5H2F

Crystal structure of the PsbM-deletion mutant of photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

Starting Model: experimental
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This is version 3.1 of the entry. See complete history


Literature

Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II.

Uto, S.Kawakami, K.Umena, Y.Iwai, M.Ikeuchi, M.Shen, J.R.Kamiya, N.

(2017) Faraday Discuss 198: 107-120

  • DOI: https://doi.org/10.1039/c6fd00213g
  • Primary Citation of Related Structures:  
    5H2F

  • PubMed Abstract: 

    Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids. After initial light excitation, the charge separation produces an electron, which is transferred to a plastoquinone molecule (Q A ) and then to another plastoquinone (Q B ). PsbM is a low-molecular-weight subunit with one transmembrane helix, and is located in the monomer-monomer interface of the PSII dimer. The function of PsbM has been reported to be stabilization of the PSII dimer and maintenance of electron transfer efficiency of PSII based on previous X-ray crystal structure analysis at a resolution of 4.2 Å. In order to elucidate the structure-function relationships of PsbM in detail, we improved the quality of PSII crystals from a PsbM-deleted mutant (ΔPsbM-PSII) of Thermosynechococcus elongatus, and succeeded in improving the diffraction quality to a resolution of 2.2 Å. X-ray crystal structure analysis of ΔPsbM-PSII showed that electron densities for the PsbM subunit and neighboring carotenoid and detergent molecules were absent in the monomer-monomer interface. The overall structure of ΔPsbM-PSII was similar to wild-type PSII, but the arrangement of the hydrophobic transmembrane subunits was significantly changed by the deletion of PsbM, resulting in a slight widening of the lipid hole involving Q B . The lipid hole-widening further induced structural changes of the bicarbonate ion coordinated to the non-heme Fe(ii) atom and destabilized the polypeptide chains around the Q B binding site located far from the position of PsbM. The fluorescence decay measurement indicated that the electron transfer rate from Q A to Q B was decreased in ΔPsbM-PSII compared with wild-type PSII. The functional change in electron transfer efficiency was fully interpreted based on structural changes caused by the deletion of the PsbM subunit.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, Japan. [email protected].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
S [auth a]
334Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
T [auth b]
505Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
U [auth c]
455Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
V [auth d]
342Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
W [auth e]
80Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
X [auth f]
33Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Y [auth h]
63Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
Z [auth i]
36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JAA [auth j],
I [auth J]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KBA [auth k],
J [auth K]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LCA [auth l],
K [auth L]
35Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideDA [auth o],
L [auth O]
243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TEA [auth t],
M [auth T]
30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinFA [auth u],
N [auth U]
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550GA [auth v],
O [auth V]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12HA [auth y],
P [auth Y]
29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinIA [auth x],
Q [auth X]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZJA [auth z],
R [auth Z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AM [auth h]
EK [auth c]
FF [auth H]
FK [auth c]
GK [auth c]
AM [auth h],
EK [auth c],
FF [auth H],
FK [auth c],
GK [auth c],
LD [auth C],
LL [auth d],
MD [auth C],
ND [auth C],
PE [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AD [auth C]
AK [auth c]
BD [auth C]
BK [auth c]
CD [auth C]
AD [auth C],
AK [auth c],
BD [auth C],
BK [auth c],
CD [auth C],
DD [auth C],
DI [auth b],
ED [auth C],
EI [auth b],
FD [auth C],
FI [auth b],
GB [auth B],
GD [auth C],
GI [auth b],
HB [auth B],
HD [auth C],
HI [auth b],
HL [auth d],
IB [auth B],
ID [auth C],
II [auth b],
IL [auth d],
JB [auth B],
JE [auth D],
JH [auth a],
JI [auth b],
KB [auth B],
KH [auth a],
KI [auth b],
LB [auth B],
LE [auth D],
LH [auth a],
LI [auth b],
MB [auth B],
ME [auth D],
MI [auth b],
NB [auth B],
NI [auth b],
OA [auth A],
OB [auth B],
OH [auth a],
OI [auth b],
PA [auth A],
PB [auth B],
PI [auth b],
PJ [auth c],
QB [auth B],
QI [auth b],
QJ [auth c],
RA [auth A],
RB [auth B],
RI [auth b],
RJ [auth c],
SB [auth B],
SI [auth b],
SJ [auth c],
TB [auth B],
TJ [auth c],
UB [auth B],
UJ [auth c],
VB [auth B],
VJ [auth c],
WC [auth C],
WJ [auth c],
XC [auth C],
XJ [auth c],
YC [auth C],
YJ [auth c],
ZC [auth C],
ZJ [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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KE [auth D],
MH [auth a],
NH [auth a],
QA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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MM [auth l]
QE [auth D]
QH [auth a]
UH [auth a]
VC [auth C]
MM [auth l],
QE [auth D],
QH [auth a],
UH [auth a],
VC [auth C],
WA [auth A],
WI [auth b],
WL [auth f]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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BM [auth i]
HK [auth c]
HM [auth j]
NF [auth J]
OD [auth C]
BM [auth i],
HK [auth c],
HM [auth j],
NF [auth J],
OD [auth C],
OL [auth d],
RK [auth c],
TA [auth A],
UE [auth D],
XI [auth b],
ZB [auth B],
ZD [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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KL [auth d],
OE [auth D],
RH [auth a],
UA [auth A]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

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GL [auth d]
ML [auth d]
NL [auth d]
NM [auth l]
QD [auth C]
GL [auth d],
ML [auth d],
NL [auth d],
NM [auth l],
QD [auth C],
RE [auth D],
SE [auth D],
SF [auth L],
SH [auth a],
TE [auth D],
VA [auth A],
ZH [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

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LN [auth v],
OG [auth V]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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CF [auth E],
VL [auth e]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
Query on RRX

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EF [auth H],
ZL [auth h]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR

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CK [auth c]
DK [auth c]
JD [auth C]
JL [auth d]
KD [auth C]
CK [auth c],
DK [auth c],
JD [auth C],
JL [auth d],
KD [auth C],
KM [auth k],
NE [auth D],
PH [auth a],
QF [auth K],
SA [auth A],
TI [auth b],
UI [auth b],
VI [auth b],
VN [auth y],
WB [auth B],
XB [auth B],
YB [auth B],
ZG [auth Y]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AC [auth B]
AN [auth t]
BF [auth E]
BH [auth Z]
IF [auth I]
AC [auth B],
AN [auth t],
BF [auth E],
BH [auth Z],
IF [auth I],
IK [auth c],
JG [auth T],
SK [auth c],
VH [auth a],
XA [auth A],
XL [auth f]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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FH [auth a],
KA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG

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AE [auth C]
BC [auth B]
BJ [auth b]
CJ [auth b]
EC [auth B]
AE [auth C],
BC [auth B],
BJ [auth b],
CJ [auth b],
EC [auth B],
FC [auth B],
HJ [auth b],
JK [auth c],
MN [auth v],
PD [auth C],
PG [auth V],
RD [auth C],
RM [auth l],
WE [auth D],
XE [auth D],
YI [auth b],
ZI [auth b]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
DMS
Query on DMS

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AB [auth A]
AF [auth D]
AG [auth O]
AI [auth a]
AL [auth c]
AB [auth A],
AF [auth D],
AG [auth O],
AI [auth a],
AL [auth c],
BB [auth A],
BE [auth C],
BG [auth O],
BI [auth a],
BL [auth c],
CB [auth A],
CE [auth C],
CG [auth O],
CL [auth c],
CN [auth t],
DB [auth A],
DE [auth C],
DF [auth F],
DG [auth O],
DH [auth a],
DL [auth c],
DN [auth t],
EE [auth C],
EG [auth O],
EH [auth a],
EJ [auth b],
EL [auth c],
EN [auth t],
FE [auth C],
FG [auth O],
FJ [auth b],
FL [auth c],
GC [auth B],
GE [auth C],
GF [auth H],
GG [auth O],
GJ [auth b],
GM [auth i],
GN [auth u],
HC [auth B],
HE [auth C],
HF [auth I],
HG [auth O],
HN [auth u],
IC [auth B],
IE [auth C],
IJ [auth b],
IN [auth u],
JC [auth B],
JJ [auth b],
JN [auth u],
KC [auth B],
KJ [auth b],
KK [auth c],
KN [auth v],
LC [auth B],
LG [auth U],
LJ [auth b],
LK [auth c],
MC [auth B],
MF [auth I],
MG [auth U],
MJ [auth b],
MK [auth c],
NC [auth B],
NG [auth V],
NJ [auth b],
NK [auth c],
NN [auth v],
OC [auth B],
OK [auth c],
OM [auth l],
ON [auth v],
PC [auth B],
PK [auth c],
PM [auth l],
PN [auth v],
QC [auth B],
QG [auth V],
QK [auth c],
QL [auth d],
QM [auth l],
QN [auth v],
RC [auth B],
RG [auth V],
RL [auth d],
RN [auth v],
SC [auth B],
SD [auth C],
SG [auth V],
SL [auth d],
SN [auth v],
TC [auth B],
TD [auth C],
TF [auth L],
TG [auth V],
TL [auth d],
TM [auth o],
TN [auth v],
UC [auth B],
UD [auth C],
UG [auth V],
UK [auth c],
UL [auth d],
UM [auth o],
UN [auth v],
VD [auth C],
VG [auth V],
VK [auth c],
VM [auth o],
WD [auth C],
WF [auth O],
WG [auth V],
WK [auth c],
WM [auth o],
XD [auth C],
XF [auth O],
XG [auth V],
XH [auth a],
XK [auth c],
XM [auth o],
YD [auth C],
YE [auth D],
YF [auth O],
YG [auth V],
YK [auth c],
YL [auth f],
YM [auth o],
ZA [auth A],
ZE [auth D],
ZF [auth O],
ZK [auth c],
ZM [auth o]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT
Query on BCT

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EB [auth A],
YH [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

Download Ideal Coordinates CCD File 
GH [auth a],
LA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CI [auth b],
FB [auth B],
OJ [auth c],
SM [auth o],
VF [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
HH [auth a],
IH [auth a],
MA [auth A],
NA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
IM [auth j],
LM [auth k],
OF [auth J],
RF [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
AH [auth X]
AJ [auth b]
BN [auth t]
CC [auth B]
CH [auth Z]
AH [auth X],
AJ [auth b],
BN [auth t],
CC [auth B],
CH [auth Z],
CM [auth i],
DC [auth B],
DJ [auth b],
DM [auth i],
EM [auth i],
FM [auth i],
FN [auth u],
IG [auth T],
JF [auth I],
JM [auth j],
KF [auth I],
KG [auth U],
LF [auth I],
PF [auth J],
PL [auth d],
TH [auth a],
TK [auth c],
UF [auth O],
VE [auth D],
WH [auth a],
WN [auth x],
YA [auth A]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
H [auth I],
Z [auth i]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.954α = 90
b = 226.993β = 90
c = 285.886γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XSCALEdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHI GrantsJapan24227002
Grant-in-Aid for Scientific Research on Innovative Areas Artificial photosynthesis (AnApple)Japan24107003

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection, Database references
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 3.0: 2023-11-08
    Changes: Data collection, Database references, Non-polymer description, Refinement description, Structure summary
  • Version 3.1: 2024-10-23
    Changes: Structure summary