28RO | pdb_000028ro

split variant of Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

An engineered closed-shell, two-component, 480-subunit nucleocapsid.

Levasseur, M.D.Terasaka, N.Steinauer, A.Tetter, S.Pfister, S.Meier, B.H.Hilvert, D.

(2026) Proc Natl Acad Sci U S A 123: e2530090123-e2530090123

  • DOI: https://doi.org/10.1073/pnas.2530090123
  • Primary Citation Related Structures: 
    28RO

  • PubMed Abstract: 

    Self-assembling protein cages are valuable nanoscale containers for biotechnology and medical applications. Two-component systems are especially attractive due to their potential for functional complexity. In this study, we demonstrate that the subunits of the 240-subunit nucleocapsid NC-4, which was previously evolved to package and protect its encoding mRNA, can be split into two fragments without disrupting cage assembly or structure, generating a two-component, 480-subunit capsid. This modification introduces additional termini on the cage's exterior surface, creating opportunities for functionalization. We exploited these new sites by genetically appending peptide and protein tags to the exterior surface of split NC-4 (spNC-4), enabling site-specific glycosylation via posttranslational modification and cell-specific delivery by targeted antibody recruitment. Our findings broaden the utility of the NC-4 nucleocapsid. By extension, splitting related protein compartments that bind diverse cargoes could offer a robust platform for biotechnological applications requiring simultaneous encapsulation and customizable surface modification.


  • Organizational Affiliation
    • Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 5,203.57 kDa 
  • Atom Count: 268,440 
  • Modeled Residue Count: 35,340 
  • Deposited Residue Count: 47,760 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
6,7-dimethyl-8-ribityllumazine synthase
A [auth 0A],
AA [auth 3C],
AD [auth FA],
AE [auth IC],
AH [auth SA],
AI [auth VC],
AL [auth fA],
AM [auth iC],
AP [auth sA],
AQ [auth vC],
B [auth 0B],
BA [auth 3D],
BD [auth FB],
BE [auth ID],
BH [auth SB],
BI [auth VD],
BL [auth fB],
BM [auth iD],
BP [auth sB],
BQ [auth vD],
C [auth 0C],
CC [auth CA],
CD [auth FC],
CG [auth PA],
CH [auth SC],
CK [auth cA],
CL [auth fC],
CO [auth pA],
CP [auth sC],
D [auth 0D],
DC [auth CB],
DD [auth FD],
DG [auth PB],
DH [auth SD],
DK [auth cB],
DL [auth fD],
DO [auth pB],
DP [auth sD],
EB [auth 7A],
EC [auth CC],
EF [auth MA],
EG [auth PC],
EJ [auth ZA],
EK [auth cC],
EN [auth mA],
EO [auth pC],
ER [auth zA],
FB [auth 7B],
FC [auth CD],
FF [auth MB],
FG [auth PD],
FJ [auth ZB],
FK [auth cD],
FN [auth mB],
FO [auth pD],
FR [auth zB],
GA [auth 4A],
GB [auth 7C],
GE [auth JA],
GF [auth MC],
GI [auth WA],
GJ [auth ZC],
GM [auth jA],
GN [auth mC],
GQ [auth wA],
GR [auth zC],
HA [auth 4B],
HB [auth 7D],
HE [auth JB],
HF [auth MD],
HI [auth WB],
HJ [auth ZD],
HM [auth jB],
HN [auth mD],
HQ [auth wB],
HR [auth zD],
I [auth 1A],
IA [auth 4C],
ID [auth GA],
IE [auth JC],
IH [auth TA],
II [auth WC],
IL [auth gA],
IM [auth jC],
IP [auth tA],
IQ [auth wC],
J [auth 1B],
JA [auth 4D],
JD [auth GB],
JE [auth JD],
JH [auth TB],
JI [auth WD],
JL [auth gB],
JM [auth jD],
JP [auth tB],
JQ [auth wD],
K [auth 1C],
KC [auth DA],
KD [auth GC],
KG [auth QA],
KH [auth TC],
KK [auth dA],
KL [auth gC],
KO [auth qA],
KP [auth tC],
L [auth 1D],
LC [auth DB],
LD [auth GD],
LG [auth QB],
LH [auth TD],
LK [auth dB],
LL [auth gD],
LO [auth qB],
LP [auth tD],
MB [auth AA],
MC [auth DC],
MF [auth NA],
MG [auth QC],
MJ [auth aA],
MK [auth dC],
MN [auth nA],
MO [auth qC],
NB [auth AB],
NC [auth DD],
NF [auth NB],
NG [auth QD],
NJ [auth aB],
NK [auth dD],
NN [auth nB],
NO [auth qD],
OA [auth 5A],
OB [auth AC],
OE [auth KA],
OF [auth NC],
OI [auth XA],
OJ [auth aC],
OM [auth kA],
ON [auth nC],
OQ [auth xA],
PA [auth 5B],
PB [auth AD],
PE [auth KB],
PF [auth ND],
PI [auth XB],
PJ [auth aD],
PM [auth kB],
PN [auth nD],
PQ [auth xB],
Q [auth 2A],
QA [auth 5C],
QD [auth HA],
QE [auth KC],
QH [auth UA],
QI [auth XC],
QL [auth hA],
QM [auth kC],
QP [auth uA],
QQ [auth xC],
R [auth 2B],
RA [auth 5D],
RD [auth HB],
RE [auth KD],
RH [auth UB],
RI [auth XD],
RL [auth hB],
RM [auth kD],
RP [auth uB],
RQ [auth xD],
S [auth 2C],
SC [auth EA],
SD [auth HC],
SG [auth RA],
SH [auth UC],
SK [auth eA],
SL [auth hC],
SO [auth rA],
SP [auth uC],
T [auth 2D],
TC [auth EB],
TD [auth HD],
TG [auth RB],
TH [auth UD],
TK [auth eB],
TL [auth hD],
TO [auth rB],
TP [auth uD],
UB [auth BA],
UC [auth EC],
UF [auth OA],
UG [auth RC],
UJ [auth bA],
UK [auth eC],
UN [auth oA],
UO [auth rC],
VB [auth BB],
VC [auth ED],
VF [auth OB],
VG [auth RD],
VJ [auth bB],
VK [auth eD],
VN [auth oB],
VO [auth rD],
WA [auth 6A],
WB [auth BC],
WE [auth LA],
WF [auth OC],
WI [auth YA],
WJ [auth bC],
WM [auth lA],
WN [auth oC],
WQ [auth yA],
XA [auth 6B],
XB [auth BD],
XE [auth LB],
XF [auth OD],
XI [auth YB],
XJ [auth bD],
XM [auth lB],
XN [auth oD],
XQ [auth yB],
Y [auth 3A],
YA [auth 6C],
YD [auth IA],
YE [auth LC],
YH [auth VA],
YI [auth YC],
YL [auth iA],
YM [auth lC],
YP [auth vA],
YQ [auth yC],
Z [auth 3B],
ZA [auth 6D],
ZD [auth IB],
ZE [auth LD],
ZH [auth VB],
ZI [auth YD],
ZL [auth iB],
ZM [auth lD],
ZP [auth vB],
ZQ [auth yD]
113Aquifex aeolicusMutation(s): 0 
Gene Names: ribHaq_132
EC: 2.5.1.78
UniProt
Find proteins for O66529 (Aquifex aeolicus (strain VF5))
Explore O66529 
Go to UniProtKB:  O66529
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66529
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
6,7-dimethyl-8-ribityllumazine synthase
AB [auth 6a],
AC [auth Bc],
AF [auth La],
AG [auth Oc],
AJ [auth Ya],
AK [auth bc],
AN [auth la],
AO [auth oc],
AR [auth ya],
BB [auth 6b],
BC [auth Bd],
BF [auth Lb],
BG [auth Od],
BJ [auth Yb],
BK [auth bd],
BN [auth lb],
BO [auth od],
BR [auth yb],
CA [auth 3a],
CB [auth 6c],
CE [auth Ia],
CF [auth Lc],
CI [auth Va],
CJ [auth Yc],
CM [auth ia],
CN [auth lc],
CQ [auth va],
CR [auth yc],
DA [auth 3b],
DB [auth 6d],
DE [auth Ib],
DF [auth Ld],
DI [auth Vb],
DJ [auth Yd],
DM [auth ib],
DN [auth ld],
DQ [auth vb],
DR [auth yd],
E [auth 0a],
EA [auth 3c],
ED [auth Fa],
EE [auth Ic],
EH [auth Sa],
EI [auth Vc],
EL [auth fa],
EM [auth ic],
EP [auth sa],
EQ [auth vc],
F [auth 0b],
FA [auth 3d],
FD [auth Fb],
FE [auth Id],
FH [auth Sb],
FI [auth Vd],
FL [auth fb],
FM [auth id],
FP [auth sb],
FQ [auth vd],
G [auth 0c],
GC [auth Ca],
GD [auth Fc],
GG [auth Pa],
GH [auth Sc],
GK [auth ca],
GL [auth fc],
GO [auth pa],
GP [auth sc],
H [auth 0d],
HC [auth Cb],
HD [auth Fd],
HG [auth Pb],
HH [auth Sd],
HK [auth cb],
HL [auth fd],
HO [auth pb],
HP [auth sd],
IB [auth 7a],
IC [auth Cc],
IF [auth Ma],
IG [auth Pc],
IJ [auth Za],
IK [auth cc],
IN [auth ma],
IO [auth pc],
IR [auth za],
JB [auth 7b],
JC [auth Cd],
JF [auth Mb],
JG [auth Pd],
JJ [auth Zb],
JK [auth cd],
JN [auth mb],
JO [auth pd],
JR [auth zb],
KA [auth 4a],
KB [auth 7c],
KE [auth Ja],
KF [auth Mc],
KI [auth Wa],
KJ [auth Zc],
KM [auth ja],
KN [auth mc],
KQ [auth wa],
KR [auth zc],
LA [auth 4b],
LB [auth 7d],
LE [auth Jb],
LF [auth Md],
LI [auth Wb],
LJ [auth Zd],
LM [auth jb],
LN [auth md],
LQ [auth wb],
LR [auth zd],
M [auth 1a],
MA [auth 4c],
MD [auth Ga],
ME [auth Jc],
MH [auth Ta],
MI [auth Wc],
ML [auth ga],
MM [auth jc],
MP [auth ta],
MQ [auth wc],
N [auth 1b],
NA [auth 4d],
ND [auth Gb],
NE [auth Jd],
NH [auth Tb],
NI [auth Wd],
NL [auth gb],
NM [auth jd],
NP [auth tb],
NQ [auth wd],
O [auth 1c],
OC [auth Da],
OD [auth Gc],
OG [auth Qa],
OH [auth Tc],
OK [auth da],
OL [auth gc],
OO [auth qa],
OP [auth tc],
P [auth 1d],
PC [auth Db],
PD [auth Gd],
PG [auth Qb],
PH [auth Td],
PK [auth db],
PL [auth gd],
PO [auth qb],
PP [auth td],
QB [auth Aa],
QC [auth Dc],
QF [auth Na],
QG [auth Qc],
QJ [auth aa],
QK [auth dc],
QN [auth na],
QO [auth qc],
RB [auth Ab],
RC [auth Dd],
RF [auth Nb],
RG [auth Qd],
RJ [auth ab],
RK [auth dd],
RN [auth nb],
RO [auth qd],
SA [auth 5a],
SB [auth Ac],
SE [auth Ka],
SF [auth Nc],
SI [auth Xa],
SJ [auth ac],
SM [auth ka],
SN [auth nc],
SQ [auth xa],
TA [auth 5b],
TB [auth Ad],
TE [auth Kb],
TF [auth Nd],
TI [auth Xb],
TJ [auth ad],
TM [auth kb],
TN [auth nd],
TQ [auth xb],
U [auth 2a],
UA [auth 5c],
UD [auth Ha],
UE [auth Kc],
UH [auth Ua],
UI [auth Xc],
UL [auth ha],
UM [auth kc],
UP [auth ua],
UQ [auth xc],
V [auth 2b],
VA [auth 5d],
VD [auth Hb],
VE [auth Kd],
VH [auth Ub],
VI [auth Xd],
VL [auth hb],
VM [auth kd],
VP [auth ub],
VQ [auth xd],
W [auth 2c],
WC [auth Ea],
WD [auth Hc],
WG [auth Ra],
WH [auth Uc],
WK [auth ea],
WL [auth hc],
WO [auth ra],
WP [auth uc],
X [auth 2d],
XC [auth Eb],
XD [auth Hd],
XG [auth Rb],
XH [auth Ud],
XK [auth eb],
XL [auth hd],
XO [auth rb],
XP [auth ud],
YB [auth Ba],
YC [auth Ec],
YF [auth Oa],
YG [auth Rc],
YJ [auth ba],
YK [auth ec],
YN [auth oa],
YO [auth rc],
ZB [auth Bb],
ZC [auth Ed],
ZF [auth Ob],
ZG [auth Rd],
ZJ [auth bb],
ZK [auth ed],
ZN [auth ob],
ZO [auth rd]
86Aquifex aeolicusMutation(s): 0 
Gene Names: ribHaq_132
EC: 2.5.1.78
UniProt
Find proteins for O66529 (Aquifex aeolicus (strain VF5))
Explore O66529 
Go to UniProtKB:  O66529
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66529
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.18

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-AdG-2012-321295

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-29
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Data collection, Database references