› 4v99

X-ray diffraction
2.9Å resolution

The Crystallographic Structure of Panicum Mosaic Virus

Released:
DOI: 10.2210/pdb4v99/pdb
PDB entry 4v99 coloured by chain, front view.
PDB entry 4v99 coloured by chain, side view.
PDB entry 4v99 coloured by chain, top view.
Source organism: Panicum mosaic virus strain Kansas 109S
Primary publication:
The crystallographic structure of Panicum Mosaic Virus (PMV).
Makino DL, Larson SB, McPherson A
J Struct Biol 181 37-52 (2013)
PMID: 23123270

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161019 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Capsid protein Chains: A1, A4, A5, A6, 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, B1, B4, B5, B6, 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, C1, C4, C5, C6, 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, D1, D4, D5, D6, 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, E1, E4, E5, E6, 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, F1, F4, F5, F6, 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, G1, G4, G5, G6, 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, H1, H4, H5, H6, 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, I1, I4, I5, I6, 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, J1, J4, J5, J6, 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
Molecule details ›
Chains: A1, A4, A5, A6, 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, B1, B4, B5, B6, 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, C1, C4, C5, C6, 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, D1, D4, D5, D6, 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, E1, E4, E5, E6, 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, F1, F4, F5, F6, 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, G1, G4, G5, G6, 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, H1, H4, H5, H6, 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, I1, I4, I5, I6, 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, J1, J4, J5, J6, 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
Length: 242 amino acids
Theoretical weight: 26.39 KDa
Source organism: Panicum mosaic virus strain Kansas 109S
UniProt:
  • Canonical: P89036 (Residues: 1-242; Coverage: 100%)
Gene name: ORF3
Sequence domains: Viral coat protein (S domain)
5'-R(P*UP*UP*AP*AP*UP*AP*UP*UP*UP*UP*UP*AP*UP*UP*UP*UP*U)-3' Chains: A2, A7, AD, AI, AN, AS, AX, Ac, Ah, Am, Ar, Aw, B2, B7, BD, BI, BN, BS, BX, Bc, Bh, Bm, Br, Bw, C2, C7, CD, CI, CN, CS, CX, Cc, Ch, Cm, Cr, Cw, D2, D7, DD, DI, DN, DS, DX, Dc, Dh, Dm, Dr, Dw, E2, E7, ED, EI, EN, ES, EX, Ec, Eh, Em, Er, Ew, F2, F7, FD, FI, FN, FS, FX, Fc, Fh, Fm, Fr, Fw, G2, G7, GD, GI, GN, GS, GX, Gc, Gh, Gm, Gr, Gw, H2, H7, HD, HI, HN, HS, HX, Hc, Hh, Hm, Hr, Hw, I2, I7, ID, II, IN, IS, IX, Ic, Ih, Im, Ir, Iw, J2, J7, JD, JI, JN, JS, JX, Jc, Jh, Jm, Jr, Jw
Molecule details ›
Chains: A2, A7, AD, AI, AN, AS, AX, Ac, Ah, Am, Ar, Aw, B2, B7, BD, BI, BN, BS, BX, Bc, Bh, Bm, Br, Bw, C2, C7, CD, CI, CN, CS, CX, Cc, Ch, Cm, Cr, Cw, D2, D7, DD, DI, DN, DS, DX, Dc, Dh, Dm, Dr, Dw, E2, E7, ED, EI, EN, ES, EX, Ec, Eh, Em, Er, Ew, F2, F7, FD, FI, FN, FS, FX, Fc, Fh, Fm, Fr, Fw, G2, G7, GD, GI, GN, GS, GX, Gc, Gh, Gm, Gr, Gw, H2, H7, HD, HI, HN, HS, HX, Hc, Hh, Hm, Hr, Hw, I2, I7, ID, II, IN, IS, IX, Ic, Ih, Im, Ir, Iw, J2, J7, JD, JI, JN, JS, JX, Jc, Jh, Jm, Jr, Jw
Length: 17 nucleotides
Theoretical weight: 5.25 KDa
Source organism: Panicum mosaic virus strain Kansas 109S

Ligands and Environments

1 bound ligand:
Ligand CA 120 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 411.74Å b: 403.9Å c: 412.46Å
α: 90° β: 89.65° γ: 90°
R-values:
R R work R free
0.255 0.251 0.285

Quick links

Citations

6 citation in other articles

Discovery of several thousand highly diverse circular DNA viruses.
Tisza et al. (2020)
5 more

2 mentions without citation

Panicum Mosaic Virus and Its Satellites Acquire RNA Modifications Associated with Host-Mediated Antiviral Degradation.
Pyle et al. (2019)
1 more