5O61

The complete structure of the Mycobacterium smegmatis 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.

Hentschel, J.Burnside, C.Mignot, I.Leibundgut, M.Boehringer, D.Ban, N.

(2017) Cell Rep 20: 149-160

  • DOI: https://doi.org/10.1016/j.celrep.2017.06.029
  • Primary Citation of Related Structures:  
    5O5J, 5O60, 5O61

  • PubMed Abstract: 

    The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein bL37A [auth 3]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10J [auth I]175Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11K [auth J]142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13L [auth K]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14M [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15N [auth M]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16O [auth N]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17P [auth O]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18Q [auth P]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSG5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19R [auth Q]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20S [auth R]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21T [auth S]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22U [auth T]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23V [auth U]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24W [auth V]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25X [auth W]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R3D2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Y [auth X]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L28PZ [auth Y]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29AA [auth Z]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30BA [auth a]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth b]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1DA [auth c]55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth d]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth e]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth f]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31HA [auth g]75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved domain proteinJA [auth BB]33Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3KA [auth BC]275Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4LA [auth BD]201Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5MA [auth BE]214Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6NA [auth BF]96Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7OA [auth BG]156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8PA [auth BH]132Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9QA [auth BI]150Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10RA [auth BJ]101Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11SA [auth BK]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12TA [auth BL]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13UA [auth BM]124Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZVA [auth BN]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15WA [auth BO]89Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16XA [auth BP]156Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17YA [auth BQ]98Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18 2ZA [auth BR]84Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AB [auth BS]93Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BB [auth BT]86Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2CB [auth BV]277Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S rRNAB [auth A]3,120Mycolicibacterium smegmatis MC2 155
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth B]118Mycolicibacterium smegmatis MC2 155
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Entity ID: 35
MoleculeChains LengthOrganismImage
16S rRNAIA [auth BA]1,528Mycolicibacterium smegmatis MC2 155
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Entity ID: 56
MoleculeChains LengthOrganismImage
P/P-site Phe-tRNA(Phe)DB [auth BW]76Mycolicibacterium smegmatis MC2 155
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Entity ID: 57
MoleculeChains LengthOrganismImage
mRNA fragmentEB [auth BX]6Mycolicibacterium smegmatis MC2 155
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

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MZ [auth BW]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ZN
Query on ZN

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AR [auth g]
JZ [auth BN]
KZ [auth BR]
WQ [auth Y]
XQ [auth c]
AR [auth g],
JZ [auth BN],
KZ [auth BR],
WQ [auth Y],
XQ [auth c],
ZQ [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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