7LX0 | pdb_00007lx0

Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light

Gisriel, C.J.Huang, H.L.Reiss, K.M.Flesher, D.A.Batista, V.S.Bryant, D.A.Brudvig, G.W.Wang, J.

(2021) BBA Adv 1: 100019

Macromolecule Content 

  • Total Structure Weight: 1,119.61 kDa 
  • Atom Count: 72,462 
  • Modeled Residue Count: 6,774 
  • Deposited Residue Count: 7,410 
  • Unique protein chains: 12

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth G],
M [auth a],
Y [auth A]
788Fischerella thermalis PCC 7521Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for G6FME9 (Fischerella thermalis JSC-11)
Explore G6FME9 
Go to UniProtKB:  G6FME9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG6FME9
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth H],
N [auth b],
Z [auth B]
741Fischerella thermalis PCC 7521Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for G6FMF0 (Fischerella thermalis JSC-11)
Explore G6FMF0 
Go to UniProtKB:  G6FMF0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG6FMF0
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerAA [auth C],
C [auth N],
O [auth c]
81Fischerella thermalis PCC 7521Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for G6FW50 (Fischerella thermalis JSC-11)
Explore G6FW50 
Go to UniProtKB:  G6FW50
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG6FW50
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I protein PsaDBA [auth D],
D [auth O],
P [auth d]
159Fischerella thermalis PCC 7521Mutation(s): 0 
UniProt
Find proteins for G6FW99 (Fischerella thermalis JSC-11)
Explore G6FW99 
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UniProt GroupG6FW99
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth E],
E [auth P],
Q [auth e]
72Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FQU3 (Fischerella thermalis JSC-11)
Explore G6FQU3 
Go to UniProtKB:  G6FQU3
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UniProt GroupG6FQU3
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center protein PsaF subunit IIIDA [auth F],
F [auth Q],
R [auth f]
159Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FMD3 (Fischerella thermalis JSC-11)
Explore G6FMD3 
Go to UniProtKB:  G6FMD3
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UniProt GroupG6FMD3
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
photosystem I subunit VIIIEA [auth I],
G [auth R],
S [auth i]
67Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FMF2 (Fischerella thermalis JSC-11)
Explore G6FMF2 
Go to UniProtKB:  G6FMF2
Entity Groups
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UniProt GroupG6FMF2
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction centre subunit IX / PsaJFA [auth J],
H [auth S],
T [auth j]
48Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FMD2 (Fischerella thermalis JSC-11)
Explore G6FMD2 
Go to UniProtKB:  G6FMD2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth K],
I [auth T],
U [auth k]
49Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FV28 (Fischerella thermalis JSC-11)
Explore G6FV28 
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UniProt GroupG6FV28
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI subunit VHA [auth L],
J [auth U],
V [auth l]
174Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FMF1 (Fischerella thermalis JSC-11)
Explore G6FMF1 
Go to UniProtKB:  G6FMF1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG6FMF1
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth M],
K [auth V],
W [auth m]
31Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FWT6 (Fischerella thermalis JSC-11)
Explore G6FWT6 
Go to UniProtKB:  G6FWT6
Entity Groups
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UniProt GroupG6FWT6
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem one PsaXJA [auth X],
L [auth W],
X [auth x]
101Fischerella thermalis PCC 7521Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G6FSH2 (Fischerella thermalis JSC-11)
Explore G6FSH2 
Go to UniProtKB:  G6FSH2
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C
(Subject of Investigation/LOI)

Query on F6C



Download:Ideal Coordinates CCD File
AE [auth H]
BE [auth H]
BG [auth a]
HB [auth G]
HN [auth B]
AE [auth H],
BE [auth H],
BG [auth a],
HB [auth G],
HN [auth B],
KM [auth B],
NI [auth b],
ON [auth B],
PN [auth B],
QH [auth b],
TD [auth H],
UI [auth b],
VI [auth b],
VK [auth A],
WC [auth H]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth G]
AC [auth G]
AD [auth H]
AG [auth a]
AI [auth b]
AB [auth G],
AC [auth G],
AD [auth H],
AG [auth a],
AI [auth b],
AK [auth A],
AL [auth A],
AN [auth B],
BB [auth G],
BD [auth H],
BI [auth b],
BK [auth A],
BL [auth A],
BM [auth B],
BN [auth B],
CB [auth G],
CD [auth H],
CE [auth H],
CG [auth a],
CI [auth b],
CK [auth A],
CL [auth A],
CM [auth B],
CN [auth B],
DB [auth G],
DD [auth H],
DF [auth W],
DG [auth a],
DI [auth b],
DK [auth A],
DL [auth A],
DM [auth B],
DN [auth B],
EB [auth G],
ED [auth H],
EG [auth a],
EI [auth b],
EK [auth A],
EL [auth A],
EM [auth B],
EN [auth B],
FB [auth G],
FD [auth H],
FF [auth a],
FG [auth a],
FI [auth b],
FK [auth A],
FL [auth A],
FM [auth B],
FN [auth B],
GB [auth G],
GD [auth H],
GF [auth a],
GG [auth a],
GI [auth b],
GK [auth A],
GL [auth A],
GM [auth B],
GN [auth B],
HD [auth H],
HF [auth a],
HG [auth a],
HH [auth b],
HI [auth b],
HK [auth A],
HL [auth A],
HM [auth B],
IB [auth G],
ID [auth H],
IF [auth a],
IG [auth a],
IH [auth b],
II [auth b],
IK [auth A],
IL [auth A],
IM [auth B],
IN [auth B],
IO [auth K],
JB [auth G],
JD [auth H],
JF [auth a],
JG [auth a],
JH [auth b],
JI [auth b],
JK [auth A],
JL [auth A],
JM [auth B],
JN [auth B],
KB [auth G],
KD [auth H],
KF [auth a],
KG [auth a],
KH [auth b],
KI [auth b],
KK [auth A],
KL [auth A],
KN [auth B],
KO [auth L],
LA [auth G],
LB [auth G],
LD [auth H],
LF [auth a],
LG [auth a],
LH [auth b],
LI [auth b],
LK [auth A],
LL [auth A],
LM [auth B],
LN [auth B],
LO [auth L],
MA [auth G],
MB [auth G],
MD [auth H],
MF [auth a],
MG [auth a],
MH [auth b],
MI [auth b],
MK [auth A],
ML [auth A],
MM [auth B],
MN [auth B],
MO [auth L],
NA [auth G],
NB [auth G],
NC [auth H],
ND [auth H],
NF [auth a],
NG [auth a],
NH [auth b],
NK [auth A],
NL [auth A],
NM [auth B],
NN [auth B],
OA [auth G],
OB [auth G],
OC [auth H],
OD [auth H],
OF [auth a],
OG [auth a],
OH [auth b],
OI [auth b],
OJ [auth k],
OK [auth A],
OL [auth A],
OM [auth B],
PA [auth G],
PB [auth G],
PC [auth H],
PD [auth H],
PF [auth a],
PG [auth a],
PH [auth b],
PI [auth b],
PK [auth A],
PM [auth B],
QA [auth G],
QB [auth G],
QC [auth H],
QD [auth H],
QF [auth a],
QG [auth a],
QI [auth b],
QJ [auth l],
QK [auth A],
QM [auth B],
QN [auth B],
RA [auth G],
RB [auth G],
RC [auth H],
RD [auth H],
RF [auth a],
RG [auth a],
RH [auth b],
RI [auth b],
RJ [auth l],
RK [auth A],
RM [auth B],
RO [auth X],
SA [auth G],
SB [auth G],
SC [auth H],
SD [auth H],
SF [auth a],
SG [auth a],
SH [auth b],
SI [auth b],
SJ [auth l],
SK [auth A],
SM [auth B],
TA [auth G],
TB [auth G],
TC [auth H],
TF [auth a],
TG [auth a],
TH [auth b],
TI [auth b],
TK [auth A],
TM [auth B],
UA [auth G],
UB [auth G],
UC [auth H],
UD [auth H],
UE [auth T],
UF [auth a],
UG [auth a],
UH [auth b],
UK [auth A],
UM [auth B],
VA [auth G],
VB [auth G],
VC [auth H],
VD [auth H],
VF [auth a],
VH [auth b],
VM [auth B],
WA [auth G],
WB [auth G],
WD [auth H],
WE [auth U],
WF [auth a],
WH [auth b],
WI [auth b],
WK [auth A],
WM [auth B],
XA [auth G],
XB [auth G],
XC [auth H],
XD [auth H],
XE [auth U],
XF [auth a],
XH [auth b],
XJ [auth x],
XK [auth A],
XM [auth B],
YA [auth G],
YB [auth G],
YC [auth H],
YD [auth H],
YE [auth U],
YF [auth a],
YH [auth b],
YK [auth A],
YM [auth B],
ZA [auth G],
ZB [auth G],
ZC [auth H],
ZD [auth H],
ZF [auth a],
ZH [auth b],
ZJ [auth A],
ZK [auth A],
ZM [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



Download:Ideal Coordinates CCD File
EF [auth a],
KA [auth G],
YJ [auth A]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG



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BF [auth U]
BO [auth B]
EH [auth a]
HJ [auth b]
HO [auth I]
BF [auth U],
BO [auth B],
EH [auth a],
HJ [auth b],
HO [auth I],
KC [auth G],
NE [auth H],
NJ [auth i],
PO [auth L],
TE [auth R],
VJ [auth l],
YL [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



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CO [auth B]
DH [auth a]
IJ [auth b]
JC [auth G]
OE [auth H]
CO [auth B],
DH [auth a],
IJ [auth b],
JC [auth G],
OE [auth H],
XL [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR



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AF [auth U]
AH [auth a]
AJ [auth b]
AO [auth B]
BH [auth a]
AF [auth U],
AH [auth a],
AJ [auth b],
AO [auth B],
BH [auth a],
BJ [auth b],
CF [auth V],
CH [auth a],
CJ [auth b],
DC [auth G],
DJ [auth b],
EC [auth G],
EE [auth H],
EJ [auth b],
FC [auth G],
FE [auth H],
FJ [auth b],
FO [auth I],
GC [auth G],
GE [auth H],
GJ [auth b],
GO [auth I],
HC [auth G],
HE [auth H],
IC [auth G],
IE [auth H],
JE [auth H],
KE [auth H],
LE [auth H],
LJ [auth i],
ME [auth H],
MJ [auth i],
NO [auth L],
OO [auth L],
QO [auth M],
RE [auth R],
RL [auth A],
SE [auth R],
SL [auth A],
SN [auth B],
TJ [auth l],
TL [auth A],
TN [auth B],
UJ [auth l],
UL [auth A],
UN [auth B],
VL [auth A],
VN [auth B],
WJ [auth m],
WL [auth A],
WN [auth B],
XG [auth a],
XN [auth B],
YG [auth a],
YI [auth b],
YN [auth B],
ZE [auth U],
ZG [auth a],
ZI [auth b],
ZN [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



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AM [auth A]
FH [auth a]
GH [auth a]
LC [auth G]
MC [auth G]
AM [auth A],
FH [auth a],
GH [auth a],
LC [auth G],
MC [auth G],
ZL [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN



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BC [auth G]
DE [auth H]
PL [auth A]
RN [auth B]
VG [auth a]
BC [auth G],
DE [auth H],
PL [auth A],
RN [auth B],
VG [auth a],
XI [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
CC [auth G]
DO [auth C]
EO [auth C]
JJ [auth c]
KJ [auth c]
CC [auth G],
DO [auth C],
EO [auth C],
JJ [auth c],
KJ [auth c],
PE [auth N],
QE [auth N],
QL [auth A],
WG [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
JO [auth L],
PJ [auth l],
VE [auth U]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary