8ZEE

Cryo-EM structure of an intermediate-state PSII-PRF2' complex during the process of photosystem II repair

PDB DOI: https://doi.org/10.2210/pdb8ZEE/pdb
EM Map EMD-60026: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Chlamydomonas reinhardtii
Mutation(s): No

Deposited: 2024-05-06 Released: 2024-06-19
Deposition Author(s): Li, A., Liu, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii

Li, A., You, T., Pang, X., Wang, Y., Tian, L., Li, X., Liu, Z.

(2024) Nat Commun 15: 5211

DOI: https://doi.org/10.1038/s41467-024-49532-2

Macromolecule Content

Total Structure Weight: 312.05 kDa
Atom Count: 20,218
Modelled Residue Count: 2,101
Deposited Residue Count: 2,345
Unique protein chains: 16

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	A [auth B]	508	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A218N8S0 (Chlamydomonas reinhardtii) Explore A0A218N8S0 Go to UniProtKB: A0A218N8S0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A218N8S0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	B [auth D]	352	Chlamydomonas reinhardtii	Mutation(s): 0 EC: 1.10.3.9
UniProt
Find proteins for P06007 (Chlamydomonas reinhardtii) Explore P06007 Go to UniProtKB: P06007
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06007
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	C [auth E]	82	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P48268 (Chlamydomonas reinhardtii) Explore P48268 Go to UniProtKB: P48268
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48268
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	D [auth F]	44	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q08363 (Chlamydomonas reinhardtii) Explore Q08363 Go to UniProtKB: Q08363
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UniProt Group	Q08363
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	E [auth H]	88	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P22666 (Chlamydomonas reinhardtii) Explore P22666 Go to UniProtKB: P22666
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22666
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	F [auth I]	37	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P59763 (Chlamydomonas reinhardtii) Explore P59763 Go to UniProtKB: P59763
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59763
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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 K	G [auth K]	46	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P18263 (Chlamydomonas reinhardtii) Explore P18263 Go to UniProtKB: P18263
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UniProt Group	P18263
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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 L	H [auth L]	38	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P32974 (Chlamydomonas reinhardtii) Explore P32974 Go to UniProtKB: P32974
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32974
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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 M	I [auth M]	34	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P92277 (Chlamydomonas reinhardtii) Explore P92277 Go to UniProtKB: P92277
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P92277
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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 T	J [auth T]	31	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P37256 (Chlamydomonas reinhardtii) Explore P37256 Go to UniProtKB: P37256
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UniProt Group	P37256
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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 Psb30	K [auth V]	33	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P50370 (Chlamydomonas reinhardtii) Explore P50370 Go to UniProtKB: P50370
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UniProt Group	P50370
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
4.1 kDa photosystem II subunit	L [auth X]	101	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8I846 (Chlamydomonas reinhardtii) Explore A8I846 Go to UniProtKB: A8I846
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UniProt Group	A8I846
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	M [auth Z]	62	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P92276 (Chlamydomonas reinhardtii) Explore P92276 Go to UniProtKB: P92276
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P92276
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	N [auth C]	461	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P10898 (Chlamydomonas reinhardtii) Explore P10898 Go to UniProtKB: P10898
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UniProt Group	P10898
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	O [auth A]	329	Chlamydomonas reinhardtii	Mutation(s): 0 EC: 1.10.3.9
UniProt
Find proteins for P07753 (Chlamydomonas reinhardtii) Explore P07753 Go to UniProtKB: P07753
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UniProt Group	P07753
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: 1	P [auth 1]	99	Chlamydomonas reinhardtii	Mutation(s): 0
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Find proteins for A8HMM7 (Chlamydomonas reinhardtii) Explore A8HMM7 Go to UniProtKB: A8HMM7
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UniProt Group	A8HMM7
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Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD (Subject of Investigation/LOI) Query on DGD Download Ideal Coordinates CCD File SDF format, chain AC [auth C] SDF format, chain YB [auth C] SDF format, chain ZB [auth C] MOL2 format, chain AC [auth C] MOL2 format, chain YB [auth C] MOL2 format, chain ZB [auth C]	AC [auth C], YB [auth C], ZB [auth C]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain AC [auth C] Focus chain YB [auth C] Focus chain ZB [auth C] Interactions & Density Focus chain AC [auth C] Focus chain YB [auth C] Focus chain ZB [auth C]
CLA (Subject of Investigation/LOI) Query on CLA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain EC [auth A] SDF format, chain FA [auth B] SDF format, chain FC [auth A] SDF format, chain GC [auth A] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain LB [auth C] SDF format, chain MB [auth C] SDF format, chain NB [auth C] SDF format, chain OA [auth D] SDF format, chain OB [auth C] SDF format, chain PA [auth D] SDF format, chain PB [auth C] SDF format, chain Q [auth B] SDF format, chain QB [auth C] SDF format, chain R [auth B] SDF format, chain RB [auth C] SDF format, chain S [auth B] SDF format, chain SB [auth C] SDF format, chain T [auth B] SDF format, chain TB [auth C] SDF format, chain U [auth B] SDF format, chain UB [auth C] SDF format, chain V [auth B] SDF format, chain VB [auth C] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain EC [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain FC [auth A] MOL2 format, chain GC [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain R [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain T [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], EC [auth A], FA [auth B], FC [auth A], GC [auth A], JB [auth C], KB [auth C], LB [auth C], MB [auth C], NB [auth C], OA [auth D], OB [auth C], PA [auth D], PB [auth C], Q [auth B], QB [auth C], R [auth B], RB [auth C], S [auth B], SB [auth C], T [auth B], TB [auth C], U [auth B], UB [auth C], V [auth B], VB [auth C], W [auth B], WA [auth D], X [auth B], Y [auth B], Z [auth B]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EC [auth A] Focus chain FA [auth B] Focus chain FC [auth A] Focus chain GC [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OA [auth D] Focus chain OB [auth C] Focus chain PA [auth D] Focus chain PB [auth C] Focus chain Q [auth B] Focus chain QB [auth C] Focus chain R [auth B] Focus chain RB [auth C] Focus chain S [auth B] Focus chain SB [auth C] Focus chain T [auth B] Focus chain TB [auth C] Focus chain U [auth B] Focus chain UB [auth C] Focus chain V [auth B] Focus chain VB [auth C] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EC [auth A] Focus chain FA [auth B] Focus chain FC [auth A] Focus chain GC [auth A] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OA [auth D] Focus chain OB [auth C] Focus chain PA [auth D] Focus chain PB [auth C] Focus chain Q [auth B] Focus chain QB [auth C] Focus chain R [auth B] Focus chain RB [auth C] Focus chain S [auth B] Focus chain SB [auth C] Focus chain T [auth B] Focus chain TB [auth C] Focus chain U [auth B] Focus chain UB [auth C] Focus chain V [auth B] Focus chain VB [auth C] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
PHO (Subject of Investigation/LOI) Query on PHO Download Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain YA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D]	XA [auth D], YA [auth D]	PHEOPHYTIN A C₅₅ H₇₄ N₄ O₅ CQIKWXUXPNUNDV-RCBXBCQGSA-N		Interactions Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain XA [auth D] Focus chain YA [auth D]
SQD (Subject of Investigation/LOI) Query on SQD Download Ideal Coordinates CCD File SDF format, chain BC [auth C] MOL2 format, chain BC [auth C]	BC [auth C]	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 BC [auth C] Interactions & Density Focus chain BC [auth C]
LMG (Subject of Investigation/LOI) Query on LMG Download Ideal Coordinates CCD File SDF format, chain BB [auth H] SDF format, chain CC [auth C] SDF format, chain DB [auth K] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain UA [auth D] MOL2 format, chain BB [auth H] MOL2 format, chain CC [auth C] MOL2 format, chain DB [auth K] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain UA [auth D]	BB [auth H] CC [auth C] DB [auth K] IB [auth C] JA [auth B] BB [auth H], CC [auth C], DB [auth K], IB [auth C], JA [auth B], UA [auth D]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain BB [auth H] Focus chain CC [auth C] Focus chain DB [auth K] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain UA [auth D] Interactions & Density Focus chain BB [auth H] Focus chain CC [auth C] Focus chain DB [auth K] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain UA [auth D]
PL9 (Subject of Investigation/LOI) Query on PL9 Download Ideal Coordinates CCD File SDF format, chain RA [auth D] MOL2 format, chain RA [auth D]	RA [auth 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 C₅₃ H₈₀ O₂ FKUYMLZIRPABFK-UHFFFAOYSA-N		Interactions Focus chain RA [auth D] Interactions & Density Focus chain RA [auth D]
LHG (Subject of Investigation/LOI) Query on LHG Download Ideal Coordinates CCD File SDF format, chain EB [auth K] SDF format, chain FB [auth L] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain VA [auth D] MOL2 format, chain EB [auth K] MOL2 format, chain FB [auth L] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain VA [auth D]	EB [auth K] FB [auth L] KA [auth B] LA [auth B] MA [auth B] EB [auth K], FB [auth L], KA [auth B], LA [auth B], MA [auth B], SA [auth D], TA [auth D], VA [auth D]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain EB [auth K] Focus chain FB [auth L] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain VA [auth D] Interactions & Density Focus chain EB [auth K] Focus chain FB [auth L] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain VA [auth D]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain ZA [auth E] MOL2 format, chain ZA [auth E]	ZA [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain ZA [auth E] Interactions & Density Focus chain ZA [auth E]
BCR (Subject of Investigation/LOI) Query on BCR Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain CB [auth K] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain HB [auth Z] SDF format, chain HC [auth A] SDF format, chain IA [auth B] SDF format, chain QA [auth D] SDF format, chain WB [auth C] SDF format, chain XB [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain CB [auth K] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth Z] MOL2 format, chain HC [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain WB [auth C] MOL2 format, chain XB [auth C]	AB [auth H] CB [auth K] GA [auth B] HA [auth B] HB [auth Z] AB [auth H], CB [auth K], GA [auth B], HA [auth B], HB [auth Z], HC [auth A], IA [auth B], QA [auth D], WB [auth C], XB [auth C]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain AB [auth H] Focus chain CB [auth K] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth Z] Focus chain HC [auth A] Focus chain IA [auth B] Focus chain QA [auth D] Focus chain WB [auth C] Focus chain XB [auth C] Interactions & Density Focus chain AB [auth H] Focus chain CB [auth K] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth Z] Focus chain HC [auth A] Focus chain IA [auth B] Focus chain QA [auth D] Focus chain WB [auth C] Focus chain XB [auth C]
VTQ (Subject of Investigation/LOI) Query on VTQ Download Ideal Coordinates CCD File SDF format, chain GB [auth X] MOL2 format, chain GB [auth X]	GB [auth X]	RRR-ALPHA-TOCOPHERYLQUINONE C₂₉ H₅₀ O₃ LTVDFSLWFKLJDQ-IEOSBIPESA-N		Interactions Focus chain GB [auth X] Interactions & Density Focus chain GB [auth X]
BCT (Subject of Investigation/LOI) Query on BCT Download Ideal Coordinates CCD File SDF format, chain NA [auth D] MOL2 format, chain NA [auth D]	NA [auth D]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain NA [auth D] Interactions & Density Focus chain NA [auth D]
FE2 (Subject of Investigation/LOI) Query on FE2 Download Ideal Coordinates CCD File SDF format, chain DC [auth A] MOL2 format, chain DC [auth A]	DC [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain DC [auth A] Interactions & Density Focus chain DC [auth A]