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- PDB-6qn1: T=4 quasi-symmetric bacterial microcompartment particle -

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Basic information

Entry
Database: PDB / ID: 6qn1
TitleT=4 quasi-symmetric bacterial microcompartment particle
Components
  • BMC domain-containing protein
  • Carbon dioxide concentrating mechanism protein CcmL
KeywordsSTRUCTURAL PROTEIN / bacterial microcompartment / protein shell / GRM2 type microcompartment / EutN / ccmK / PduA
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
BMC domain-containing protein / Carbon dioxide concentrating mechanism protein CcmL
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsKalnins, G.
CitationJournal: Nat Commun / Year: 2020
Title: Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles.
Authors: Gints Kalnins / Eva-Emilija Cesle / Juris Jansons / Janis Liepins / Anatolij Filimonenko / Kaspars Tars /
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, ...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.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 12, 2020Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.phase_plate

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Structure visualization

Movie
  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
AA: Carbon dioxide concentrating mechanism protein CcmL
AB: BMC domain-containing protein
AC: BMC domain-containing protein
AD: BMC domain-containing protein
AE: Carbon dioxide concentrating mechanism protein CcmL
AF: BMC domain-containing protein
AG: BMC domain-containing protein
AH: BMC domain-containing protein
AI: Carbon dioxide concentrating mechanism protein CcmL
AJ: BMC domain-containing protein
AK: BMC domain-containing protein
AL: BMC domain-containing protein
AM: Carbon dioxide concentrating mechanism protein CcmL
AN: BMC domain-containing protein
AO: BMC domain-containing protein
AP: BMC domain-containing protein
AQ: Carbon dioxide concentrating mechanism protein CcmL
AR: BMC domain-containing protein
AS: BMC domain-containing protein
AT: BMC domain-containing protein
AU: Carbon dioxide concentrating mechanism protein CcmL
AV: BMC domain-containing protein
AW: BMC domain-containing protein
AX: BMC domain-containing protein
AY: Carbon dioxide concentrating mechanism protein CcmL
AZ: BMC domain-containing protein
BA: BMC domain-containing protein
BB: BMC domain-containing protein
BC: Carbon dioxide concentrating mechanism protein CcmL
BD: BMC domain-containing protein
BE: BMC domain-containing protein
BF: BMC domain-containing protein
BG: Carbon dioxide concentrating mechanism protein CcmL
BH: BMC domain-containing protein
BI: BMC domain-containing protein
BJ: BMC domain-containing protein
BK: Carbon dioxide concentrating mechanism protein CcmL
BL: BMC domain-containing protein
BM: BMC domain-containing protein
BN: BMC domain-containing protein
BO: Carbon dioxide concentrating mechanism protein CcmL
BP: BMC domain-containing protein
BQ: BMC domain-containing protein
BR: BMC domain-containing protein
BS: Carbon dioxide concentrating mechanism protein CcmL
BT: BMC domain-containing protein
BU: BMC domain-containing protein
BV: BMC domain-containing protein
BW: Carbon dioxide concentrating mechanism protein CcmL
BX: BMC domain-containing protein
BY: BMC domain-containing protein
BZ: BMC domain-containing protein
CA: Carbon dioxide concentrating mechanism protein CcmL
CB: BMC domain-containing protein
CC: BMC domain-containing protein
CD: BMC domain-containing protein
CE: Carbon dioxide concentrating mechanism protein CcmL
CF: BMC domain-containing protein
CG: BMC domain-containing protein
CH: BMC domain-containing protein
CI: Carbon dioxide concentrating mechanism protein CcmL
CJ: BMC domain-containing protein
CK: BMC domain-containing protein
CL: BMC domain-containing protein
CM: Carbon dioxide concentrating mechanism protein CcmL
CN: BMC domain-containing protein
CO: BMC domain-containing protein
CP: BMC domain-containing protein
CQ: Carbon dioxide concentrating mechanism protein CcmL
CR: BMC domain-containing protein
CS: BMC domain-containing protein
CT: BMC domain-containing protein
CU: Carbon dioxide concentrating mechanism protein CcmL
CV: BMC domain-containing protein
CW: BMC domain-containing protein
CX: BMC domain-containing protein
CY: Carbon dioxide concentrating mechanism protein CcmL
CZ: BMC domain-containing protein
DA: BMC domain-containing protein
DB: BMC domain-containing protein
DC: Carbon dioxide concentrating mechanism protein CcmL
DD: BMC domain-containing protein
DE: BMC domain-containing protein
DF: BMC domain-containing protein
DG: Carbon dioxide concentrating mechanism protein CcmL
DH: BMC domain-containing protein
DI: BMC domain-containing protein
DJ: BMC domain-containing protein
DK: Carbon dioxide concentrating mechanism protein CcmL
DL: BMC domain-containing protein
DM: BMC domain-containing protein
DN: BMC domain-containing protein
DO: Carbon dioxide concentrating mechanism protein CcmL
DP: BMC domain-containing protein
DQ: BMC domain-containing protein
DR: BMC domain-containing protein
DS: Carbon dioxide concentrating mechanism protein CcmL
DT: BMC domain-containing protein
DU: BMC domain-containing protein
DV: BMC domain-containing protein
DW: Carbon dioxide concentrating mechanism protein CcmL
DX: BMC domain-containing protein
DY: BMC domain-containing protein
DZ: BMC domain-containing protein
EA: Carbon dioxide concentrating mechanism protein CcmL
EB: BMC domain-containing protein
EC: BMC domain-containing protein
ED: BMC domain-containing protein
EE: Carbon dioxide concentrating mechanism protein CcmL
EF: BMC domain-containing protein
EG: BMC domain-containing protein
EH: BMC domain-containing protein
EI: Carbon dioxide concentrating mechanism protein CcmL
EJ: BMC domain-containing protein
EK: BMC domain-containing protein
EL: BMC domain-containing protein
EM: Carbon dioxide concentrating mechanism protein CcmL
EN: BMC domain-containing protein
EO: BMC domain-containing protein
EP: BMC domain-containing protein
EQ: Carbon dioxide concentrating mechanism protein CcmL
ER: BMC domain-containing protein
ES: BMC domain-containing protein
ET: BMC domain-containing protein
EU: Carbon dioxide concentrating mechanism protein CcmL
EV: BMC domain-containing protein
EW: BMC domain-containing protein
EX: BMC domain-containing protein
EY: Carbon dioxide concentrating mechanism protein CcmL
EZ: BMC domain-containing protein
FA: BMC domain-containing protein
FB: BMC domain-containing protein
FC: Carbon dioxide concentrating mechanism protein CcmL
FD: BMC domain-containing protein
FE: BMC domain-containing protein
FF: BMC domain-containing protein
FG: Carbon dioxide concentrating mechanism protein CcmL
FH: BMC domain-containing protein
FI: BMC domain-containing protein
FJ: BMC domain-containing protein
FK: Carbon dioxide concentrating mechanism protein CcmL
FL: BMC domain-containing protein
FM: BMC domain-containing protein
FN: BMC domain-containing protein
FO: Carbon dioxide concentrating mechanism protein CcmL
FP: BMC domain-containing protein
FQ: BMC domain-containing protein
FR: BMC domain-containing protein
FS: Carbon dioxide concentrating mechanism protein CcmL
FT: BMC domain-containing protein
FU: BMC domain-containing protein
FV: BMC domain-containing protein
FW: Carbon dioxide concentrating mechanism protein CcmL
FX: BMC domain-containing protein
FY: BMC domain-containing protein
FZ: BMC domain-containing protein
GA: Carbon dioxide concentrating mechanism protein CcmL
GB: BMC domain-containing protein
GC: BMC domain-containing protein
GD: BMC domain-containing protein
GE: Carbon dioxide concentrating mechanism protein CcmL
GF: BMC domain-containing protein
GG: BMC domain-containing protein
GH: BMC domain-containing protein
GI: Carbon dioxide concentrating mechanism protein CcmL
GJ: BMC domain-containing protein
GK: BMC domain-containing protein
GL: BMC domain-containing protein
GM: Carbon dioxide concentrating mechanism protein CcmL
GN: BMC domain-containing protein
GO: BMC domain-containing protein
GP: BMC domain-containing protein
GQ: Carbon dioxide concentrating mechanism protein CcmL
GR: BMC domain-containing protein
GS: BMC domain-containing protein
GT: BMC domain-containing protein
GU: Carbon dioxide concentrating mechanism protein CcmL
GV: BMC domain-containing protein
GW: BMC domain-containing protein
GX: BMC domain-containing protein
GY: Carbon dioxide concentrating mechanism protein CcmL
GZ: BMC domain-containing protein
HA: BMC domain-containing protein
HB: BMC domain-containing protein
HC: Carbon dioxide concentrating mechanism protein CcmL
HD: BMC domain-containing protein
HE: BMC domain-containing protein
HF: BMC domain-containing protein
HG: Carbon dioxide concentrating mechanism protein CcmL
HH: BMC domain-containing protein
HI: BMC domain-containing protein
HJ: BMC domain-containing protein
HK: Carbon dioxide concentrating mechanism protein CcmL
HL: BMC domain-containing protein
HM: BMC domain-containing protein
HN: BMC domain-containing protein
HO: Carbon dioxide concentrating mechanism protein CcmL
HP: BMC domain-containing protein
HQ: BMC domain-containing protein
HR: BMC domain-containing protein
HS: Carbon dioxide concentrating mechanism protein CcmL
HT: BMC domain-containing protein
HU: BMC domain-containing protein
HV: BMC domain-containing protein
HW: Carbon dioxide concentrating mechanism protein CcmL
HX: BMC domain-containing protein
HY: BMC domain-containing protein
HZ: BMC domain-containing protein
IA: Carbon dioxide concentrating mechanism protein CcmL
IB: BMC domain-containing protein
IC: BMC domain-containing protein
ID: BMC domain-containing protein
IE: Carbon dioxide concentrating mechanism protein CcmL
IF: BMC domain-containing protein
IG: BMC domain-containing protein
IH: BMC domain-containing protein
II: Carbon dioxide concentrating mechanism protein CcmL
IJ: BMC domain-containing protein
IK: BMC domain-containing protein
IL: BMC domain-containing protein
IM: Carbon dioxide concentrating mechanism protein CcmL
IN: BMC domain-containing protein
IO: BMC domain-containing protein
IP: BMC domain-containing protein
IQ: Carbon dioxide concentrating mechanism protein CcmL
IR: BMC domain-containing protein
IS: BMC domain-containing protein
IT: BMC domain-containing protein
IU: Carbon dioxide concentrating mechanism protein CcmL
IV: BMC domain-containing protein
IW: BMC domain-containing protein
IX: BMC domain-containing protein
IY: Carbon dioxide concentrating mechanism protein CcmL
IZ: BMC domain-containing protein
JA: BMC domain-containing protein
JB: BMC domain-containing protein
JC: Carbon dioxide concentrating mechanism protein CcmL
JD: BMC domain-containing protein
JE: BMC domain-containing protein
JF: BMC domain-containing protein


Theoretical massNumber of molelcules
Total (without water)2,453,538240
Polymers2,453,538240
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Carbon dioxide concentrating mechanism protein CcmL / Ethanolamine utilization protein EutN (BMC-P)


Mass: 9962.463 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ccmL, SAMEA4873648_04509 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A486QTH6
#2: Protein ...
BMC domain-containing protein / Ethanolamine utilization polyhedral-body-like protein EutM / Propanediol utilization protein PduA / ...Ethanolamine utilization polyhedral-body-like protein EutM / Propanediol utilization protein PduA / Propanediol utilization protein PduJ


Mass: 10309.946 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J4R4X1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: T=4 quasi-symmetric bacterial microcompartment particle
Type: COMPLEX
Details: Bacterial microcompartment particle made by coexpression of shell proteins
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.45 MDa / Experimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMNaClSodium chloride1
220 mMTris-HClTris1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was purified with gel filtration
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 291 K / Details: blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1400 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1316
EM imaging opticsPhase plate: VOLTA PHASE PLATE
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4RELION3CTF correction
7UCSF Chimera1.13.1model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
19REFMAC5.8.0238model refinement
20PHENIX1.16-3549model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 62533
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45915 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 149.892 / Protocol: RIGID BODY FIT / Space: RECIPROCAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
14N8XAA1
24QIVAB1

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