4V99

The Crystallographic Structure of Panicum Mosaic Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


This is version 1.1 of the entry. See complete history


Literature

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:  
    4V99

  • 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.



Macromolecules

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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
UniProt
Find proteins for P89036 (Panicum mosaic virus (strain United States/Kansas 109S))
Explore P89036 
Go to UniProtKB:  P89036
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(P*UP*UP*AP*AP*UP*AP*UP*UP*UP*UP*UP*AP*UP*UP*UP*UP*U)-3'
    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
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CA
    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]
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • 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
    CNSrefinement
    PDB_EXTRACTdata extraction
    ADSCdata collection
    d*TREKdata reduction
    CNSphasing

    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