], SA [auth A4], TA [auth A5], UA [auth A6], A [auth AA], B [auth AB], C [auth AC], E [auth AF], F [auth AG], G [auth AH], I [auth AK], J [auth AL], K [auth AM], M [auth AP], N [auth AQ], O [auth AR], Q [auth AU], R [auth AV], S [auth AW], U [auth AZ], V [auth Aa], W [auth Ab], Y [auth Ae], Z [auth Af], AA [auth Ag], CA [auth Aj], DA [auth Ak], EA [auth Al], GA [auth Ao], HA [auth Ap], IA [auth Aq], KA [auth At], LA [auth Au], MA [auth Av], OA [auth Ay], PA [auth Az], MC [auth B1], OC [auth B4], PC [auth B5], QC [auth B6], WA [auth BA], XA [auth BB], YA [auth BC], AB [auth BF], BB [auth BG], CB [auth BH], EB [auth BK], FB [auth BL], GB [auth BM], IB [auth BP], JB [auth BQ], KB [auth BR], MB [auth BU], NB [auth BV], OB [auth BW], QB [auth BZ], RB [auth Ba], SB [auth Bb], UB [auth Be], VB [auth Bf], WB [auth Bg], YB [auth Bj], ZB [auth Bk], AC [auth Bl], CC [auth Bo], DC [auth Bp], EC [auth Bq], GC [auth Bt], HC [auth Bu], IC [auth Bv], KC [auth By], LC [auth Bz], IE [auth C1], KE [auth C4], LE [auth C5], ME [auth C6], SC [auth CA], TC [auth CB], UC [auth CC], WC [auth CF], XC [auth CG], YC [auth CH], AD [auth CK], BD [auth CL], CD [auth CM], ED [auth CP], FD [auth CQ], GD [auth CR], ID [auth CU], JD [auth CV], KD [auth CW], MD [auth CZ], ND [auth Ca], OD [auth Cb], QD [auth Ce], RD [auth Cf], SD [auth Cg], UD [auth Cj], VD [auth Ck], WD [auth Cl], YD [auth Co], ZD [auth Cp], AE [auth Cq], CE [auth Ct], DE [auth Cu], EE [auth Cv], GE [auth Cy], HE [auth Cz], EG [auth D1], GG [auth D4], HG [auth D5], IG [auth D6], OE [auth DA], PE [auth DB], QE [auth DC], SE [auth DF], TE [auth DG], UE [auth DH], WE [auth DK], XE [auth DL], YE [auth DM], AF [auth DP], BF [auth DQ], CF [auth DR], EF [auth DU], FF [auth DV], GF [auth DW], IF [auth DZ], JF [auth Da], KF [auth Db], MF [auth De], NF [auth Df], OF [auth Dg], QF [auth Dj], RF [auth Dk], SF [auth Dl], UF [auth Do], VF [auth Dp], WF [auth Dq], YF [auth Dt], ZF [auth Du], AG [auth Dv], CG [auth Dy], DG [auth Dz], AI [auth E1], CI [auth E4], DI [auth E5], EI [auth E6], KG [auth EA], LG [auth EB], MG [auth EC], OG [auth EF], PG [auth EG], QG [auth EH], SG [auth EK], TG [auth EL], UG [auth EM], WG [auth EP], XG [auth EQ], YG [auth ER], AH [auth EU], BH [auth EV], CH [auth EW], EH [auth EZ], FH [auth Ea], GH [auth Eb], IH [auth Ee], JH [auth Ef], KH [auth Eg], MH [auth Ej], NH [auth Ek], OH [auth El], QH [auth Eo], RH [auth Ep], SH [auth Eq], UH [auth Et], VH [auth Eu], WH [auth Ev], YH [auth Ey], ZH [auth Ez], WJ [auth F1], YJ [auth F4], ZJ [auth F5], AK [auth F6], GI [auth FA], HI [auth FB], II [auth FC], KI [auth FF], LI [auth FG], MI [auth FH], OI [auth FK], PI [auth FL], QI [auth FM], SI [auth FP], TI [auth FQ], UI [auth FR], WI [auth FU], XI [auth FV], YI [auth FW], AJ [auth FZ], BJ [auth Fa], CJ [auth Fb], EJ [auth Fe], FJ [auth Ff], GJ [auth Fg], IJ [auth Fj], JJ [auth Fk], KJ [auth Fl], MJ [auth Fo], NJ [auth Fp], OJ [auth Fq], QJ [auth Ft], RJ [auth Fu], SJ [auth Fv], UJ [auth Fy], VJ [auth Fz], SL [auth G1], UL [auth G4], VL [auth G5], WL [auth G6], CK [auth GA], DK [auth GB], EK [auth GC], GK [auth GF], HK [auth GG], IK [auth GH], KK [auth GK], LK [auth GL], MK [auth GM], OK [auth GP], PK [auth GQ], QK [auth GR], SK [auth GU], TK [auth GV], UK [auth GW], WK [auth GZ], XK [auth Ga], YK [auth Gb], AL [auth Ge], BL [auth Gf], CL [auth Gg], EL [auth Gj], FL [auth Gk], GL [auth Gl], IL [auth Go], JL [auth Gp], KL [auth Gq], ML [auth Gt], NL [auth Gu], OL [auth Gv], QL [auth Gy], RL [auth Gz], ON [auth H1], QN [auth H4], RN [auth H5], SN [auth H6], YL [auth HA], ZL [auth HB], AM [auth HC], CM [auth HF], DM [auth HG], EM [auth HH], GM [auth HK], HM [auth HL], IM [auth HM], KM [auth HP], LM [auth HQ], MM [auth HR], OM [auth HU], PM [auth HV], QM [auth HW], SM [auth HZ], TM [auth Ha], UM [auth Hb], WM [auth He], XM [auth Hf], YM [auth Hg], AN [auth Hj], BN [auth Hk], CN [auth Hl], EN [auth Ho], FN [auth Hp], GN [auth Hq], IN [auth Ht], JN [auth Hu], KN [auth Hv], MN [auth Hy], NN [auth Hz], KP [auth I1], MP [auth I4], NP [auth I5], OP [auth I6], UN [auth IA], VN [auth IB], WN [auth IC], YN [auth IF], ZN [auth IG], AO [auth IH], CO [auth IK], DO [auth IL], EO [auth IM], GO [auth IP], HO [auth IQ], IO [auth IR], KO [auth IU], LO [auth IV], MO [auth IW], OO [auth IZ], PO [auth Ia], QO [auth Ib], SO [auth Ie], TO [auth If], UO [auth Ig], WO [auth Ij], XO [auth Ik], YO [auth Il], AP [auth Io], BP [auth Ip], CP [auth Iq], EP [auth It], FP [auth Iu], GP [auth Iv], IP [auth Iy], JP [auth Iz], GR [auth J1], IR [auth J4], JR [auth J5], KR [auth J6], QP [auth JA], RP [auth JB], SP [auth JC], UP [auth JF], VP [auth JG], WP [auth JH], YP [auth JK], ZP [auth JL], AQ [auth JM], CQ [auth JP], DQ [auth JQ], EQ [auth JR], GQ [auth JU], HQ [auth JV], IQ [auth JW], KQ [auth JZ], LQ [auth Ja], MQ [auth Jb], OQ [auth Je], PQ [auth Jf], QQ [auth Jg], SQ [auth Jj], TQ [auth Jk], UQ [auth Jl], WQ [auth Jo], XQ [auth Jp], YQ [auth Jq], AR [auth Jt], BR [auth Ju], CR [auth Jv], ER [auth Jy], FR [auth Jz]
242Panicum mosaic virus strain Kansas 109SMutation(s): 0 
Gene Names: ORF3
Find proteins for P89036 (Panicum mosaic virus (strain United States/Kansas 109S))
Explore P89036 
Go to UniProtKB:  P89036
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    RA [auth A2], VA [auth A7], D [auth AD], H [auth AI], L [auth AN], P [auth AS], T [auth AX], X [auth Ac], BA [auth Ah], FA [auth Am], JA [auth Ar], NA [auth Aw], NC [auth B2], RC [auth B7], ZA [auth BD], DB [auth BI], HB [auth BN], LB [auth BS], PB [auth BX], TB [auth Bc], XB [auth Bh], BC [auth Bm], FC [auth Br], JC [auth Bw], JE [auth C2], NE [auth C7], VC [auth CD], ZC [auth CI], DD [auth CN], HD [auth CS], LD [auth CX], PD [auth Cc], TD [auth Ch], XD [auth Cm], BE [auth Cr], FE [auth Cw], FG [auth D2], JG [auth D7], RE [auth DD], VE [auth DI], ZE [auth DN], DF [auth DS], HF [auth DX], LF [auth Dc], PF [auth Dh], TF [auth Dm], XF [auth Dr], BG [auth Dw], BI [auth E2], FI [auth E7], NG [auth ED], RG [auth EI], VG [auth EN], ZG [auth ES], DH [auth EX], HH [auth Ec], LH [auth Eh], PH [auth Em], TH [auth Er], XH [auth Ew], XJ [auth F2], BK [auth F7], JI [auth FD], NI [auth FI], RI [auth FN], VI [auth FS], ZI [auth FX], DJ [auth Fc], HJ [auth Fh], LJ [auth Fm], PJ [auth Fr], TJ [auth Fw], TL [auth G2], XL [auth G7], FK [auth GD], JK [auth GI], NK [auth GN], RK [auth GS], VK [auth GX], ZK [auth Gc], DL [auth Gh], HL [auth Gm], LL [auth Gr], PL [auth Gw], PN [auth H2], TN [auth H7], BM [auth HD], FM [auth HI], JM [auth HN], NM [auth HS], RM [auth HX], VM [auth Hc], ZM [auth Hh], DN [auth Hm], HN [auth Hr], LN [auth Hw], LP [auth I2], PP [auth I7], XN [auth ID], BO [auth II], FO [auth IN], JO [auth IS], NO [auth IX], RO [auth Ic], VO [auth Ih], ZO [auth Im], DP [auth Ir], HP [auth Iw], HR [auth J2], LR [auth J7], TP [auth JD], XP [auth JI], BQ [auth JN], FQ [auth JS], JQ [auth JX], NQ [auth Jc], RQ [auth Jh], VQ [auth Jm], ZQ [auth Jr], DR [auth Jw]
    17Panicum mosaic virus strain Kansas 109S
    Protein Feature View
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    Query on CA

    Download Ideal Coordinates CCD File 
    AS [auth BK] , AT [auth DU] , AU [auth Fe] , AV [auth Ho] , AW [auth Jy] , BS [auth BQ] , BT [auth DZ] , BU [auth Fk] , 
    AS [auth BK],  AT [auth DU],  AU [auth Fe],  AV [auth Ho],  AW [auth Jy],  BS [auth BQ],  BT [auth DZ],  BU [auth Fk],  BV [auth Ht],  BW [auth J4],  CS [auth BU],  CT [auth Df],  CU [auth Fo],  CV [auth Hy],  DS [auth BZ],  DT [auth Dj],  DU [auth Ft],  DV [auth H4],  ES [auth Be],  ET [auth Do],  EU [auth F1],  EV [auth IA],  FS [auth Bk],  FT [auth Dt],  FU [auth F4],  FV [auth IF],  GS [auth Bo],  GT [auth Dy],  GU [auth GA],  GV [auth IK],  HS [auth Bt],  HT [auth D4],  HU [auth GF],  HV [auth IR],  IS [auth By],  IT [auth EC],  IU [auth GK],  IV [auth IU],  JS [auth B5],  JT [auth EF],  JU [auth GP],  JV [auth IZ],  KS [auth CA],  KT [auth EK],  KU [auth GU],  KV [auth If],  LS [auth CG],  LT [auth EP],  LU [auth GZ],  LV [auth Ij],  MR [auth AA],  MS [auth CK],  MT [auth EU],  MU [auth Ge],  MV [auth Io],  NR [auth AF],  NS [auth CP],  NT [auth EZ],  NU [auth Gj],  NV [auth It],  OR [auth AL],  OS [auth CU],  OT [auth Ee],  OU [auth Go],  OV [auth I1],  PR [auth AP],  PS [auth CZ],  PT [auth Ek],  PU [auth Gt],  PV [auth I4],  QR [auth AU],  QS [auth Ce],  QT [auth Eo],  QU [auth G1],  QV [auth JA],  RR [auth AZ],  RS [auth Cj],  RT [auth Et],  RU [auth G4],  RV [auth JF],  SR [auth Af],  SS [auth Co],  ST [auth Ey],  SU [auth HA],  SV [auth JL],  TR [auth Aj],  TS [auth Ct],  TT [auth E4],  TU [auth HF],  TV [auth JP],  UR [auth Ao],  US [auth Cy],  UT [auth FA],  UU [auth HK],  UV [auth JU],  VR [auth At],  VS [auth C4],  VT [auth FF],  VU [auth HP],  VV [auth JZ],  WR [auth A1],  WS [auth DA],  WT [auth FK],  WU [auth HU],  WV [auth Je],  XR [auth A4],  XS [auth DF],  XT [auth FP],  XU [auth HZ],  XV [auth Jj],  YR [auth BB],  YS [auth DK],  YT [auth FU],  YU [auth Hg],  YV [auth Jo],  ZR [auth BF],  ZS [auth DP],  ZT [auth FZ],  ZU [auth Hj],  ZV [auth Jt]
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Resolution: 2.90 Å
    • R-Value Free: 0.285 
    • R-Value Work: 0.251 
    • R-Value Observed: 0.255 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 411.74α = 90
    b = 403.9β = 89.65
    c = 412.46γ = 90
    Software Package:
    Software NamePurpose
    d*TREKdata scaling
    PDB_EXTRACTdata extraction
    ADSCdata collection
    d*TREKdata reduction

    Structure Validation

    View Full Validation Report

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other