5V74

Structure of the intact Haliangium ochraceum microcompartment shell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell.

Sutter, M.Greber, B.Aussignargues, C.Kerfeld, C.A.

(2017) Science 356: 1293-1297

  • DOI: https://doi.org/10.1126/science.aan3289
  • Primary Citation of Related Structures:  
    5V74, 5V75, 5V76

  • PubMed Abstract: 

    Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable protein shell; prominent examples include the carboxysome for CO 2 fixation and catabolic microcompartments found in many pathogenic microbes. The shell sequesters enzymatic reactions from the cytosol, analogous to the lipid-based membrane of eukaryotic organelles. Despite available structural information for single building blocks, the principles of shell assembly have remained elusive. We present the crystal structure of an intact shell from Haliangium ochraceum , revealing the basic principles of bacterial microcompartment shell construction. Given the conservation among shell proteins of all bacterial microcompartments, these principles apply to functionally diverse organelles and can inform the design and engineering of shells with new functionalities.


  • Organizational Affiliation

    Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ethanolamine utilization protein EutN/carboxysome structural protein Ccml96Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_5814
UniProt
Find proteins for D0LHE5 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LHE5 
Go to UniProtKB:  D0LHE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0LHE5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Microcompartments protein
AC [auth I7],
AD [auth L6],
AE [auth O5],
AF [auth R4],
AG [auth U3],
AH [auth X2],
B [auth A2],
BD [auth L7],
BE [auth O6],
BF [auth R5],
BG [auth U4],
BH [auth X3],
BI [auth 12],
C [auth A3],
CA [auth D2],
CE [auth O7],
CF [auth R6],
CG [auth U5],
CH [auth X4],
CI [auth 13],
CJ [auth 42],
D [auth A4],
DA [auth D3],
DB [auth G2],
DF [auth R7],
DG [auth U6],
DH [auth X5],
DI [auth 14],
DJ [auth 43],
E [auth A5],
EA [auth D4],
EB [auth G3],
EC [auth J2],
EG [auth U7],
EH [auth X6],
EI [auth 15],
EJ [auth 44],
F [auth A6],
FA [auth D5],
FB [auth G4],
FC [auth J3],
FD [auth M2],
FH [auth X7],
FI [auth 16],
FJ [auth 45],
G [auth A7],
GA [auth D6],
GB [auth G5],
GC [auth J4],
GD [auth M3],
GE [auth P2],
GI [auth 17],
GJ [auth 46],
HA [auth D7],
HB [auth G6],
HC [auth J5],
HD [auth M4],
HE [auth P3],
HF [auth S2],
HJ [auth 47],
IB [auth G7],
IC [auth J6],
ID [auth M5],
IE [auth P4],
IF [auth S3],
IG [auth V2],
JC [auth J7],
JD [auth M6],
JE [auth P5],
JF [auth S4],
JG [auth V3],
JH [auth Y2],
K [auth B2],
KD [auth M7],
KE [auth P6],
KF [auth S5],
KG [auth V4],
KH [auth Y3],
KI [auth 22],
L [auth B3],
LA [auth E2],
LE [auth P7],
LF [auth S6],
LG [auth V5],
LH [auth Y4],
LI [auth 23],
M [auth B4],
MA [auth E3],
MB [auth H2],
MF [auth S7],
MG [auth V6],
MH [auth Y5],
MI [auth 24],
N [auth B5],
NA [auth E4],
NB [auth H3],
NC [auth K2],
NG [auth V7],
NH [auth Y6],
NI [auth 25],
O [auth B6],
OA [auth E5],
OB [auth H4],
OC [auth K3],
OD [auth N2],
OH [auth Y7],
OI [auth 26],
P [auth B7],
PA [auth E6],
PB [auth H5],
PC [auth K4],
PD [auth N3],
PE [auth Q2],
PI [auth 27],
QA [auth E7],
QB [auth H6],
QC [auth K5],
QD [auth N4],
QE [auth Q3],
QF [auth T2],
RB [auth H7],
RC [auth K6],
RD [auth N5],
RE [auth Q4],
RF [auth T3],
RG [auth W2],
SC [auth K7],
SD [auth N6],
SE [auth Q5],
SF [auth T4],
SG [auth W3],
SH [auth Z2],
T [auth C2],
TD [auth N7],
TE [auth Q6],
TF [auth T5],
TG [auth W4],
TH [auth Z3],
TI [auth 32],
U [auth C3],
UA [auth F2],
UE [auth Q7],
UF [auth T6],
UG [auth W5],
UH [auth Z4],
UI [auth 33],
V [auth C4],
VA [auth F3],
VB [auth I2],
VF [auth T7],
VG [auth W6],
VH [auth Z5],
VI [auth 34],
W [auth C5],
WA [auth F4],
WB [auth I3],
WC [auth L2],
WG [auth W7],
WH [auth Z6],
WI [auth 35],
X [auth C6],
XA [auth F5],
XB [auth I4],
XC [auth L3],
XD [auth O2],
XH [auth Z7],
XI [auth 36],
Y [auth C7],
YA [auth F6],
YB [auth I5],
YC [auth L4],
YD [auth O3],
YE [auth R2],
YI [auth 37],
ZA [auth F7],
ZB [auth I6],
ZC [auth L5],
ZD [auth O4],
ZE [auth R3],
ZF [auth U2]
99Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_5815
UniProt
Find proteins for D0LID5 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LID5 
Go to UniProtKB:  D0LID5
Entity Groups  
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UniProt GroupD0LID5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Microcompartments protein212Haliangium ochraceum DSM 14365Mutation(s): 0 
Gene Names: Hoch_5816
UniProt
Find proteins for D0LID6 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2))
Explore D0LID6 
Go to UniProtKB:  D0LID6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0LID6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 394.34α = 90
b = 638.09β = 90
c = 642.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-04-03
    Changes: Refinement description