9OP9 | pdb_00009op9

Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Subtomogram Averaged 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: 2025-05-17 Released: 2026-05-20 
  • Deposition Author(s): DiMaio, F., Chmielewski, D., 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: 31.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9OP9

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

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 [auth ZA],
AB [auth AY],
AD [auth CW],
AF [auth EV],
AH [auth GT],
AJ [auth IO],
AL [auth KL],
B [auth YC],
BC [auth BY],
BE [auth DX],
BG [auth FV],
BI [auth HR],
BK [auth JO],
BM [auth LL],
CA [auth YY],
CB [auth ZC],
CD [auth CY],
CF [auth EX],
CH [auth GV],
CJ [auth IQ],
CL [auth KN],
D [auth ZY],
DB [auth BA],
DE [auth DZ],
DG [auth FX],
DI [auth HT],
DK [auth JQ],
DM [auth LN],
EA [auth AC],
EC [auth CA],
ED [auth ZE],
EF [auth EZ],
EH [auth GX],
EJ [auth IS],
EL [auth KP],
F [auth YE],
FB [auth BC],
FD [auth DA],
FG [auth FZ],
FI [auth HV],
FK [auth JS],
FM [auth LP],
GA [auth AE],
GC [auth CC],
GE [auth EB],
GF [auth ZG],
GH [auth GZ],
GJ [auth IU],
GL [auth KR],
H [auth YG],
HB [auth BE],
HD [auth DC],
HF [auth FB],
HI [auth HX],
HM [auth LR],
IA [auth AG],
IC [auth CE],
IE [auth ED],
IG [auth GB],
IH [auth ZI],
IJ [auth IW],
IK [auth WD],
IL [auth KT],
J [auth YI],
JB [auth BG],
JD [auth DE],
JF [auth FD],
JH [auth HB],
JI [auth HZ],
JK [auth JV],
KA [auth AI],
KC [auth CG],
KE [auth EF],
KG [auth GD],
KJ [auth IY],
KL [auth KV],
KM [auth ZO],
L [auth YK],
LB [auth BI],
LD [auth DG],
LF [auth FF],
LH [auth HD],
LK [auth JX],
MA [auth AK],
MC [auth CI],
ME [auth EH],
MG [auth GF],
MJ [auth JA],
ML [auth KX],
MM [auth ZQ],
N [auth YM],
NB [auth BK],
ND [auth DI],
NF [auth FH],
NI [auth WC],
NJ [auth ZK],
NK [auth JZ],
OA [auth AM],
OC [auth CK],
OE [auth EJ],
OG [auth GH],
OH [auth WB],
OI [auth IC],
OL [auth KZ],
OM [auth ZS],
P [auth YO],
PB [auth BM],
PD [auth DK],
PF [auth FJ],
PH [auth HG],
PJ [auth JC],
QC [auth CM],
QE [auth EL],
QG [auth GJ],
QI [auth IE],
QK [auth KB],
QL [auth ZM],
QM [auth ZU],
R [auth YQ],
RA [auth AP],
RB [auth BO],
RD [auth DM],
RF [auth FL],
RH [auth HI],
RJ [auth JE],
RL [auth LB],
SC [auth CO],
SE [auth EN],
SG [auth GL],
SK [auth KD],
SM [auth ZW],
T [auth YS],
TA [auth AR],
TB [auth BQ],
TD [auth DO],
TF [auth FN],
TI [auth IH],
TJ [auth JG],
TL [auth LD],
UA [auth AS],
UC [auth CQ],
UE [auth EP],
UG [auth GN],
UH [auth WA],
UI [auth II],
UK [auth KF],
UM [auth YA],
V [auth YU],
VB [auth BS],
VD [auth DQ],
VF [auth FP],
VH [auth HL],
VJ [auth JI],
VL [auth LF],
WA [auth AU],
WC [auth CS],
WE [auth ER],
WG [auth GP],
WI [auth IK],
WK [auth KH],
X [auth AA],
XB [auth BU],
XD [auth DS],
XF [auth FR],
XH [auth HN],
XJ [auth JK],
XL [auth LH],
YA [auth AW],
YC [auth CU],
YE [auth ET],
YG [auth GR],
YI [auth IM],
YK [auth KJ],
Z [auth YW],
ZB [auth BW],
ZD [auth DU],
ZF [auth FT],
ZH [auth HP],
ZJ [auth JM],
ZL [auth LJ]
114synthetic constructMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
C3-A
AA [auth YX],
AC [auth BX],
AE [auth DW],
AG [auth FU],
AI [auth HQ],
AK [auth JN],
AM [auth LK],
BA [auth ZB],
BB [auth AZ],
BD [auth CX],
BF [auth EW],
BH [auth GU],
BJ [auth IP],
BL [auth KM],
C [auth YD],
CC [auth BZ],
CE [auth DY],
CG [auth FW],
CI [auth HS],
CK [auth JP],
CM [auth LM],
DA [auth YZ],
DC [auth ZD],
DD [auth CZ],
DF [auth EY],
DH [auth GW],
DJ [auth IR],
DL [auth KO],
E [auth ZZ],
EB [auth BB],
EE [auth EA],
EG [auth FY],
EI [auth HU],
EK [auth JR],
EM [auth LO],
FA [auth AD],
FC [auth CB],
FE [auth ZF],
FF [auth FA],
FH [auth GY],
FJ [auth IT],
FL [auth KQ],
G [auth YF],
GB [auth BD],
GD [auth DB],
GG [auth GA],
GI [auth HW],
GK [auth JT],
GM [auth LQ],
HA [auth AF],
HC [auth CD],
HE [auth EC],
HG [auth ZH],
HH [auth HA],
HJ [auth IV],
HK [auth JU],
HL [auth KS],
I [auth YH],
IB [auth BF],
ID [auth DD],
IF [auth FC],
II [auth HY],
IM [auth LS],
JA [auth AH],
JC [auth CF],
JE [auth EE],
JG [auth GC],
JJ [auth IX],
JL [auth KU],
JM [auth ZN],
K [auth YJ],
KB [auth BH],
KD [auth DF],
KF [auth FE],
KH [auth HC],
KI [auth IA],
KK [auth JW],
LA [auth AJ],
LC [auth CH],
LE [auth EG],
LG [auth GE],
LI [auth ZJ],
LJ [auth IZ],
LL [auth KW],
LM [auth ZP],
M [auth YL],
MB [auth BJ],
MD [auth DH],
MF [auth FG],
MH [auth HE],
MI [auth IB],
MK [auth JY],
NA [auth AL],
NC [auth CJ],
NE [auth EI],
NG [auth GG],
NH [auth HF],
NL [auth KY],
NM [auth ZR],
O [auth YN],
OB [auth BL],
OD [auth DJ],
OF [auth FI],
OJ [auth JB],
OK [auth KA],
PA [auth AN],
PC [auth CL],
PE [auth EK],
PG [auth GI],
PI [auth ID],
PK [auth ZL],
PL [auth LA],
PM [auth ZT],
Q [auth YP],
QA [auth AO],
QB [auth BN],
QD [auth DL],
QF [auth FK],
QH [auth HH],
QJ [auth JD],
RC [auth CN],
RE [auth EM],
RG [auth GK],
RI [auth IF],
RK [auth KC],
RM [auth ZV],
S [auth YR],
SA [auth AQ],
SB [auth BP],
SD [auth DN],
SF [auth FM],
SH [auth HJ],
SI [auth IG],
SJ [auth JF],
SL [auth LC],
TC [auth CP],
TE [auth EO],
TG [auth GM],
TH [auth HK],
TK [auth KE],
TM [auth ZX],
U [auth YT],
UB [auth BR],
UD [auth DP],
UF [auth FO],
UJ [auth JH],
UL [auth LE],
VA [auth AT],
VC [auth CR],
VE [auth EQ],
VG [auth GO],
VI [auth IJ],
VK [auth KG],
VM [auth YB],
W [auth YV],
WB [auth BT],
WD [auth DR],
WF [auth FQ],
WH [auth HM],
WJ [auth JJ],
WL [auth LG],
XA [auth AV],
XC [auth CT],
XE [auth ES],
XG [auth GQ],
XI [auth IL],
XK [auth KI],
Y [auth AB],
YB [auth BV],
YD [auth DT],
YF [auth FS],
YH [auth HO],
YJ [auth JL],
YL [auth LI],
ZA [auth AX],
ZC [auth CV],
ZE [auth EU],
ZG [auth GS],
ZI [auth IN],
ZK [auth KK]
300synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 31.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONEMAN2

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