7DR1

Structure of Wild-type PSI monomer2 from Cyanophora paradoxa

PDB DOI: https://doi.org/10.2210/pdb7DR1/pdb
EM Map EMD-30821: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Cyanophora paradoxa
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2020-12-25 Released: 2022-02-16
Deposition Author(s): Kato, K., Nagao, R., Akita, F., Miyazaki, N., Shen, J.R.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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

Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes

Kato, K., Nagao, R., Ueno, Y., Yokono, M., Suzuki, T., Jiang, T.Y., Dohmae, N., Akita, F., Akimoto, S., Miyazaki, N., Shen, J.R.

(2022) Biorxiv

DOI: https://doi.org/10.1101/2022.01.03.474851

Macromolecule Content

Total Structure Weight: 340.74 kDa
Atom Count: 22,177
Modelled Residue Count: 2,114
Deposited Residue Count: 2,298
Unique protein chains: 10

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A	752	Cyanophora paradoxa	Mutation(s): 0 EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P48112 (Cyanophora paradoxa) Explore P48112 Go to UniProtKB: P48112
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48112
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B	737	Cyanophora paradoxa	Mutation(s): 0 EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P48113 (Cyanophora paradoxa) Explore P48113 Go to UniProtKB: P48113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48113
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C	81	Cyanophora paradoxa	Mutation(s): 0 EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P31173 (Cyanophora paradoxa) Explore P31173 Go to UniProtKB: P31173
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31173
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II, cyanelle	D	220	Cyanophora paradoxa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9T4W8 (Cyanophora paradoxa) Explore Q9T4W8 Go to UniProtKB: Q9T4W8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9T4W8
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	E	70	Cyanophora paradoxa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P48114 (Cyanophora paradoxa) Explore P48114 Go to UniProtKB: P48114
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48114
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	F	186	Cyanophora paradoxa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P48115 (Cyanophora paradoxa) Explore P48115 Go to UniProtKB: P48115
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48115
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	G [auth I]	35	Cyanophora paradoxa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P48116 (Cyanophora paradoxa) Explore P48116 Go to UniProtKB: P48116
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48116
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	H [auth J]	40	Cyanophora paradoxa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P48117 (Cyanophora paradoxa) Explore P48117 Go to UniProtKB: P48117
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48117
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	I [auth L]	146	Cyanophora paradoxa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	J [auth M]	31	Cyanophora paradoxa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P48185 (Cyanophora paradoxa) Explore P48185 Go to UniProtKB: P48185
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UniProt Group	P48185
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Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA Query on CLA Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth A] SDF format, chain AC [auth B] SDF format, chain BA [auth A] SDF format, chain BC [auth B] SDF format, chain BD [auth F] SDF format, chain CA [auth A] SDF format, chain CC [auth B] SDF format, chain DA [auth A] SDF format, chain DC [auth B] SDF format, chain DD [auth J] SDF format, chain EA [auth A] SDF format, chain EC [auth B] SDF format, chain FA [auth A] SDF format, chain FC [auth B] SDF format, chain GA [auth A] SDF format, chain GC [auth B] SDF format, chain HA [auth A] SDF format, chain HC [auth B] SDF format, chain IA [auth A] SDF format, chain IC [auth B] SDF format, chain ID [auth L] SDF format, chain JA [auth A] SDF format, chain JC [auth B] SDF format, chain JD [auth L] SDF format, chain KA [auth A] SDF format, chain KC [auth B] SDF format, chain KD [auth L] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth A] SDF format, chain LC [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain MB [auth B] SDF format, chain MC [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain NB [auth B] SDF format, chain NC [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain OB [auth B] SDF format, chain OC [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth A] SDF format, chain PB [auth B] SDF format, chain PC [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain QC [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain RB [auth B] SDF format, chain RC [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth A] SDF format, chain SB [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain TB [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth A] SDF format, chain UB [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth A] SDF format, chain VB [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth A] SDF format, chain WB [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth A] SDF format, chain XB [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth A] SDF format, chain YB [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth A] SDF format, chain ZB [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BC [auth B] MOL2 format, chain BD [auth F] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DC [auth B] MOL2 format, chain DD [auth J] MOL2 format, chain EA [auth A] MOL2 format, chain EC [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FC [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GC [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HC [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain IC [auth B] MOL2 format, chain ID [auth L] MOL2 format, chain JA [auth A] MOL2 format, chain JC [auth B] MOL2 format, chain JD [auth L] MOL2 format, chain KA [auth A] MOL2 format, chain KC [auth B] MOL2 format, chain KD [auth L] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain LC [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain MC [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain NC [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain OC [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain PC [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain QC [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain RC [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth B]	AA [auth A] AB [auth A] AC [auth B] BA [auth A] BC [auth B] AA [auth A], AB [auth A], AC [auth B], BA [auth A], BC [auth B], BD [auth F], CA [auth A], CC [auth B], DA [auth A], DC [auth B], DD [auth J], EA [auth A], EC [auth B], FA [auth A], FC [auth B], GA [auth A], GC [auth B], HA [auth A], HC [auth B], IA [auth A], IC [auth B], ID [auth L], JA [auth A], JC [auth B], JD [auth L], KA [auth A], KC [auth B], KD [auth L], L [auth A], LA [auth A], LB [auth A], LC [auth B], M [auth A], MA [auth A], MB [auth B], MC [auth B], N [auth A], NA [auth A], NB [auth B], NC [auth B], O [auth A], OA [auth A], OB [auth B], OC [auth B], P [auth A], PA [auth A], PB [auth B], PC [auth B], Q [auth A], QA [auth A], QB [auth B], QC [auth B], R [auth A], RA [auth A], RB [auth B], RC [auth B], S [auth A], SA [auth A], SB [auth B], T [auth A], TA [auth A], TB [auth B], U [auth A], UA [auth A], UB [auth B], V [auth A], VA [auth A], VB [auth B], W [auth A], WA [auth A], WB [auth B], X [auth A], XA [auth A], XB [auth B], Y [auth A], YA [auth A], YB [auth B], Z [auth A], ZA [auth A], ZB [auth B]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BC [auth B] Focus chain BD [auth F] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DC [auth B] Focus chain DD [auth J] Focus chain EA [auth A] Focus chain EC [auth B] Focus chain FA [auth A] Focus chain FC [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain IA [auth A] Focus chain IC [auth B] Focus chain ID [auth L] Focus chain JA [auth A] Focus chain JC [auth B] Focus chain JD [auth L] Focus chain KA [auth A] Focus chain KC [auth B] Focus chain KD [auth L] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain MC [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain NC [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain OC [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain PC [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain QC [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain RC [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth B] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BC [auth B] Focus chain BD [auth F] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DC [auth B] Focus chain DD [auth J] Focus chain EA [auth A] Focus chain EC [auth B] Focus chain FA [auth A] Focus chain FC [auth B] Focus chain GA [auth A] Focus chain GC [auth B] Focus chain HA [auth A] Focus chain HC [auth B] Focus chain IA [auth A] Focus chain IC [auth B] Focus chain ID [auth L] Focus chain JA [auth A] Focus chain JC [auth B] Focus chain JD [auth L] Focus chain KA [auth A] Focus chain KC [auth B] Focus chain KD [auth L] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain MC [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain NC [auth B] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain OC [auth B] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain PC [auth B] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain QC [auth B] Focus chain R [auth A] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain RC [auth B] Focus chain S [auth A] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth B] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth B]
CL0 Query on CL0 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	CHLOROPHYLL A ISOMER C₅₅ H₇₂ Mg N₄ O₅ VIQFHHZSLDFWDU-DVXFRRMCSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
LMG Query on LMG Download Ideal Coordinates CCD File SDF format, chain WC [auth B] MOL2 format, chain WC [auth B]	WC [auth B]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain WC [auth B] Interactions & Density Focus chain WC [auth B]
LHG Query on LHG Download Ideal Coordinates CCD File SDF format, chain JB [auth A] SDF format, chain KB [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain KB [auth A]	JB [auth A], KB [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain JB [auth A] Focus chain KB [auth A] Interactions & Density Focus chain JB [auth A] Focus chain KB [auth A]
BCR Query on BCR Download Ideal Coordinates CCD File SDF format, chain AD [auth F] SDF format, chain CD [auth I] SDF format, chain DB [auth A] SDF format, chain EB [auth A] SDF format, chain ED [auth J] SDF format, chain FB [auth A] SDF format, chain FD [auth J] SDF format, chain GB [auth A] SDF format, chain GD [auth J] SDF format, chain HB [auth A] SDF format, chain HD [auth L] SDF format, chain IB [auth A] SDF format, chain LD [auth L] SDF format, chain MD [auth L] SDF format, chain ND [auth M] SDF format, chain TC [auth B] SDF format, chain UC [auth B] SDF format, chain VC [auth B] SDF format, chain ZC [auth F] MOL2 format, chain AD [auth F] MOL2 format, chain CD [auth I] MOL2 format, chain DB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain ED [auth J] MOL2 format, chain FB [auth A] MOL2 format, chain FD [auth J] MOL2 format, chain GB [auth A] MOL2 format, chain GD [auth J] MOL2 format, chain HB [auth A] MOL2 format, chain HD [auth L] MOL2 format, chain IB [auth A] MOL2 format, chain LD [auth L] MOL2 format, chain MD [auth L] MOL2 format, chain ND [auth M] MOL2 format, chain TC [auth B] MOL2 format, chain UC [auth B] MOL2 format, chain VC [auth B] MOL2 format, chain ZC [auth F]	AD [auth F] CD [auth I] DB [auth A] EB [auth A] ED [auth J] AD [auth F], CD [auth I], DB [auth A], EB [auth A], ED [auth J], FB [auth A], FD [auth J], GB [auth A], GD [auth J], HB [auth A], HD [auth L], IB [auth A], LD [auth L], MD [auth L], ND [auth M], TC [auth B], UC [auth B], VC [auth B], ZC [auth F]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain AD [auth F] Focus chain CD [auth I] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain ED [auth J] Focus chain FB [auth A] Focus chain FD [auth J] Focus chain GB [auth A] Focus chain GD [auth J] Focus chain HB [auth A] Focus chain HD [auth L] Focus chain IB [auth A] Focus chain LD [auth L] Focus chain MD [auth L] Focus chain ND [auth M] Focus chain TC [auth B] Focus chain UC [auth B] Focus chain VC [auth B] Focus chain ZC [auth F] Interactions & Density Focus chain AD [auth F] Focus chain CD [auth I] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain ED [auth J] Focus chain FB [auth A] Focus chain FD [auth J] Focus chain GB [auth A] Focus chain GD [auth J] Focus chain HB [auth A] Focus chain HD [auth L] Focus chain IB [auth A] Focus chain LD [auth L] Focus chain MD [auth L] Focus chain ND [auth M] Focus chain TC [auth B] Focus chain UC [auth B] Focus chain VC [auth B] Focus chain ZC [auth F]
PQN Query on PQN Download Ideal Coordinates CCD File SDF format, chain BB [auth A] SDF format, chain SC [auth B] MOL2 format, chain BB [auth A] MOL2 format, chain SC [auth B]	BB [auth A], SC [auth B]	PHYLLOQUINONE C₃₁ H₄₆ O₂ MBWXNTAXLNYFJB-NKFFZRIASA-N		Interactions Focus chain BB [auth A] Focus chain SC [auth B] Interactions & Density Focus chain BB [auth A] Focus chain SC [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain CB [auth A] SDF format, chain XC [auth C] SDF format, chain YC [auth C] MOL2 format, chain CB [auth A] MOL2 format, chain XC [auth C] MOL2 format, chain YC [auth C]	CB [auth A], XC [auth C], YC [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CB [auth A] Focus chain XC [auth C] Focus chain YC [auth C] Interactions & Density Focus chain CB [auth A] Focus chain XC [auth C] Focus chain YC [auth C]