PDB-8wql: In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis

Basic information

• Entry: Database: PDB / ID: 8wql
• Title: In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis

Components

• (Allophycocyanin ...) x 3
• (Cytochrome b559 subunit ...) x 2
• (Photosystem II ...) x 17
• Allophycocyanin-B alpha subunit
• C-phycocyanin alpha subunit
• LCM
• LPP1
• LPP2
• LRC1
• Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
• Phycocyanin beta subunit
• PsbQ protein
• PsbU

• Keywords: PHOTOSYNTHESIS / complex

Function / homology

Function:

phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis

Domain/homology:

Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily

Component:

BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / PHYCOCYANOBILIN / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / Phycocyanin beta subunit

• Biological species: Arthrospira sp. FACHB-439 (bacteria)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
• Authors: You, X. / Zhang, X. / Xiao, Y.N. / Sun, S. / Sui, S.F.

Funding support

1items

Organization	Grant number	Country
Not funded

• Citation: Journal: To Be Published; Title: Structure of in situ PBS-PSII supercomplex at 3.5 Angstroms resolution.; Authors: You, X. / Zhang, X. / Xiao, Y.N. / Sun, S. / Sui, S.F.

History

Deposition	Oct 11, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 31, 2024	Provider: repository / Type: Initial release

Assembly

Deposited unit

BA: LRC1

BB: LCM

CB: LCM

OB: Allophycocyanin alpha chain

PB: Allophycocyanin beta chain

QB: Allophycocyanin alpha chain

RB: Allophycocyanin beta chain

SB: Allophycocyanin alpha chain

TB: Allophycocyanin beta chain

UB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

VB: Allophycocyanin alpha chain

WB: Allophycocyanin beta chain

XB: Allophycocyanin alpha chain

YB: Allophycocyanin beta chain

ZB: Allophycocyanin alpha chain

BC: LRC1

AD: Photosystem II protein D1

BD: Photosystem II CP47 reaction center protein

CD: Photosystem II CP43 reaction center protein

DD: Photosystem II D2 protein

ED: Cytochrome b559 subunit alpha

FD: Cytochrome b559 subunit beta

HD: Photosystem II reaction center protein H

ID: Photosystem II reaction center protein I

JD: Photosystem II reaction center protein J

KD: Photosystem II reaction center protein K

LD: Photosystem II reaction center protein L

MD: Photosystem II reaction center protein M

OD: Photosystem II extrinsic protein O

QD: PsbQ protein

RD: Photosystem II reaction center protein Y

SD: LPP1

TD: Photosystem II reaction center protein T

UD: PsbU

VD: Photosystem II extrinsic protein V

XD: Photosystem II reaction center protein X

YD: Photosystem II reaction center protein Psb30

ZD: Photosystem II reaction center protein Z

AE: Photosystem II protein D1

BE: Photosystem II CP47 reaction center protein

CE: Photosystem II CP43 reaction center protein

DE: Photosystem II D2 protein

EE: Cytochrome b559 subunit alpha

FE: Cytochrome b559 subunit beta

HE: Photosystem II reaction center protein H

IE: Photosystem II reaction center protein I

JE: Photosystem II reaction center protein J

KE: Photosystem II reaction center protein K

LE: Photosystem II reaction center protein L

ME: Photosystem II reaction center protein M

OE: Photosystem II extrinsic protein O

QE: PsbQ protein

RE: Photosystem II reaction center protein Y

SE: LPP1

TE: Photosystem II reaction center protein T

UE: PsbU

VE: Photosystem II extrinsic protein V

XE: Photosystem II reaction center protein X

YE: Photosystem II reaction center protein Psb30

ZE: Photosystem II reaction center protein Z

EF: LPP2

IF: Allophycocyanin beta chain

JF: Allophycocyanin alpha chain

KF: Allophycocyanin beta chain

LF: Allophycocyanin alpha chain

MF: Allophycocyanin beta chain

NF: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

XF: Allophycocyanin alpha chain

YF: Allophycocyanin beta chain

ZF: Allophycocyanin alpha chain

AG: Allophycocyanin alpha chain

BG: LPP2

GG: Allophycocyanin alpha chain

HG: Allophycocyanin beta chain

IG: Allophycocyanin alpha chain

JG: Allophycocyanin beta chain

KG: Allophycocyanin alpha chain

LG: Allophycocyanin beta chain

MG: Allophycocyanin beta chain

NG: Allophycocyanin alpha chain

OG: Allophycocyanin beta chain

PG: Allophycocyanin alpha chain

QG: Allophycocyanin beta-18 subunit

RG: Allophycocyanin alpha chain

SG: Allophycocyanin beta chain

TG: Allophycocyanin alpha chain

UG: Allophycocyanin beta chain

VG: Allophycocyanin-B alpha subunit

WG: Allophycocyanin beta chain

BH: LRC1

BI: LRC1

BJ: LRC1

EK: LPP2

IK: Allophycocyanin beta chain

JK: Allophycocyanin alpha chain

KK: Allophycocyanin beta chain

LK: Allophycocyanin alpha chain

MK: Allophycocyanin beta chain

NK: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

XK: Allophycocyanin alpha chain

YK: Allophycocyanin beta chain

ZK: Allophycocyanin alpha chain

AL: Allophycocyanin alpha chain

BL: LPP2

GL: Allophycocyanin alpha chain

HL: Allophycocyanin beta chain

IL: Allophycocyanin alpha chain

JL: Allophycocyanin beta chain

KL: Allophycocyanin alpha chain

LL: Allophycocyanin beta chain

ML: Allophycocyanin beta chain

NL: Allophycocyanin alpha chain

OL: Allophycocyanin beta chain

PL: Allophycocyanin alpha chain

QL: Allophycocyanin beta-18 subunit

RL: Allophycocyanin alpha chain

SL: Allophycocyanin beta chain

TL: Allophycocyanin alpha chain

UL: Allophycocyanin beta chain

VL: Allophycocyanin-B alpha subunit

WL: Allophycocyanin beta chain

A1: Photosystem II protein D1

B1: Photosystem II CP47 reaction center protein

C1: Photosystem II CP43 reaction center protein

D1: Photosystem II D2 protein

E1: Cytochrome b559 subunit alpha

F1: Cytochrome b559 subunit beta

H1: Photosystem II reaction center protein H

I1: Photosystem II reaction center protein I

J1: Photosystem II reaction center protein J

K1: Photosystem II reaction center protein K

L1: Photosystem II reaction center protein L

M1: Photosystem II reaction center protein M

O1: Photosystem II extrinsic protein O

Q1: PsbQ protein

R1: Photosystem II reaction center protein Y

T1: Photosystem II reaction center protein T

U1: PsbU

V1: Photosystem II extrinsic protein V

X1: Photosystem II reaction center protein X

Y1: Photosystem II reaction center protein Psb30

Z1: Photosystem II reaction center protein Z

a1: Photosystem II protein D1

b1: Photosystem II CP47 reaction center protein

c1: Photosystem II CP43 reaction center protein

d1: Photosystem II D2 protein

e1: Cytochrome b559 subunit alpha

f1: Cytochrome b559 subunit beta

h1: Photosystem II reaction center protein H

i1: Photosystem II reaction center protein I

j1: Photosystem II reaction center protein J

k1: Photosystem II reaction center protein K

l1: Photosystem II reaction center protein L

m1: Photosystem II reaction center protein M

o1: Photosystem II extrinsic protein O

q1: PsbQ protein

r1: Photosystem II reaction center protein Y

S1: LPP1

t1: Photosystem II reaction center protein T

u1: PsbU

v1: Photosystem II extrinsic protein V

x1: Photosystem II reaction center protein X

y1: Photosystem II reaction center protein Psb30

z1: Photosystem II reaction center protein Z

b2: C-phycocyanin alpha subunit

c2: Phycocyanin beta subunit

d2: C-phycocyanin alpha subunit

e2: Phycocyanin beta subunit

f2: C-phycocyanin alpha subunit

g2: Phycocyanin beta subunit

h2: C-phycocyanin alpha subunit

i2: Phycocyanin beta subunit

j2: C-phycocyanin alpha subunit

k2: Phycocyanin beta subunit

l2: C-phycocyanin alpha subunit

m2: Phycocyanin beta subunit

B2: LRC1

b3: C-phycocyanin alpha subunit

c3: Phycocyanin beta subunit

d3: C-phycocyanin alpha subunit

e3: Phycocyanin beta subunit

f3: C-phycocyanin alpha subunit

g3: Phycocyanin beta subunit

h3: C-phycocyanin alpha subunit

i3: Phycocyanin beta subunit

j3: C-phycocyanin alpha subunit

k3: Phycocyanin beta subunit

l3: C-phycocyanin alpha subunit

m3: Phycocyanin beta subunit

B3: LRC1

Z4: Allophycocyanin alpha chain

a4: Allophycocyanin beta chain

b4: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

S4: Allophycocyanin alpha chain

T4: Allophycocyanin beta chain

U4: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

V4: Allophycocyanin alpha chain

W4: Allophycocyanin beta chain

X4: Allophycocyanin alpha chain

Y4: Allophycocyanin beta chain

s4: Allophycocyanin alpha chain

t4: Allophycocyanin beta chain

u4: Allophycocyanin alpha chain

v4: Allophycocyanin beta chain

w4: Allophycocyanin alpha chain

o4: Allophycocyanin alpha chain

p4: Allophycocyanin beta chain

q4: Allophycocyanin alpha chain

r4: Allophycocyanin beta chain

x4: Allophycocyanin beta chain

y4: Allophycocyanin alpha chain

z4: Allophycocyanin beta chain

B4: LCM

C4: LCM

O4: Allophycocyanin alpha chain

P4: Allophycocyanin beta chain

Q4: Allophycocyanin alpha chain

R4: Allophycocyanin beta chain

B5: LRC1

b5: C-phycocyanin alpha subunit

c5: Phycocyanin beta subunit

d5: C-phycocyanin alpha subunit

e5: Phycocyanin beta subunit

f5: C-phycocyanin alpha subunit

g5: Phycocyanin beta subunit

h5: C-phycocyanin alpha subunit

i5: Phycocyanin beta subunit

j5: C-phycocyanin alpha subunit

k5: Phycocyanin beta subunit

l5: C-phycocyanin alpha subunit

m5: Phycocyanin beta subunit

b6: C-phycocyanin alpha subunit

c6: Phycocyanin beta subunit

d6: C-phycocyanin alpha subunit

e6: Phycocyanin beta subunit

f6: C-phycocyanin alpha subunit

g6: Phycocyanin beta subunit

h6: C-phycocyanin alpha subunit

i6: Phycocyanin beta subunit

j6: C-phycocyanin alpha subunit

k6: Phycocyanin beta subunit

l6: C-phycocyanin alpha subunit

m6: Phycocyanin beta subunit

B6: LRC1

b7: C-phycocyanin alpha subunit

c7: Phycocyanin beta subunit

d7: C-phycocyanin alpha subunit

e7: Phycocyanin beta subunit

f7: C-phycocyanin alpha subunit

g7: Phycocyanin beta subunit

h7: C-phycocyanin alpha subunit

i7: Phycocyanin beta subunit

j7: C-phycocyanin alpha subunit

k7: Phycocyanin beta subunit

l7: C-phycocyanin alpha subunit

m7: Phycocyanin beta subunit

B7: LRC1

B8: LRC1

b8: C-phycocyanin alpha subunit

c8: Phycocyanin beta subunit

d8: C-phycocyanin alpha subunit

e8: Phycocyanin beta subunit

f8: C-phycocyanin alpha subunit

g8: Phycocyanin beta subunit

h8: C-phycocyanin alpha subunit

i8: Phycocyanin beta subunit

j8: C-phycocyanin alpha subunit

k8: Phycocyanin beta subunit

l8: C-phycocyanin alpha subunit

m8: Phycocyanin beta subunit

b9: C-phycocyanin alpha subunit

c9: Phycocyanin beta subunit

d9: C-phycocyanin alpha subunit

e9: Phycocyanin beta subunit

f9: C-phycocyanin alpha subunit

g9: Phycocyanin beta subunit

h9: C-phycocyanin alpha subunit

i9: Phycocyanin beta subunit

j9: C-phycocyanin alpha subunit

k9: Phycocyanin beta subunit

l9: C-phycocyanin alpha subunit

m9: Phycocyanin beta subunit

B9: LRC1

bA: C-phycocyanin alpha subunit

cA: Phycocyanin beta subunit

dA: C-phycocyanin alpha subunit

eA: Phycocyanin beta subunit

fA: C-phycocyanin alpha subunit

gA: Phycocyanin beta subunit

hA: C-phycocyanin alpha subunit

iA: Phycocyanin beta subunit

jA: C-phycocyanin alpha subunit

kA: Phycocyanin beta subunit

lA: C-phycocyanin alpha subunit

mA: Phycocyanin beta subunit

aB: Allophycocyanin beta chain

bB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

sB: Allophycocyanin alpha chain

tB: Allophycocyanin beta chain

uB: Allophycocyanin alpha chain

vB: Allophycocyanin beta chain

wB: Allophycocyanin alpha chain

oB: Allophycocyanin alpha chain

pB: Allophycocyanin beta chain

qB: Allophycocyanin alpha chain

rB: Allophycocyanin beta chain

xB: Allophycocyanin beta chain

yB: Allophycocyanin alpha chain

zB: Allophycocyanin beta chain

bC: C-phycocyanin alpha subunit

cC: Phycocyanin beta subunit

dC: C-phycocyanin alpha subunit

eC: Phycocyanin beta subunit

fC: C-phycocyanin alpha subunit

gC: Phycocyanin beta subunit

hC: C-phycocyanin alpha subunit

iC: Phycocyanin beta subunit

jC: C-phycocyanin alpha subunit

kC: Phycocyanin beta subunit

lC: C-phycocyanin alpha subunit

mC: Phycocyanin beta subunit

aD: Photosystem II protein D1

bD: Photosystem II CP47 reaction center protein

cD: Photosystem II CP43 reaction center protein

dD: Photosystem II D2 protein

eD: Cytochrome b559 subunit alpha

fD: Cytochrome b559 subunit beta

hD: Photosystem II reaction center protein H

iD: Photosystem II reaction center protein I

jD: Photosystem II reaction center protein J

kD: Photosystem II reaction center protein K

lD: Photosystem II reaction center protein L

mD: Photosystem II reaction center protein M

oD: Photosystem II extrinsic protein O

qD: PsbQ protein

rD: Photosystem II reaction center protein Y

tD: Photosystem II reaction center protein T

uD: PsbU

vD: Photosystem II extrinsic protein V

xD: Photosystem II reaction center protein X

yD: Photosystem II reaction center protein Psb30

zD: Photosystem II reaction center protein Z

aE: Photosystem II protein D1

bE: Photosystem II CP47 reaction center protein

cE: Photosystem II CP43 reaction center protein

dE: Photosystem II D2 protein

eE: Cytochrome b559 subunit alpha

fE: Cytochrome b559 subunit beta

hE: Photosystem II reaction center protein H

iE: Photosystem II reaction center protein I

jE: Photosystem II reaction center protein J

kE: Photosystem II reaction center protein K

lE: Photosystem II reaction center protein L

mE: Photosystem II reaction center protein M

oE: Photosystem II extrinsic protein O

qE: PsbQ protein

rE: Photosystem II reaction center protein Y

tE: Photosystem II reaction center protein T

uE: PsbU

vE: Photosystem II extrinsic protein V

xE: Photosystem II reaction center protein X

yE: Photosystem II reaction center protein Psb30

zE: Photosystem II reaction center protein Z

aF: Allophycocyanin beta chain

bF: Allophycocyanin alpha chain

cF: Allophycocyanin beta chain

dF: Allophycocyanin alpha chain

eF: Allophycocyanin beta chain

3F: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

fF: Allophycocyanin alpha chain

gF: Allophycocyanin beta-18 subunit

hF: Allophycocyanin beta chain

iF: Allophycocyanin alpha chain

jF: Allophycocyanin beta chain

kF: Allophycocyanin alpha chain

lF: Allophycocyanin beta chain

mF: Allophycocyanin-B alpha subunit

nF: Allophycocyanin beta chain

9F: Allophycocyanin alpha chain

2G: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

1G: Allophycocyanin beta chain

4G: Allophycocyanin alpha chain

5G: Allophycocyanin beta chain

6G: Allophycocyanin alpha chain

7G: Allophycocyanin beta chain

8G: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

bH: C-phycocyanin alpha subunit

cH: Phycocyanin beta subunit

dH: C-phycocyanin alpha subunit

eH: Phycocyanin beta subunit

fH: C-phycocyanin alpha subunit

gH: Phycocyanin beta subunit

hH: C-phycocyanin alpha subunit

iH: Phycocyanin beta subunit

jH: C-phycocyanin alpha subunit

kH: Phycocyanin beta subunit

lH: C-phycocyanin alpha subunit

mH: Phycocyanin beta subunit

bI: C-phycocyanin alpha subunit

cI: Phycocyanin beta subunit

dI: C-phycocyanin alpha subunit

eI: Phycocyanin beta subunit

fI: C-phycocyanin alpha subunit

gI: Phycocyanin beta subunit

hI: C-phycocyanin alpha subunit

iI: Phycocyanin beta subunit

jI: C-phycocyanin alpha subunit

kI: Phycocyanin beta subunit

lI: C-phycocyanin alpha subunit

mI: Phycocyanin beta subunit

bJ: C-phycocyanin alpha subunit

cJ: Phycocyanin beta subunit

dJ: C-phycocyanin alpha subunit

eJ: Phycocyanin beta subunit

fJ: C-phycocyanin alpha subunit

gJ: Phycocyanin beta subunit

hJ: C-phycocyanin alpha subunit

iJ: Phycocyanin beta subunit

jJ: C-phycocyanin alpha subunit

kJ: Phycocyanin beta subunit

lJ: C-phycocyanin alpha subunit

mJ: Phycocyanin beta subunit

aK: Allophycocyanin beta chain

bK: Allophycocyanin alpha chain

cK: Allophycocyanin beta chain

dK: Allophycocyanin alpha chain

eK: Allophycocyanin beta chain

3K: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

fK: Allophycocyanin alpha chain

gK: Allophycocyanin beta-18 subunit

hK: Allophycocyanin beta chain

iK: Allophycocyanin alpha chain

jK: Allophycocyanin beta chain

kK: Allophycocyanin alpha chain

lK: Allophycocyanin beta chain

mK: Allophycocyanin-B alpha subunit

nK: Allophycocyanin beta chain

9K: Allophycocyanin alpha chain

2L: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

1L: Allophycocyanin beta chain

4L: Allophycocyanin alpha chain

5L: Allophycocyanin beta chain

6L: Allophycocyanin alpha chain

7L: Allophycocyanin beta chain

8L: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

hetero molecules

Summary:

• 8.52 MDa, 445 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,522,496	1327
Polymers	7,937,928	445
Non-polymers	584,569	882
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author&software
• Evidence: electron microscopy, not applicable

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Components

Protein , 9 types, 192 molecules BA BC BH BI BJ B2 B3 B5 B6 B7 B8 B9 BB CB B4 C4 UB NF NK b4 U4 bB 3F 2G 8G 3K 2L 8L QD QE ...

#1: Protein

BA BC BH BI BJ B2 B3 B5 B6 B7 B8 B9
LRC1

Details:

Mass: 29443.213 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)

#2: Protein

BB CB B4 C4
LCM

Details:

Mass: 102100.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)

#5: Protein

UB NF NK b4 U4 bB 3F 2G 8G 3K 2L 8L
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

Details:

Mass: 7775.107 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcC / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZBQ2

#19: Protein

QD QE Q1 q1 qD qE
PsbQ protein

Details:

Mass: 18641.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbQ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZQ11

#23: Protein

UD UE U1 u1 uD uE
PsbU

Details:

Mass: 10733.153 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)

#28: Protein

EF BG EK BL
LPP2

Details:

Mass: 15788.175 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZJ52

#30: Protein

VG VL mF mK
Allophycocyanin-B alpha subunit

Details:

Mass: 18022.709 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcD / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZH43

#31: Protein

b2 d2 f2 h2 j2 l2 b3 d3 f3 h3 j3 l3 b5 d5 f5 h5 j5 l5 b6 ...
C-phycocyanin alpha subunit

Details:

Mass: 17616.848 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: cpcA / Production host: Arthrospira sp. FACHB-439 (bacteria)

#32: Protein

c2 e2 g2 i2 k2 m2 c3 e3 g3 i3 k3 m3 c5 e5 g5 i5 k5 m5 c6 ...
Phycocyanin beta subunit

Details:

Mass: 18062.441 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: cpcB / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A9UKJ0

Allophycocyanin ... , 3 types, 136 molecules OB QB SB VB XB ZB JF LF XF ZF AG GG IG KG NG PG RG TG JK LK XK ZK AL GL IL KL NL PL RL TL ...

#3: Protein

OB QB SB VB XB ZB JF LF XF ZF AG GG IG KG NG PG RG TG JK ...
Allophycocyanin alpha chain

Details:

Mass: 17409.799 Da / Num. of mol.: 64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcA / Production host: Arthrospira sp. FACHB-439 (bacteria)

#4: Protein

PB RB TB WB YB IF KF MF YF HG JG LG MG OG SG UG WG IK KK ...
Allophycocyanin beta chain

Details:

Mass: 17345.748 Da / Num. of mol.: 68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcB / Production host: Arthrospira sp. FACHB-439 (bacteria)

#29: Protein

QG QL gF gK
Allophycocyanin beta-18 subunit

Details:

Mass: 18446.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcF / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZN25

Photosystem II ... , 17 types, 102 molecules AD AE A1 a1 aD aE BD BE B1 b1 bD bE CD CE C1 c1 cD cE DD DE D1 d1 dD dE HD HE H1 h1 hD hE ...

#6: Protein

AD AE A1 a1 aD aE
Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein

Details:

Mass: 39675.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbA1 / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4ENJ6, photosystem II

#7: Protein

BD BE B1 b1 bD bE
Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47

Details:

Mass: 56256.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbB / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP29

#8: Protein

CD CE C1 c1 cD cE
Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43

Details:

Mass: 51545.973 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbC / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EL13

#9: Protein

DD DE D1 d1 dD dE
Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein

Details:

Mass: 39521.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbD1, psbD / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EL11, photosystem II

#12: Protein

HD HE H1 h1 hD hE
Photosystem II reaction center protein H / PSII-H

Details:

Mass: 7636.935 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbH / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZFR1

#13: Protein/peptide

ID IE I1 i1 iD iE
Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein

Details:

Mass: 4414.285 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbI / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EN47

#14: Protein/peptide

JD JE J1 j1 jD jE
Photosystem II reaction center protein J / PSII-J

Details:

Mass: 3914.632 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbJ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZEX7

#15: Protein/peptide

KD KE K1 k1 kD kE
Photosystem II reaction center protein K / PSII-K

Details:

Mass: 4979.012 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbK / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP73

#16: Protein/peptide

LD LE L1 l1 lD lE
Photosystem II reaction center protein L / PSII-L

Details:

Mass: 4581.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbL / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZAC5

#17: Protein/peptide

MD ME M1 m1 mD mE
Photosystem II reaction center protein M / PSII-M

Details:

Mass: 4128.829 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbM / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZMZ9

#18: Protein

OD OE O1 o1 oD oE
Photosystem II extrinsic protein O / Photosystem II manganese-stabilizing polypeptide

Details:

Mass: 30064.770 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbO / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZRB6

#20: Protein/peptide

RD RE R1 r1 rD rE
Photosystem II reaction center protein Y

Details:

Mass: 4189.124 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbY / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZG21

#22: Protein/peptide

TD TE T1 t1 tD tE
Photosystem II reaction center protein T / PSII-T

Details:

Mass: 3439.182 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbTc, psbT / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP38

#24: Protein

VD VE V1 v1 vD vE
Photosystem II extrinsic protein V / PsbV / Cytochrome c-550 / Cytochrome c550 / Low-potential cytochrome c

Details:

Mass: 18165.770 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbV1, psbV / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4ELM7

#25: Protein/peptide

XD XE X1 x1 xD xE
Photosystem II reaction center protein X

Details:

Mass: 5427.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbX / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZPA1

#26: Protein/peptide

YD YE Y1 y1 yD yE
Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12

Details:

Mass: 4692.648 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psb30 / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZL09

#27: Protein

ZD ZE Z1 z1 zD zE
Photosystem II reaction center protein Z / PSII-Z

Details:

Mass: 6848.350 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbZ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZFP8

Cytochrome b559 subunit ... , 2 types, 12 molecules ED EE E1 e1 eD eE FD FE F1 f1 fD fE

#10: Protein

ED EE E1 e1 eD eE
Cytochrome b559 subunit alpha / PSII reaction center subunit V

Details:

Mass: 9344.573 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbE / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EIR1

#11: Protein/peptide

FD FE F1 f1 fD fE
Cytochrome b559 subunit beta / PSII reaction center subunit VI

Details:

Mass: 4994.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbF / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZAF8

Protein/peptide , 1 types, 3 molecules SD SE S1

#21: Protein/peptide

SD SE S1 LPP1

Details:

Mass: 4017.944 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)

Sugars , 2 types, 78 molecules

#40: Sugar

AD-409 AD-412 BD-619 BD-622 BD-623 CD-522 DD-404 DD-412 DD-413 AE-409 AE-412 BE-619 BE-622 BE-623 DE-404 DE-412 DE-413 A1-409 A1-413 B1-619 ...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE

Details:

Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM

#44: Sugar

CD-517 CD-518 HD-103 JD-101 CE-517 CE-518 HE-103 JE-101 C1-517 C1-518 H1-103 J1-101 c1-516 c1-517 c1-518 h1-104 cD-516 cD-517 cD-518 hD-104 ...
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)

Details:

Type: saccharide / Mass: 949.299 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₅₁H₉₆O₁₅

Non-polymers , 14 types, 804 molecules

#33: Chemical

BA-301 BB-1001 BB-1002 BB-1003 BB-1004 CB-1001 CB-1002 CB-1003 OB-201 PB-201 QB-201 RB-201 SB-201 TB-201 VB-201 WB-201 XB-201 ZB-201 BC-301 IF-201 ...
ChemComp-CYC / PHYCOCYANOBILIN

Details:

Mass: 588.694 Da / Num. of mol.: 348 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆

#34: Chemical

AD-401 AE-401 A1-401 a1-402 aD-401 aE-401
ChemComp-OEX / CA-MN4-O5 CLUSTER

Details:

Mass: 339.827 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CaMn₄O₅

#35: Chemical

AD-402 AD-403 AE-402 AE-403 A1-402 A1-403 a1-403 a1-404 aD-402 aD-403 aE-402 aE-403
ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl

#36: Chemical

AD-404 AD-405 BD-601 BD-602 BD-603 BD-604 BD-605 BD-606 BD-607 BD-608 BD-609 BD-610 BD-611 BD-612 BD-613 BD-614 CD-503 CD-504 CD-505 CD-506 ...
ChemComp-CLA / CHLOROPHYLL A

Details:

Mass: 893.489 Da / Num. of mol.: 210 / Source method: obtained synthetically / Formula: C₅₅H₇₂MgN₄O₅

#37: Chemical

AD-406 DD-408 AE-406 DE-408 A1-406 D1-407 a1-409 d1-408 aD-408 dD-408 aE-408 dE-408
ChemComp-PL9 / 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 / PLASTOQUINONE 9

Details:

Mass: 749.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₅₃H₈₀O₂

#38: Chemical

AD-407 BD-621 CD-501 DD-414 LD-101 LD-102 AE-407 BE-621 CE-501 DE-414 LE-101 LE-102 A1-407 B1-622 C1-501 D1-413 L1-101 L1-102 c1-501 d1-414 ...
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL

Details:

Mass: 795.116 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₄₁H₇₈O₁₂S

#39: Chemical

AD-408 BD-618 CD-502 CD-519 DD-411 JD-102 MD-101 TD-101 AE-408 BE-618 CE-502 CE-519 DE-411 JE-102 ME-101 TE-101 A1-408 B1-618 C1-502 C1-519 ...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

Details:

Mass: 787.158 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C₄₅H₈₆O₁₀

#41: Chemical

AD-410 AE-410 A1-410 a1-411 aD-410 aE-410
ChemComp-BCT / BICARBONATE ION

Details:

Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM

#42: Chemical

AD-411 BD-620 DD-409 DD-410 AE-411 BE-620 DE-409 DE-410 A1-411 B1-621 D1-408 D1-409 a1-412 d1-409 d1-410 e1-101 l1-101 aD-411 dD-409 dD-410 ...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

Details:

Mass: 722.970 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₃₈H₇₅O₁₀P / Comment: phospholipid*YM

#43: Chemical

BD-615 BD-616 BD-617 CD-516 CD-520 CD-521 DD-407 ID-102 XD-102 ZD-101 BE-615 BE-616 BE-617 CE-516 CE-520 DE-407 IE-102 XE-102 ZE-101 ZE-102 ...
ChemComp-BCR / BETA-CAROTENE

Details:

Mass: 536.873 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C₄₀H₅₆ / Feature type: SUBJECT OF INVESTIGATION

#45: Chemical

DD-401 DD-403 DE-401 DE-403 A1-412 D1-402 a1-413 d1-402 aD-412 dD-402 aE-412 dE-402
ChemComp-PHO / PHEOPHYTIN A

Details:

Mass: 871.200 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₅₅H₇₄N₄O₅

#46: Chemical

DD-402 DE-402 D1-401 d1-401 dD-401 dE-401
ChemComp-FE2 / FE (II) ION

Details:

Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe

#47: Chemical

ED-101 VD-201 EE-101 VE-201 E1-101 V1-201 f1-101 v1-201 fD-101 vD-201 fE-101 vE-201
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME

Details:

Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄

#48: Chemical

KD-101 UD-201 VD-202 KE-101 UE-201 VE-202 K1-101 U1-201 V1-202 k1-101 u1-201 v1-202 kD-101 uD-201 vD-202 kE-101 uE-201 vE-202
ChemComp-CA / CALCIUM ION

Details:

Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca

Details

• Has ligand of interest: Y

Experimental details

Experiment

• Experiment: Method: ELECTRON MICROSCOPY
• EM experiment: Aggregation state: CELL / 3D reconstruction method: single particle reconstruction

Sample preparation

• Component: Name: In situ PBS-PSII supercomplex / Type: CELL / Entity ID: #1-#32 / Source: NATURAL
• Source (natural): Organism: Arthrospira platensis (bacteria)
• Buffer solution: pH: 7.6
• Specimen: Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
• Vitrification: Cryogen name: ETHANE

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Microscopy: Model: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
• Electron lens: Mode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 6000 nm
• Image recording: Electron dose: 35 e/Ų / Film or detector model: GATAN K3 (6k x 4k)

Processing

• CTF correction: Type: NONE
• 3D reconstruction: Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168000 / Symmetry type: POINT