Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.

Nakajima, Y.; Umena, Y.; Nagao, R.; Endo, K.; Kobayashi, K.; Akita, F.; Suga, M.; Wada, H.; Noguchi, T.; Shen, J.R.

doi:10.2210/pdb5zzn/pdb

Macromolecule Content

Total Structure Weight: 756983.88
Atom Count: 51444
Residue Count: 5270
Unique protein chains: 19

5ZZN

Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus

DOI: 10.2210/pdb5ZZN/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Thermosynechococcus elongatus (strain BP-1)

Deposited: 2018-06-03 Released: 2018-08-01
Deposition Author(s): Nakajima, Y., Umena, Y., Nagao, R., Endo, K., Kobayashi, K., Akita, F., Suga, M., Wada, H., Noguchi, T., Shen, J.R.
Funding Organization(s): Japan Society for the Promotion of Science; Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.1 Å
R-Value Free: 0.197
R-Value Work: 0.154

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.

Nakajima, Y., Umena, Y., Nagao, R., Endo, K., Kobayashi, K., Akita, F., Suga, M., Wada, H., Noguchi, T., Shen, J.R.

(2018) J. Biol. Chem. 293: 14786-14797

PubMed: 30076221 Search on PubMed

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II protein D1 1	A, a	334	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbA1 (psbA-1) EC: 1.10.3.9
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: P0A444
Protein Feature View Full Protein Feature View for P0A444

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II CP47 reaction center protein	B, b	505	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbB
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DIQ1
Protein Feature View Full Protein Feature View for Q8DIQ1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II CP43 reaction center protein	C, c	455	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbC
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DIF8
Protein Feature View Full Protein Feature View for Q8DIF8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II D2 protein	D, d	342	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbD1, psbD2 EC: 1.10.3.9
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8CM25
Protein Feature View Full Protein Feature View for Q8CM25

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome b559 subunit alpha	E, e	81	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbE
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DIP0
Protein Feature View Full Protein Feature View for Q8DIP0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome b559 subunit beta	F, f	34	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbF
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DIN9
Protein Feature View Full Protein Feature View for Q8DIN9

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein H	H, h	63	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbH
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DJ43
Protein Feature View Full Protein Feature View for Q8DJ43

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein I	I, i	37	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbI
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DJZ6
Protein Feature View Full Protein Feature View for Q8DJZ6

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein J	J, j	40	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbJ
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: P59087
Protein Feature View Full Protein Feature View for P59087

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein K	K, k	37	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbK
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q9F1K9
Protein Feature View Full Protein Feature View for Q9F1K9

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein L	L, l	36	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbL
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DIN8
Protein Feature View Full Protein Feature View for Q8DIN8

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein M	M, m	34	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbM
Find proteins for Q8DHA7 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DHA7
Protein Feature View Full Protein Feature View for Q8DHA7

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II manganese-stabilizing polypeptide	O, o	243	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbO
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: P0A431
Protein Feature View Full Protein Feature View for P0A431

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein T	T, t	30	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbT
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DIQ0
Protein Feature View Full Protein Feature View for Q8DIQ0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II 12 kDa extrinsic protein	U, u	97	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbU
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q9F1L5
Protein Feature View Full Protein Feature View for Q9F1L5

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome c-550	V, v	137	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbV
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: P0A386
Protein Feature View Full Protein Feature View for P0A386

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein Ycf12	Y, y	29	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: ycf12
Find proteins for Q8DJI1 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DJI1
Protein Feature View Full Protein Feature View for Q8DJI1

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center X protein	X, x	39	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbX
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q9F1R6
Protein Feature View Full Protein Feature View for Q9F1R6

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
Photosystem II reaction center protein Z	Z, z	62	Thermosynechococcus elongatus (strain BP-1)	Mutation(s): 0 Gene Names: psbZ
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1)) Go to UniProtKB: Q8DHJ2
Protein Feature View Full Protein Feature View for Q8DHJ2

Small Molecules

Ligands 19 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
CLA Query on CLA Download SDF File Download CCD File	a, A, B, b, c, C, D, d	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ VIQFHHZSLDFWDU-AENOIHSZSA-M		Ligand Interaction
PL9 Query on PL9 Download SDF File Download CCD File	a, A, D, d	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 C₅₃ H₈₀ O₂ FKUYMLZIRPABFK-UHFFFAOYSA-N		Ligand Interaction
OEX Query on OEX Download SDF File Download CCD File	a, A	CA-MN4-O5 CLUSTER Ca Mn₄ O₅ SEXWDHMBWJEXOJ-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download SDF File Download CCD File	a, A, v	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
GOL Query on GOL Download SDF File Download CCD File	b, c, C, D, e	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
HTG Query on HTG Download SDF File Download CCD File	B, b, c, C, d, D, o, O, U, V, v	HEPTYL 1-THIOHEXOPYRANOSIDE C₁₃ H₂₆ O₅ S HPEGNLMTTNTJSP-LBELIVKGSA-N		Ligand Interaction
CA Query on CA Download SDF File Download CCD File	B, b, c, O, o, V, v	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction
DGD Query on DGD Download SDF File Download CCD File	c, C, d, D, H, h	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Ligand Interaction
LMG Query on LMG Download SDF File Download CCD File	A, a, b, B, C, c, D, d	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Ligand Interaction
BCT Query on BCT Download SDF File Download CCD File	D, d	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Ligand Interaction
MG Query on MG Download SDF File Download CCD File	j, J, k, K	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction
HEM Query on HEM Download SDF File Download CCD File	f, F, v, V	PROTOPORPHYRIN IX CONTAINING FE HEME C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction
BCR Query on BCR Download SDF File Download CCD File	a, A, B, b, c, C, D, d, K, k, t, T, y, Y	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Ligand Interaction
PHO Query on PHO Download SDF File Download CCD File	A, a, d, D	PHEOPHYTIN A C₅₅ H₇₄ N₄ O₅ CQIKWXUXPNUNDV-RCBXBCQGSA-N		Ligand Interaction
FE2 Query on FE2 Download SDF File Download CCD File	a, D	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Ligand Interaction
LMT Query on LMT Download SDF File Download CCD File	A, a, b, B, c, C, F, J, j, l, m, M, t, T, Z, z	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Ligand Interaction
DMS Query on DMS Download SDF File Download CCD File	A, a, b, B, c, C, d, D, E, e, h, I, O, o, U, u, V, v	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction
RRX Query on RRX Download SDF File Download CCD File	H, h	(3R)-beta,beta-caroten-3-ol beta-Cryptoxanthin C₄₀ H₅₆ O DMASLKHVQRHNES-FKKUPVFPSA-N		Ligand Interaction
LHG Query on LHG Download SDF File Download CCD File	B, b, d, D, E, e, F, f	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Ligand Interaction

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	I, i, m, M, T, t	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
HSK Query on HSK	d, D	L-PEPTIDE LINKING	C₆ H₉ N₃ O₃		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.1 Å
R-Value Free: 0.197
R-Value Work: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 122.250	α = 90.00
b = 228.430	β = 90.00
c = 287.120	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-06-03
Released Date: 2018-08-01
Deposition Author(s): Nakajima, Y., Umena, Y., Nagao, R., Endo, K., Kobayashi, K., Akita, F., Suga, M., Wada, H., Noguchi, T., Shen, J.R.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP17H06434
Japan Society for the Promotion of Science	Japan	JP16K21181
Japan Science and Technology	Japan	JPMJPR16P1

Revision History

Version 1.0: 2018-08-01
Type: Initial release
Version 1.1: 2018-09-05
Type: Data collection, Database references
Version 1.2: 2018-10-03
Type: Data collection, Database references

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

148969 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

5ZZN

Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus

Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.

Entity ID: 1

Entity ID: 2

Entity ID: 3

Entity ID: 4

Entity ID: 5

Entity ID: 6

Entity ID: 7

Entity ID: 8

Entity ID: 9

Entity ID: 10

Entity ID: 11

Entity ID: 12

Entity ID: 13

Entity ID: 14

Entity ID: 15

Entity ID: 16

Entity ID: 17

Entity ID: 18

Entity ID: 19

Experimental Data

Structure Validation

Deposition Data

Revision History