6GSN

Structure of a partial yeast 48S preinitiation complex in closed conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3JAP


Literature

Large-scale movement of eIF3 domains during translation initiation modulate start codon selection.

Llacer, J.L.Hussain, T.Dong, J.Villamayor, L.Gordiyenko, Y.Hinnebusch, A.G.

(2021) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gkab908
  • Primary Citation of Related Structures:  
    6GSM, 6GSN

  • PubMed Abstract: 

    The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia 46010, Spain.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F09812pB [auth C]217Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0D08305pC [auth D]223Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CRK7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0D10659pD [auth F]206Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B08173pE [auth K]96Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12F [auth M]118Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F07843pG [auth P]117Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16H [auth Q]141Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B01474pI [auth R]130Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CWU3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B01562pJ [auth S]145Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CWT9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0A07194pK [auth T]143Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CXM0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F25542pL [auth U]106Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B06182pM [auth Z]70Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28N [auth c]62Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P33285 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aO [auth f]69Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P69061 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0E12277pP [auth g]324Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CNI7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29Q [auth d]53Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CPG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30R [auth e]58Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CUH5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AS [auth h]25Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1AU [auth i]111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF11YMR260CYM8156.02C
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor eIF-1V [auth m]90Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI1RFR1YNL244CN0905
UniProt
Find proteins for P32911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit A,eIF3aW [auth o]567Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPG1TIF32YBR079CYBR0734
UniProt
Find proteins for P38249 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CX [auth q]699Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NIP1YMR309CYM9924.01CYM9952.11C
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit gammaY [auth k]430Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GCD11TIF213YER025W
EC: 3.6.5.3
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit betaZ [auth l]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI3TIF212YPL237W
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Find proteins for P09064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alphaAA [auth j]263Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI2TIF211YJR007WJ1429
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0CA [auth A]219Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1DA [auth B]231Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4EA [auth E]260Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6FA [auth G]226Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7GA [auth H]184Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8HA [auth I]200Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0E23673pIA [auth J]182Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0A10483pJA [auth L]155Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CX80 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F18040pKA [auth N]150Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14LA [auth O]127Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21MA [auth V]87Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22NA [auth W]129Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CW21 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24OA [auth Y]134Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CU44 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
RPS23PA [auth X]144Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q875M3 (Kluyveromyces lactis)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26QA [auth a]98Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CS01 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27RA [auth b]81Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CNL2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BSA [auth p]666Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRT1CDC63YOR361C
UniProt
Find proteins for P06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ITA [auth s]342Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF34SCY_4321
UniProt
Find proteins for P40217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GUA [auth r]49Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF35SCY_1313
UniProt
Find proteins for A6ZZ25 (Saccharomyces cerevisiae (strain YJM789))
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNA (1798-MER)A [auth 2]1,798Kluyveromyces lactis NRRL Y-1140
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Entity ID: 20
MoleculeChains LengthOrganismImage
mRNAT [auth 3]14Saccharomyces cerevisiae S288C
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Entity ID: 28
MoleculeChains LengthOrganismImage
tRNAi (75-MER)BA [auth 1]75Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

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XD [auth k]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
MET
Query on MET

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YD [auth k]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN
Query on ZN

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BE [auth a],
DE [auth b],
UD [auth f],
ZD [auth l]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 2]
AC [auth 2]
AD [auth 2]
AE [auth B]
BB [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth B],
BB [auth 2],
BC [auth 2],
BD [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CE [auth a],
DB [auth 2],
DC [auth 2],
DD [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth C],
UB [auth 2],
UC [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth h],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth k],
XA [auth 2],
XB [auth 2],
XC [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTREFMAC5.8

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection
  • Version 1.2: 2021-10-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-07-10
    Changes: Data collection