4V99

The Crystallographic Structure of Panicum Mosaic Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 

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:  

  • 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, ...

    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.,Sect.D 61: 173


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
AA, AB, AC, AF, AG, AH, AK, AL, AM, AP, AQ, AR, AU, AV, AW, AZ, Aa, Ab, Ae, Af, Ag, Aj, Ak, Al, Ao, Ap, Aq, At, Au, Av, Ay, Az, A1, A4, A5, A6, BA, BB, BC, BF, BG, BH, BK, BL, BM, BP, BQ, BR, BU, BV, BW, BZ, Ba, Bb, Be, Bf, Bg, Bj, Bk, Bl, Bo, Bp, Bq, Bt, Bu, Bv, By, Bz, B1, B4, B5, B6, CA, CB, CC, CF, CG, CH, CK, CL, CM, CP, CQ, CR, CU, CV, CW, CZ, Ca, Cb, Ce, Cf, Cg, Cj, Ck, Cl, Co, Cp, Cq, Ct, Cu, Cv, Cy, Cz, C1, C4, C5, C6, DA, DB, DC, DF, DG, DH, DK, DL, DM, DP, DQ, DR, DU, DV, DW, DZ, Da, Db, De, Df, Dg, Dj, Dk, Dl, Do, Dp, Dq, Dt, Du, Dv, Dy, Dz, D1, D4, D5, D6, EA, EB, EC, EF, EG, EH, EK, EL, EM, EP, EQ, ER, EU, EV, EW, EZ, Ea, Eb, Ee, Ef, Eg, Ej, Ek, El, Eo, Ep, Eq, Et, Eu, Ev, Ey, Ez, E1, E4, E5, E6, FA, FB, FC, FF, FG, FH, FK, FL, FM, FP, FQ, FR, FU, FV, FW, FZ, Fa, Fb, Fe, Ff, Fg, Fj, Fk, Fl, Fo, Fp, Fq, Ft, Fu, Fv, Fy, Fz, F1, F4, F5, F6, GA, GB, GC, GF, GG, GH, GK, GL, GM, GP, GQ, GR, GU, GV, GW, GZ, Ga, Gb, Ge, Gf, Gg, Gj, Gk, Gl, Go, Gp, Gq, Gt, Gu, Gv, Gy, Gz, G1, G4, G5, G6, HA, HB, HC, HF, HG, HH, HK, HL, HM, HP, HQ, HR, HU, HV, HW, HZ, Ha, Hb, He, Hf, Hg, Hj, Hk, Hl, Ho, Hp, Hq, Ht, Hu, Hv, Hy, Hz, H1, H4, H5, H6, IA, IB, IC, IF, IG, IH, IK, IL, IM, IP, IQ, IR, IU, IV, IW, IZ, Ia, Ib, Ie, If, Ig, Ij, Ik, Il, Io, Ip, Iq, It, Iu, Iv, Iy, Iz, I1, I4, I5, I6, JA, JB, JC, JF, JG, JH, JK, JL, JM, JP, JQ, JR, JU, JV, JW, JZ, Ja, Jb, Je, Jf, Jg, Jj, Jk, Jl, Jo, Jp, Jq, Jt, Ju, Jv, Jy, Jz, J1, J4, J5, J6
242Panicum mosaic virus (strain United States/Kansas 109S)Mutation(s): 0 
Find proteins for P89036 (Panicum mosaic virus (strain United States/Kansas 109S))
Go to UniProtKB:  P89036
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(P*UP*UP*AP*AP*UP*AP*UP*UP*UP*UP*UP*AP*UP*UP*UP*UP*U)-3'AD,AI,AN,AS,AX,Ac,Ah,Am,Ar,Aw,A2,A7,BD,BI,BN,BS,BX,Bc,Bh,Bm,Br,Bw,B2,B7,CD,CI,CN,CS,CX,Cc,Ch,Cm,Cr,Cw,C2,C7,DD,DI,DN,DS,DX,Dc,Dh,Dm,Dr,Dw,D2,D7,ED,EI,EN,ES,EX,Ec,Eh,Em,Er,Ew,E2,E7,FD,FI,FN,FS,FX,Fc,Fh,Fm,Fr,Fw,F2,F7,GD,GI,GN,GS,GX,Gc,Gh,Gm,Gr,Gw,G2,G7,HD,HI,HN,HS,HX,Hc,Hh,Hm,Hr,Hw,H2,H7,ID,II,IN,IS,IX,Ic,Ih,Im,Ir,Iw,I2,I7,JD,JI,JN,JS,JX,Jc,Jh,Jm,Jr,Jw,J2,J717Panicum mosaic virus strain Kansas 109S
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A1, A4, AA, Af, AF, Aj, AL, Ao, AP, At, AU, AZ, B5, BB, Be, BF, Bk, BK, Bo, BQ, Bt, BU, By, BZ, C4, CA, Ce, CG, Cj, CK, Co, CP, Ct, CU, Cy, CZ, D4, DA, DF, Df, Dj, DK, Do, DP, Dt, DU, Dy, DZ, E4, EC, Ee, EF, Ek, EK, Eo, EP, Et, EU, Ey, EZ, F1, F4, FA, Fe, FF, Fk, FK, Fo, FP, Ft, FU, FZ, G1, G4, GA, Ge, GF, Gj, GK, Go, GP, Gt, GU, GZ, H4, HA, HF, Hg, Hj, HK, Ho, HP, Ht, HU, Hy, HZ, I1, I4, IA, IF, If, Ij, IK, Io, IR, It, IU, IZ, J4, JA, Je, JF, Jj, JL, Jo, JP, Jt, JU, Jy, JZ
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 411.740α = 90.00
b = 403.900β = 89.65
c = 412.460γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
CNSphasing
PDB_EXTRACTdata extraction
ADSCdata collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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