8BCW

Photosystem I assembly intermediate of Avena sativa

PDB DOI: https://doi.org/10.2210/pdb8BCW/pdb
EM Map EMD-15970: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Avena sativa
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2022-10-17 Released: 2023-11-01
Deposition Author(s): Naschberger, A., Amunts, A., Nelson, N.
Funding Organization(s): The Swedish Foundation for Strategic Research, Knut and Alice Wallenberg Foundation, Israel Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.11 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

Photosystem I assembly intermediate of Avena sativa

Naschberger, A., Amunts, A., Nelson, N.

To be published.

Macromolecule Content

Total Structure Weight: 341.47 kDa
Atom Count: 22,313
Modelled Residue Count: 2,029
Deposited Residue Count: 2,254
Unique protein chains: 8

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A	750	Avena sativa	Mutation(s): 0 EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A0A3G1AUL2 (Avena sativa) Explore A0A3G1AUL2 Go to UniProtKB: A0A3G1AUL2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3G1AUL2
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	734	Avena sativa	Mutation(s): 0 EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A0A3G1AZK6 (Avena sativa) Explore A0A3G1AZK6 Go to UniProtKB: A0A3G1AZK6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3G1AZK6
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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	Avena sativa	Mutation(s): 0 EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A0A3G1ATU7 (Avena sativa) Explore A0A3G1ATU7 Go to UniProtKB: A0A3G1ATU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3G1ATU7
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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, chloroplastic	D	206	Avena sativa	Mutation(s): 0
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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 A, chloroplastic	E	143	Avena sativa	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VI, chloroplastic	F [auth H]	94	Avena sativa	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	G [auth I]	33	Avena sativa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A3G1AZM6 (Avena sativa) Explore A0A3G1AZM6 Go to UniProtKB: A0A3G1AZM6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3G1AZM6
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PSI subunit V	H [auth L]	213	Avena sativa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Small Molecules

Ligands 9 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 GD [auth B] MOL2 format, chain GD [auth B]	GD [auth B]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain GD [auth B] Interactions & Density Focus chain GD [auth B]
CLA (Subject of Investigation/LOI) 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 AD [auth B] SDF format, chain BA [auth A] SDF format, chain BC [auth B] 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 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 J [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth A] SDF format, chain JC [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain KC [auth B] 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 MC [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain NC [auth B] SDF format, chain ND [auth L] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain OC [auth B] SDF format, chain OD [auth L] 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 PD [auth L] 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 SC [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain TB [auth B] SDF format, chain TC [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth A] SDF format, chain UB [auth B] SDF format, chain UC [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth A] SDF format, chain VB [auth B] SDF format, chain VC [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth A] SDF format, chain WB [auth B] SDF format, chain WC [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth A] SDF format, chain XB [auth B] SDF format, chain XC [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth A] SDF format, chain YB [auth B] SDF format, chain YC [auth B] SDF format, chain Z [auth A] SDF format, chain ZB [auth B] SDF format, chain ZC [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth B] MOL2 format, chain AD [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BC [auth B] 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 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 J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain JC [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KC [auth B] 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 MC [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NC [auth B] MOL2 format, chain ND [auth L] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OC [auth B] MOL2 format, chain OD [auth L] 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 PD [auth L] 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 SC [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain TC [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain UC [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain VC [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth B] MOL2 format, chain WC [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth B] MOL2 format, chain XC [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth B] MOL2 format, chain YC [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZB [auth B] MOL2 format, chain ZC [auth B]	AA [auth A] AB [auth A] AC [auth B] AD [auth B] BA [auth A] AA [auth A], AB [auth A], AC [auth B], AD [auth B], BA [auth A], BC [auth B], CA [auth A], CC [auth B], DA [auth A], DC [auth B], 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], J [auth A], JA [auth A], JB [auth A], JC [auth B], K [auth A], KA [auth A], KC [auth B], L [auth A], LA [auth A], LB [auth A], LC [auth B], M [auth A], MA [auth A], MC [auth B], N [auth A], NA [auth A], NC [auth B], ND [auth L], O [auth A], OA [auth A], OC [auth B], OD [auth L], P [auth A], PA [auth A], PB [auth B], PC [auth B], PD [auth L], 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], SC [auth B], T [auth A], TA [auth A], TB [auth B], TC [auth B], U [auth A], UA [auth A], UB [auth B], UC [auth B], V [auth A], VA [auth A], VB [auth B], VC [auth B], W [auth A], WA [auth A], WB [auth B], WC [auth B], X [auth A], XA [auth A], XB [auth B], XC [auth B], Y [auth A], YA [auth A], YB [auth B], YC [auth B], Z [auth A], ZB [auth B], ZC [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 AD [auth B] Focus chain BA [auth A] Focus chain BC [auth B] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DC [auth B] 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 J [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KC [auth B] 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 MC [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NC [auth B] Focus chain ND [auth L] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OC [auth B] Focus chain OD [auth L] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain PC [auth B] Focus chain PD [auth L] 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 SC [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain UC [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain VC [auth B] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth B] Focus chain WC [auth B] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain XC [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth B] Focus chain YC [auth B] Focus chain Z [auth A] Focus chain ZB [auth B] Focus chain ZC [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth B] Focus chain AD [auth B] Focus chain BA [auth A] Focus chain BC [auth B] Focus chain CA [auth A] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DC [auth B] 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 J [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KC [auth B] 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 MC [auth B] Focus chain N [auth A] Focus chain NA [auth A] Focus chain NC [auth B] Focus chain ND [auth L] Focus chain O [auth A] Focus chain OA [auth A] Focus chain OC [auth B] Focus chain OD [auth L] Focus chain P [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain PC [auth B] Focus chain PD [auth L] 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 SC [auth B] Focus chain T [auth A] Focus chain TA [auth A] Focus chain TB [auth B] Focus chain TC [auth B] Focus chain U [auth A] Focus chain UA [auth A] Focus chain UB [auth B] Focus chain UC [auth B] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth B] Focus chain VC [auth B] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth B] Focus chain WC [auth B] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth B] Focus chain XC [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth B] Focus chain YC [auth B] Focus chain Z [auth A] Focus chain ZB [auth B] Focus chain ZC [auth B]
CL0 (Subject of Investigation/LOI) Query on CL0 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain KD [auth H] MOL2 format, chain I [auth A] MOL2 format, chain KD [auth H]	I [auth A], KD [auth H]	CHLOROPHYLL A ISOMER C₅₅ H₇₂ Mg N₄ O₅ VIQFHHZSLDFWDU-DVXFRRMCSA-M		Interactions Focus chain I [auth A] Focus chain KD [auth H] Interactions & Density Focus chain I [auth A] Focus chain KD [auth H]
LMG (Subject of Investigation/LOI) Query on LMG Download Ideal Coordinates CCD File SDF format, chain NB [auth A] MOL2 format, chain NB [auth A]	NB [auth A]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain NB [auth A] Interactions & Density Focus chain NB [auth A]
LHG (Subject of Investigation/LOI) Query on LHG Download Ideal Coordinates CCD File SDF format, chain BB [auth A] SDF format, chain CB [auth A] SDF format, chain HD [auth B] MOL2 format, chain BB [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain HD [auth B]	BB [auth A], CB [auth A], HD [auth B]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain BB [auth A] Focus chain CB [auth A] Focus chain HD [auth B] Interactions & Density Focus chain BB [auth A] Focus chain CB [auth A] Focus chain HD [auth B]
BCR (Subject of Investigation/LOI) Query on BCR Download Ideal Coordinates CCD File SDF format, chain CD [auth B] SDF format, chain DB [auth A] SDF format, chain DD [auth B] SDF format, chain EB [auth A] SDF format, chain ED [auth B] SDF format, chain FB [auth A] SDF format, chain FD [auth B] SDF format, chain GB [auth A] SDF format, chain HB [auth A] SDF format, chain LD [auth I] SDF format, chain MD [auth L] SDF format, chain QD [auth L] SDF format, chain RD [auth L] MOL2 format, chain CD [auth B] MOL2 format, chain DB [auth A] MOL2 format, chain DD [auth B] MOL2 format, chain EB [auth A] MOL2 format, chain ED [auth B] MOL2 format, chain FB [auth A] MOL2 format, chain FD [auth B] MOL2 format, chain GB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain LD [auth I] MOL2 format, chain MD [auth L] MOL2 format, chain QD [auth L] MOL2 format, chain RD [auth L]	CD [auth B] DB [auth A] DD [auth B] EB [auth A] ED [auth B] CD [auth B], DB [auth A], DD [auth B], EB [auth A], ED [auth B], FB [auth A], FD [auth B], GB [auth A], HB [auth A], LD [auth I], MD [auth L], QD [auth L], RD [auth L]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain CD [auth B] Focus chain DB [auth A] Focus chain DD [auth B] Focus chain EB [auth A] Focus chain ED [auth B] Focus chain FB [auth A] Focus chain FD [auth B] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain LD [auth I] Focus chain MD [auth L] Focus chain QD [auth L] Focus chain RD [auth L] Interactions & Density Focus chain CD [auth B] Focus chain DB [auth A] Focus chain DD [auth B] Focus chain EB [auth A] Focus chain ED [auth B] Focus chain FB [auth A] Focus chain FD [auth B] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain LD [auth I] Focus chain MD [auth L] Focus chain QD [auth L] Focus chain RD [auth L]
LMU Query on LMU Download Ideal Coordinates CCD File SDF format, chain KB [auth A] SDF format, chain MB [auth A] SDF format, chain OB [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain OB [auth A]	KB [auth A], MB [auth A], OB [auth A]	DODECYL-ALPHA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-YHBSTRCHSA-N		Interactions Focus chain KB [auth A] Focus chain MB [auth A] Focus chain OB [auth A] Interactions & Density Focus chain KB [auth A] Focus chain MB [auth A] Focus chain OB [auth A]
PQN (Subject of Investigation/LOI) Query on PQN Download Ideal Coordinates CCD File SDF format, chain BD [auth B] SDF format, chain ZA [auth A] MOL2 format, chain BD [auth B] MOL2 format, chain ZA [auth A]	BD [auth B], ZA [auth A]	PHYLLOQUINONE C₃₁ H₄₆ O₂ MBWXNTAXLNYFJB-NKFFZRIASA-N		Interactions Focus chain BD [auth B] Focus chain ZA [auth A] Interactions & Density Focus chain BD [auth B] Focus chain ZA [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain IB [auth A] SDF format, chain ID [auth C] SDF format, chain JD [auth C] MOL2 format, chain IB [auth A] MOL2 format, chain ID [auth C] MOL2 format, chain JD [auth C]	IB [auth A], ID [auth C], JD [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain IB [auth A] Focus chain ID [auth C] Focus chain JD [auth C] Interactions & Density Focus chain IB [auth A] Focus chain ID [auth C] Focus chain JD [auth C]