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

This is version 1.1 of the entry. See complete history


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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP89036
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D 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],
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