9OM3 | pdb_00009om3

Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Single Particle CryoEM Map with Icosahedral Symmetry Applied

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
  • Mutation(s): No 

  • Deposited: 2025-05-13 Released: 2026-05-20 
  • Deposition Author(s): DiMaio, F., Weidle, C.
  • Funding Organization(s): Defense Threat Reduction Agency (DTRA), Burroughs Wellcome Fund, Human Frontier Science Program (HFSP), Bill & Melinda Gates Foundation, Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute on Aging (NIH/NIA), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9OM3

This is version 1.0 of the entry. See complete history. 

Literature

Macromolecule Content 

  • Total Structure Weight: 8,275.13 kDa 
  • Atom Count: 553,500 
  • Modeled Residue Count: 71,640 
  • Deposited Residue Count: 74,520 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C2-B
A,
AA [auth a],
AB [auth ZA],
AC [auth AQ],
AD [auth Aq],
AE [auth BG],
AF [auth Bg],
AG [auth YA],
AH [auth CW],
AI [auth Cw],
AJ [auth DM],
AK [auth Dm],
AL [auth EC],
AM [auth Ec],
C,
CA [auth c],
CB [auth ZC],
CC [auth AS],
CD [auth As],
CE [auth BI],
CF [auth Bi],
CG [auth YC],
CH [auth CY],
CI [auth Cy],
CJ [auth DO],
CK [auth Do],
CL [auth EE],
CM [auth Ee],
E,
EA [auth e],
EB [auth ZE],
EC [auth AU],
ED [auth Au],
EE [auth BK],
EF [auth Bk],
EG [auth CA],
EH [auth Ca],
EI [auth YE],
EJ [auth DQ],
EK [auth Dq],
EL [auth EG],
EM [auth Eg],
G,
GA [auth g],
GB [auth ZG],
GC [auth AW],
GD [auth Aw],
GE [auth BM],
GF [auth Bm],
GG [auth CC],
GH [auth Cc],
GI [auth YG],
GJ [auth DS],
GK [auth Ds],
GL [auth EI],
GM [auth Ei],
I,
IA [auth i],
IB [auth ZI],
IC [auth AY],
ID [auth Ay],
IE [auth BO],
IF [auth Bo],
IG [auth CE],
IH [auth Ce],
II [auth YI],
IJ [auth DU],
IK [auth Du],
IL [auth EK],
IM [auth Ek],
K,
KA [auth k],
KB [auth AA],
KC [auth Aa],
KD [auth ZK],
KE [auth BQ],
KF [auth Bq],
KG [auth CG],
KH [auth Cg],
KI [auth YK],
KJ [auth DW],
KK [auth Dw],
KL [auth EM],
KM [auth Em],
M,
MA [auth m],
MB [auth AC],
MC [auth Ac],
MD [auth ZM],
ME [auth BS],
MF [auth Bs],
MG [auth CI],
MH [auth Ci],
MI [auth YM],
MJ [auth DY],
MK [auth Dy],
ML [auth EO],
MM [auth Eo],
O,
OA [auth o],
OB [auth AE],
OC [auth Ae],
OD [auth ZO],
OE [auth BU],
OF [auth Bu],
OG [auth CK],
OH [auth Ck],
OI [auth DA],
OJ [auth Da],
OK [auth YO],
OL [auth EQ],
OM [auth Eq],
Q,
QA [auth q],
QB [auth AG],
QC [auth Ag],
QD [auth ZQ],
QE [auth BW],
QF [auth Bw],
QG [auth CM],
QH [auth Cm],
QI [auth DC],
QJ [auth Dc],
QK [auth YQ],
QL [auth ES],
QM [auth Es],
S,
SA [auth s],
SB [auth AI],
SC [auth Ai],
SD [auth ZS],
SE [auth BY],
SF [auth By],
SG [auth CO],
SH [auth Co],
SI [auth DE],
SJ [auth De],
SK [auth YS],
SL [auth EU],
SM [auth Eu],
U,
UA [auth u],
UB [auth AK],
UC [auth Ak],
UD [auth BA],
UE [auth Ba],
UF [auth ZU],
UG [auth CQ],
UH [auth Cq],
UI [auth DG],
UJ [auth Dg],
UK [auth YU],
UL [auth EW],
UM [auth Ew],
W,
WA [auth w],
WB [auth AM],
WC [auth Am],
WD [auth BC],
WE [auth Bc],
WF [auth ZW],
WG [auth CS],
WH [auth Cs],
WI [auth DI],
WJ [auth Di],
WK [auth YW],
WL [auth EY],
Y,
YA [auth y],
YB [auth AO],
YC [auth Ao],
YD [auth BE],
YE [auth Be],
YF [auth ZY],
YG [auth CU],
YH [auth Cu],
YI [auth DK],
YJ [auth Dk],
YK [auth EA],
YL [auth Ea]
114synthetic constructMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
C3-A
B,
BA [auth b],
BB [auth ZB],
BC [auth AR],
BD [auth Ar],
BE [auth BH],
BF [auth Bh],
BG [auth YB],
BH [auth CX],
BI [auth Cx],
BJ [auth DN],
BK [auth Dn],
BL [auth ED],
BM [auth Ed],
D,
DA [auth d],
DB [auth ZD],
DC [auth AT],
DD [auth At],
DE [auth BJ],
DF [auth Bj],
DG [auth YD],
DH [auth CZ],
DI [auth Cz],
DJ [auth DP],
DK [auth Dp],
DL [auth EF],
DM [auth Ef],
F,
FA [auth f],
FB [auth ZF],
FC [auth AV],
FD [auth Av],
FE [auth BL],
FF [auth Bl],
FG [auth CB],
FH [auth Cb],
FI [auth YF],
FJ [auth DR],
FK [auth Dr],
FL [auth EH],
FM [auth Eh],
H,
HA [auth h],
HB [auth ZH],
HC [auth AX],
HD [auth Ax],
HE [auth BN],
HF [auth Bn],
HG [auth CD],
HH [auth Cd],
HI [auth YH],
HJ [auth DT],
HK [auth Dt],
HL [auth EJ],
HM [auth Ej],
J,
JA [auth j],
JB [auth ZJ],
JC [auth AZ],
JD [auth Az],
JE [auth BP],
JF [auth Bp],
JG [auth CF],
JH [auth Cf],
JI [auth YJ],
JJ [auth DV],
JK [auth Dv],
JL [auth EL],
JM [auth El],
L,
LA [auth l],
LB [auth AB],
LC [auth Ab],
LD [auth ZL],
LE [auth BR],
LF [auth Br],
LG [auth CH],
LH [auth Ch],
LI [auth YL],
LJ [auth DX],
LK [auth Dx],
LL [auth EN],
LM [auth En],
N,
NA [auth n],
NB [auth AD],
NC [auth Ad],
ND [auth ZN],
NE [auth BT],
NF [auth Bt],
NG [auth CJ],
NH [auth Cj],
NI [auth YN],
NJ [auth DZ],
NK [auth Dz],
NL [auth EP],
NM [auth Ep],
P,
PA [auth p],
PB [auth AF],
PC [auth Af],
PD [auth ZP],
PE [auth BV],
PF [auth Bv],
PG [auth CL],
PH [auth Cl],
PI [auth DB],
PJ [auth Db],
PK [auth YP],
PL [auth ER],
PM [auth Er],
R,
RA [auth r],
RB [auth AH],
RC [auth Ah],
RD [auth ZR],
RE [auth BX],
RF [auth Bx],
RG [auth CN],
RH [auth Cn],
RI [auth DD],
RJ [auth Dd],
RK [auth YR],
RL [auth ET],
RM [auth Et],
T,
TA [auth t],
TB [auth AJ],
TC [auth Aj],
TD [auth ZT],
TE [auth BZ],
TF [auth Bz],
TG [auth CP],
TH [auth Cp],
TI [auth DF],
TJ [auth Df],
TK [auth YT],
TL [auth EV],
TM [auth Ev],
V,
VA [auth v],
VB [auth AL],
VC [auth Al],
VD [auth BB],
VE [auth Bb],
VF [auth ZV],
VG [auth CR],
VH [auth Cr],
VI [auth DH],
VJ [auth Dh],
VK [auth YV],
VL [auth EX],
VM [auth Ex],
X,
XA [auth x],
XB [auth AN],
XC [auth An],
XD [auth BD],
XE [auth Bd],
XF [auth ZX],
XG [auth CT],
XH [auth Ct],
XI [auth DJ],
XJ [auth Dj],
XK [auth YX],
XL [auth EZ],
Z,
ZA [auth z],
ZB [auth AP],
ZC [auth Ap],
ZD [auth BF],
ZE [auth Bf],
ZF [auth ZZ],
ZG [auth CV],
ZH [auth Cv],
ZI [auth DL],
ZJ [auth Dl],
ZK [auth EB],
ZL [auth Eb]
300synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1-19-1-0003
Burroughs Wellcome FundUnited States--
Human Frontier Science Program (HFSP)FranceRGP0061/2019
Bill & Melinda Gates FoundationUnited StatesINV-043758
Bill & Melinda Gates FoundationUnited StatesOPP1156262
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01AG063845
Department of Energy (DOE, United States)United StatesKP1607011

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release