6TRC

Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of cytochrome c6

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I

Koelsch, A., Radon, C., Golub, M., Baumert, A., Burger, J., Miehlke, T., Lisdat, F., Feoktystov, A., Pieper, J., Zouni, A., Wendler, P.

(2020) Curr Opin Struct Biol 2: 171-179


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
M [auth a],
Y [auth 1]		755Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A405 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
N [auth b],
Z [auth 2]		741Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A407 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerAA [auth 3],
C,
O [auth c]		81Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A415 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIBA [auth 4],
D,
P [auth d]		139Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A420 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth 5],
E,
Q [auth e]		76Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A423 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIDA [auth 6],
F,
R [auth f]		141Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A401 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIEA [auth 7],
G [auth I],
S [auth i]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A427 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth 8],
H [auth J],
T [auth j]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A429 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth 9],
I [auth K],
U [auth k]		83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A425 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIHA [auth 0],
J [auth L],
V [auth l]		155Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DGB4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth y],
K [auth M],
W [auth m]		31Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A403 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I 4.8K proteinJA [auth z],
L [auth X],
X [auth x]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKP6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA
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AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AG [auth a]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth B],
AG [auth a],
AH [auth a],
AI [auth b],
AJ [auth b],
AL [auth 1],
AM [auth 1],
AN [auth 2],
AO [auth 2],
BB [auth A],
BC [auth A],
BD [auth B],
BE [auth B],
BF [auth K],
BG [auth a],
BH [auth a],
BI [auth b],
BJ [auth b],
BL [auth 1],
BM [auth 1],
BN [auth 2],
BO [auth 2],
BP [auth 8],
CB [auth A],
CD [auth B],
CE [auth B],
CF [auth K],
CG [auth a],
CH [auth a],
CI [auth b],
CJ [auth b],
CL [auth 1],
CM [auth 1],
CN [auth 2],
CO [auth 2],
CP [auth 8],
DB [auth A],
DD [auth B],
DG [auth a],
DH [auth a],
DI [auth b],
DJ [auth b],
DK [auth k],
DL [auth 1],
DM [auth 1],
DN [auth 2],
DO [auth 2],
EB [auth A],
ED [auth B],
EF [auth L],
EG [auth a],
EH [auth a],
EI [auth b],
EJ [auth b],
EK [auth k],
EL [auth 1],
EM [auth 1],
EN [auth 2],
EO [auth 2],
FB [auth A],
FD [auth B],
FG [auth a],
FH [auth a],
FI [auth b],
FJ [auth b],
FL [auth 1],
FM [auth 1],
FN [auth 2],
FO [auth 2],
FP [auth 9],
GB [auth A],
GD [auth B],
GF [auth L],
GG [auth a],
GI [auth b],
GL [auth 1],
GM [auth 1],
GN [auth 2],
GO [auth 2],
HB [auth A],
HD [auth B],
HF [auth L],
HG [auth a],
HI [auth b],
HL [auth 1],
HM [auth 1],
HN [auth 2],
HO [auth 2],
HP [auth 9],
IB [auth A],
ID [auth B],
IF [auth L],
IG [auth a],
II [auth b],
IK [auth l],
IL [auth 1],
IM [auth 1],
IN [auth 2],
IO [auth 2],
JB [auth A],
JD [auth B],
JG [auth a],
JI [auth b],
JL [auth 1],
JM [auth 1],
JN [auth 2],
KB [auth A],
KD [auth B],
KG [auth a],
KI [auth b],
KL [auth 1],
KN [auth 2],
LA [auth A],
LB [auth A],
LD [auth B],
LG [auth a],
LI [auth b],
LK [auth l],
LL [auth 1],
LN [auth 2],
LP [auth 0],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth B],
MF [auth M],
MG [auth a],
MI [auth b],
MK [auth l],
ML [auth 1],
MN [auth 2],
MP [auth 0],
NA [auth A],
NB [auth A],
ND [auth B],
NG [auth a],
NI [auth b],
NK [auth l],
NL [auth 1],
NN [auth 2],
OA [auth A],
OB [auth A],
OD [auth B],
OF [auth X],
OG [auth a],
OI [auth b],
OL [auth 1],
ON [auth 2],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PG [auth a],
PI [auth b],
PL [auth 1],
PN [auth 2],
PP [auth 0],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth F],
QF [auth a],
QG [auth a],
QI [auth b],
QL [auth 1],
QN [auth 2],
QP [auth 0],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth a],
RG [auth a],
RI [auth b],
RJ [auth f],
RK [auth x],
RL [auth 1],
RN [auth 2],
RP [auth 0],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth F],
SF [auth a],
SG [auth a],
SH [auth b],
SI [auth b],
SL [auth 1],
SN [auth 2],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TE [auth F],
TF [auth a],
TG [auth a],
TH [auth b],
TI [auth b],
TJ [auth f],
TK [auth 1],
TL [auth 1],
TN [auth 2],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth a],
UG [auth a],
UH [auth b],
UI [auth b],
UJ [auth f],
UK [auth 1],
UL [auth 1],
UN [auth 2],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VF [auth a],
VG [auth a],
VH [auth b],
VI [auth b],
VK [auth 1],
VL [auth 1],
VM [auth 2],
VN [auth 2],
VO [auth 6],
VP [auth z],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WF [auth a],
WG [auth a],
WH [auth b],
WI [auth b],
WK [auth 1],
WL [auth 1],
WM [auth 2],
WN [auth 2],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XE [auth J],
XF [auth a],
XG [auth a],
XH [auth b],
XI [auth b],
XJ [auth j],
XK [auth 1],
XL [auth 1],
XM [auth 2],
XN [auth 2],
XO [auth 6],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YE [auth J],
YF [auth a],
YG [auth a],
YH [auth b],
YI [auth b],
YJ [auth j],
YK [auth 1],
YL [auth 1],
YM [auth 2],
YN [auth 2],
YO [auth 6],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZF [auth a],
ZG [auth a],
ZH [auth b],
ZI [auth b],
ZJ [auth j],
ZK [auth 1],
ZL [auth 1],
ZM [auth 2],
ZN [auth 2]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0
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KA [auth A],
PF [auth a],
SK [auth 1]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG
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KE [auth B],
NJ [auth b],
QO [auth 2]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
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GK [auth l]
HK [auth l]
JP [auth 0]
KC [auth A]
KF [auth L]
GK [auth l],
HK [auth l],
JP [auth 0],
KC [auth A],
KF [auth L],
KP [auth 0],
LC [auth A],
LE [auth B],
LF [auth L],
OH [auth a],
OJ [auth b],
PH [auth a],
RM [auth 1],
RO [auth 2],
SM [auth 1]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR
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AF [auth J]
AK [auth j]
AP [auth 7]
BK [auth j]
CK [auth j]
AF [auth J],
AK [auth j],
AP [auth 7],
BK [auth j],
CK [auth j],
DC [auth A],
DF [auth K],
DP [auth 8],
EC [auth A],
EE [auth B],
EP [auth 8],
FC [auth A],
FE [auth B],
FK [auth k],
GC [auth A],
GE [auth B],
GP [auth 9],
HC [auth A],
HE [auth B],
HH [auth a],
HJ [auth b],
IC [auth A],
IE [auth B],
IH [auth a],
IJ [auth b],
IP [auth 9],
JC [auth A],
JE [auth B],
JF [auth L],
JH [auth a],
JJ [auth b],
JK [auth l],
KH [auth a],
KJ [auth b],
KO [auth 2],
LH [auth a],
LJ [auth b],
LM [auth 1],
LO [auth 2],
ME [auth B],
MH [auth a],
MJ [auth b],
MM [auth 1],
MO [auth 2],
NE [auth B],
NF [auth M],
NH [auth a],
NM [auth 1],
NO [auth 2],
NP [auth 0],
OK [auth l],
OM [auth 1],
OO [auth 2],
PK [auth l],
PM [auth 1],
PO [auth 2],
QK [auth m],
QM [auth 1],
RE [auth F],
SJ [auth f],
SO [auth 2],
SP [auth 0],
TP [auth 0],
UE [auth F],
UP [auth y],
VE [auth I],
VJ [auth f],
WE [auth I],
WJ [auth i],
WO [auth 6],
ZE [auth J],
ZO [auth 6]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN
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CC [auth A]
DE [auth B]
GH [auth a]
GJ [auth b]
JO [auth 2]
CC [auth A],
DE [auth B],
GH [auth a],
GJ [auth b],
JO [auth 2],
KM [auth 1]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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NC [auth B]
OE [auth C]
PE [auth C]
PJ [auth c]
QH [auth b]
NC [auth B],
OE [auth C],
PE [auth C],
PJ [auth c],
QH [auth b],
QJ [auth c],
TM [auth 2],
TO [auth 3],
UO [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA
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FF [auth L]
KK [auth l]
OC [auth B]
OP [auth 0]
RH [auth b]
FF [auth L],
KK [auth l],
OC [auth B],
OP [auth 0],
RH [auth b],
UM [auth 2]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME		EA [auth 7],
G [auth I],
S [auth i]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2008/1
German Research Foundation (DFG)GermanyEXC 314/2
German Federal Ministry for Education and ResearchGermany031B0557 A+B

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release