6WJ6

Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803

PDB DOI: https://doi.org/10.2210/pdb6WJ6/pdb
EM Map EMD-21690: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2020-04-12 Released: 2020-08-26
Deposition Author(s): Gisriel, C.J.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.58 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex

Gisriel, C.J., Zhou, K., Huang, H., Debus, R.J., Xiong, Y., Brudvig, G.W.

(2020) Joule

DOI: https://doi.org/10.1016/j.joule.2020.07.016

Macromolecule Content

Total Structure Weight: 286.96 kDa
Atom Count: 18,884
Modelled Residue Count: 1,898
Deposited Residue Count: 2,095
Unique protein chains: 13

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1 2	A	360	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P16033 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P16033 Go to UniProtKB: P16033
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16033
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B	507	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P05429 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P05429 Go to UniProtKB: P05429
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05429
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	C	460	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P09193 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P09193 Go to UniProtKB: P09193
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09193
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D	352	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P09192 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P09192 Go to UniProtKB: P09192
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09192
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E	81	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P09190 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P09190 Go to UniProtKB: P09190
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09190
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F	44	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P09191 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P09191 Go to UniProtKB: P09191
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UniProt Group	P09191
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	G [auth H]	64	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P14835 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P14835 Go to UniProtKB: P14835
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UniProt Group	P14835
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	H [auth I]	38	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q54697 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q54697 Go to UniProtKB: Q54697
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UniProt Group	Q54697
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	I [auth K]	45	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P15819 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P15819 Go to UniProtKB: P15819
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UniProt Group	P15819
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	J [auth L]	39	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q55354 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55354 Go to UniProtKB: Q55354
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UniProt Group	Q55354
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	K [auth M]	35	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P72701 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P72701 Go to UniProtKB: P72701
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UniProt Group	P72701
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	L [auth T]	31	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P74787 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P74787 Go to UniProtKB: P74787
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UniProt Group	P74787
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	M [auth X]	39	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P72575 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P72575 Go to UniProtKB: P72575
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UniProt Group	P72575
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Reference Sequence

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD Query on DGD Download Ideal Coordinates CCD File SDF format, chain JB [auth C] SDF format, chain ZB [auth H] MOL2 format, chain JB [auth C] MOL2 format, chain ZB [auth H]	JB [auth C], ZB [auth H]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain JB [auth C] Focus chain ZB [auth H] Interactions & Density Focus chain JB [auth C] Focus chain ZB [auth H]
CLA (Subject of Investigation/LOI) Query on CLA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RB [auth D] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain W [auth B] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], NB [auth D], O [auth A], P [auth A], QB [auth D], R [auth A], RB [auth D], UA [auth C], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
PHO Query on PHO Download Ideal Coordinates CCD File SDF format, chain OB [auth D] SDF format, chain Q [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain Q [auth A]	OB [auth D], Q [auth A]	PHEOPHYTIN A C₅₅ H₇₄ N₄ O₅ CQIKWXUXPNUNDV-RCBXBCQGSA-N		Interactions Focus chain OB [auth D] Focus chain Q [auth A] Interactions & Density Focus chain OB [auth D] Focus chain Q [auth A]
SQD Query on SQD Download Ideal Coordinates CCD File SDF format, chain DC [auth T] SDF format, chain FC [auth T] SDF format, chain GC [auth X] SDF format, chain KB [auth C] SDF format, chain PA [auth B] SDF format, chain T [auth A] SDF format, chain V [auth A] MOL2 format, chain DC [auth T] MOL2 format, chain FC [auth T] MOL2 format, chain GC [auth X] MOL2 format, chain KB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A]	DC [auth T] FC [auth T] GC [auth X] KB [auth C] PA [auth B] DC [auth T], FC [auth T], GC [auth X], KB [auth C], PA [auth B], T [auth A], V [auth A]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C₄₁ H₇₈ O₁₂ S RVUUQPKXGDTQPG-JUDHQOGESA-N		Interactions Focus chain DC [auth T] Focus chain FC [auth T] Focus chain GC [auth X] Focus chain KB [auth C] Focus chain PA [auth B] Focus chain T [auth A] Focus chain V [auth A] Interactions & Density Focus chain DC [auth T] Focus chain FC [auth T] Focus chain GC [auth X] Focus chain KB [auth C] Focus chain PA [auth B] Focus chain T [auth A] Focus chain V [auth A]
LMG Query on LMG Download Ideal Coordinates CCD File SDF format, chain QA [auth B] SDF format, chain TA [auth C] SDF format, chain XB [auth D] MOL2 format, chain QA [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain XB [auth D]	QA [auth B], TA [auth C], XB [auth D]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain QA [auth B] Focus chain TA [auth C] Focus chain XB [auth D] Interactions & Density Focus chain QA [auth B] Focus chain TA [auth C] Focus chain XB [auth D]
PL9 Query on PL9 Download Ideal Coordinates CCD File SDF format, chain TB [auth D] SDF format, chain U [auth A] MOL2 format, chain TB [auth D] MOL2 format, chain U [auth A]	TB [auth D], U [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		Interactions Focus chain TB [auth D] Focus chain U [auth A] Interactions & Density Focus chain TB [auth D] Focus chain U [auth A]
LHG Query on LHG Download Ideal Coordinates CCD File SDF format, chain BC [auth L] SDF format, chain UB [auth D] SDF format, chain VB [auth D] SDF format, chain WB [auth D] MOL2 format, chain BC [auth L] MOL2 format, chain UB [auth D] MOL2 format, chain VB [auth D] MOL2 format, chain WB [auth D]	BC [auth L], UB [auth D], VB [auth D], WB [auth D]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain BC [auth L] Focus chain UB [auth D] Focus chain VB [auth D] Focus chain WB [auth D] Interactions & Density Focus chain BC [auth L] Focus chain UB [auth D] Focus chain VB [auth D] Focus chain WB [auth D]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain YB [auth E] MOL2 format, chain YB [auth E]	YB [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain YB [auth E] Interactions & Density Focus chain YB [auth E]
BCR Query on BCR Download Ideal Coordinates CCD File SDF format, chain HB [auth C] SDF format, chain HC [auth X] SDF format, chain IB [auth C] SDF format, chain LB [auth C] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain S [auth A] SDF format, chain SB [auth D] MOL2 format, chain HB [auth C] MOL2 format, chain HC [auth X] MOL2 format, chain IB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth D]	HB [auth C] HC [auth X] IB [auth C] LB [auth C] MA [auth B] HB [auth C], HC [auth X], IB [auth C], LB [auth C], MA [auth B], NA [auth B], OA [auth B], S [auth A], SB [auth D]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain HB [auth C] Focus chain HC [auth X] Focus chain IB [auth C] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain S [auth A] Focus chain SB [auth D] Interactions & Density Focus chain HB [auth C] Focus chain HC [auth X] Focus chain IB [auth C] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain S [auth A] Focus chain SB [auth D]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain RA [auth B] SDF format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B]	RA [auth B], SA [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain RA [auth B] Focus chain SA [auth B] Interactions & Density Focus chain RA [auth B] Focus chain SA [auth B]
FME Query on FME Download Ideal Coordinates CCD File SDF format, chain AC [auth I] SDF format, chain CC [auth M] SDF format, chain EC [auth T] MOL2 format, chain AC [auth I] MOL2 format, chain CC [auth M] MOL2 format, chain EC [auth T]	AC [auth I], CC [auth M], EC [auth T]	N-FORMYLMETHIONINE C₆ H₁₁ N O₃ S PYUSHNKNPOHWEZ-YFKPBYRVSA-N		Interactions Focus chain AC [auth I] Focus chain CC [auth M] Focus chain EC [auth T] Interactions & Density Focus chain AC [auth I] Focus chain CC [auth M] Focus chain EC [auth T]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain PB [auth D] MOL2 format, chain PB [auth D]	PB [auth D]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain PB [auth D] Interactions & Density Focus chain PB [auth D]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A]	N [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain MB [auth D] MOL2 format, chain MB [auth D]	MB [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain MB [auth D] Interactions & Density Focus chain MB [auth D]