6QN1

T=4 quasi-symmetric bacterial microcompartment particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles.

Kalnins, G.Cesle, E.E.Jansons, J.Liepins, J.Filimonenko, A.Tars, K.

(2020) Nat Commun 11: 388-388

  • DOI: https://doi.org/10.1038/s41467-019-14205-y
  • Primary Citation of Related Structures:  
    6QN1

  • PubMed Abstract: 

    Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.


  • Organizational Affiliation

    Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia. gints@biomed.lu.lv.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon dioxide concentrating mechanism protein CcmL88Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ccmLSAMEA4873648_04509
UniProt
Find proteins for A0A486QTH6 (Klebsiella pneumoniae)
Explore A0A486QTH6 
Go to UniProtKB:  A0A486QTH6
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UniProt GroupA0A486QTH6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BMC domain-containing protein
AA [auth BA],
AC [auth DA],
AE [auth FA],
AG [auth HA],
AI [auth JA],
B [auth AB],
BA [auth BB],
BB [auth CB],
BC [auth DB],
BD [auth EB],
BE [auth FB],
BF [auth GB],
BG [auth HB],
BH [auth IB],
BI [auth JB],
C [auth AC],
CB [auth CC],
CD [auth EC],
CF [auth GC],
CH [auth IC],
D [auth AD],
DA [auth BD],
DB [auth CD],
DC [auth DD],
DD [auth ED],
DE [auth FD],
DF [auth GD],
DG [auth HD],
DH [auth ID],
DI [auth JD],
EA [auth BE],
EC [auth DE],
EE [auth FE],
EG [auth HE],
EI [auth JE],
F [auth AF],
FA [auth BF],
FB [auth CF],
FC [auth DF],
FD [auth EF],
FE [auth FF],
FF [auth GF],
FG [auth HF],
FH [auth IF],
FI [auth JF],
G [auth AG],
GB [auth CG],
GD [auth EG],
GF [auth GG],
GH [auth IG],
H [auth AH],
HA [auth BH],
HB [auth CH],
HC [auth DH],
HD [auth EH],
HE [auth FH],
HF [auth GH],
HG [auth HH],
HH [auth IH],
IA [auth BI],
IC [auth DI],
IE [auth FI],
IG [auth HI],
J [auth AJ],
JA [auth BJ],
JB [auth CJ],
JC [auth DJ],
JD [auth EJ],
JE [auth FJ],
JF [auth GJ],
JG [auth HJ],
JH [auth IJ],
K [auth AK],
KB [auth CK],
KD [auth EK],
KF [auth GK],
KH [auth IK],
L [auth AL],
LA [auth BL],
LB [auth CL],
LC [auth DL],
LD [auth EL],
LE [auth FL],
LF [auth GL],
LG [auth HL],
LH [auth IL],
MA [auth BM],
MC [auth DM],
ME [auth FM],
MG [auth HM],
N [auth AN],
NA [auth BN],
NB [auth CN],
NC [auth DN],
ND [auth EN],
NE [auth FN],
NF [auth GN],
NG [auth HN],
NH [auth IN],
O [auth AO],
OB [auth CO],
OD [auth EO],
OF [auth GO],
OH [auth IO],
P [auth AP],
PA [auth BP],
PB [auth CP],
PC [auth DP],
PD [auth EP],
PE [auth FP],
PF [auth GP],
PG [auth HP],
PH [auth IP],
QA [auth BQ],
QC [auth DQ],
QE [auth FQ],
QG [auth HQ],
R [auth AR],
RA [auth BR],
RB [auth CR],
RC [auth DR],
RD [auth ER],
RE [auth FR],
RF [auth GR],
RG [auth HR],
RH [auth IR],
S [auth AS],
SB [auth CS],
SD [auth ES],
SF [auth GS],
SH [auth IS],
T [auth AT],
TA [auth BT],
TB [auth CT],
TC [auth DT],
TD [auth ET],
TE [auth FT],
TF [auth GT],
TG [auth HT],
TH [auth IT],
UA [auth BU],
UC [auth DU],
UE [auth FU],
UG [auth HU],
V [auth AV],
VA [auth BV],
VB [auth CV],
VC [auth DV],
VD [auth EV],
VE [auth FV],
VF [auth GV],
VG [auth HV],
VH [auth IV],
W [auth AW],
WB [auth CW],
WD [auth EW],
WF [auth GW],
WH [auth IW],
X [auth AX],
XA [auth BX],
XB [auth CX],
XC [auth DX],
XD [auth EX],
XE [auth FX],
XF [auth GX],
XG [auth HX],
XH [auth IX],
YA [auth BY],
YC [auth DY],
YE [auth FY],
YG [auth HY],
Z [auth AZ],
ZA [auth BZ],
ZB [auth CZ],
ZC [auth DZ],
ZD [auth EZ],
ZE [auth FZ],
ZF [auth GZ],
ZG [auth HZ],
ZH [auth IZ]
100Klebsiella pneumoniaeMutation(s): 0 
UniProt
Find proteins for A0A0J4R4X1 (Klebsiella pneumoniae)
Explore A0A0J4R4X1 
Go to UniProtKB:  A0A0J4R4X1
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UniProt GroupA0A0J4R4X1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTREFMAC5.8.0238
MODEL REFINEMENTPHENIX1.16-3549

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2019-12-25 
  • Deposition Author(s): Kalnins, G.

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2020-02-12
    Changes: Data collection