9LTU | pdb_00009ltu

Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 1)

PDB DOI: https://doi.org/10.2210/pdb9LTU/pdb
EM Map EMD-63381: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Dinoroseobacter shibae DFL 12 = DSM 16493
Mutation(s): No

Deposited: 2025-02-06 Released: 2025-10-01
Deposition Author(s): Liu, Z.K., Wang, P., Liu, L.N.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.44 Å
Resolution: 2.44 Å
Resolution: 2.44 Å
Resolution: 2.44 Å
Resolution: 2.44 Å
Resolution: 2.44 Å
Resolution: 2.44 Å
Resolution: 2.44 Å
Resolution: 2.44 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

Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 1)

Liu, Z.K., Wang, P., Liu, L.N.

To be published.

Macromolecule Content

Total Structure Weight: 286.23 kDa
Atom Count: 20,306
Modeled Residue Count: 2,160
Deposited Residue Count: 2,160
Unique protein chains: 6

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein beta chain	A [auth 0] C [auth 8] J [auth b] L [auth d] N [auth f] A [auth 0], C [auth 8], J [auth b], L [auth d], N [auth f], P [auth h], R [auth j], T [auth l], V [auth n], X [auth p]	44	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0
UniProt
Find proteins for A8LQ14 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LQ14 Go to UniProtKB: A8LQ14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LQ14
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein alpha chain	B [auth 7] D [auth 9] I [auth a] K [auth c] M [auth e] B [auth 7], D [auth 9], I [auth a], K [auth c], M [auth e], O [auth g], Q [auth i], S [auth k], U [auth m], W [auth o]	51	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0
UniProt
Find proteins for A8LQ15 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LQ15 Go to UniProtKB: A8LQ15
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LQ15
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	E [auth C]	357	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0
UniProt
Find proteins for A8LQ18 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LQ18 Go to UniProtKB: A8LQ18
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LQ18
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	F [auth H]	255	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0
UniProt
Find proteins for A8LQ33 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LQ33 Go to UniProtKB: A8LQ33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LQ33
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	G [auth L]	273	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0
UniProt
Find proteins for A8LQ16 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LQ16 Go to UniProtKB: A8LQ16
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LQ16
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	H [auth M]	325	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0
UniProt
Find proteins for A8LQ17 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LQ17 Go to UniProtKB: A8LQ17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LQ17
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL (Subject of Investigation/LOI) Query on BCL Download Ideal Coordinates CCD File SDF format, chain ZA [auth d] SDF format, chain YA [auth c] SDF format, chain Y [auth 0] SDF format, chain XA [auth b] SDF format, chain WB [auth p] SDF format, chain VB [auth o] SDF format, chain TB [auth n] SDF format, chain TA [auth a] SDF format, chain RB [auth m] SDF format, chain RA [auth M] SDF format, chain PB [auth l] SDF format, chain OB [auth k] SDF format, chain OA [auth M] SDF format, chain NB [auth j] SDF format, chain KB [auth i] SDF format, chain KA [auth L] SDF format, chain IB [auth h] SDF format, chain IA [auth L] SDF format, chain FB [auth g] SDF format, chain EA [auth 9] SDF format, chain DB [auth f] SDF format, chain BA [auth 8] SDF format, chain AB [auth e] SDF format, chain AA [auth 7] MOL2 format, chain ZA [auth d] MOL2 format, chain YA [auth c] MOL2 format, chain Y [auth 0] MOL2 format, chain XA [auth b] MOL2 format, chain WB [auth p] MOL2 format, chain VB [auth o] MOL2 format, chain TB [auth n] MOL2 format, chain TA [auth a] MOL2 format, chain RB [auth m] MOL2 format, chain RA [auth M] MOL2 format, chain PB [auth l] MOL2 format, chain OB [auth k] MOL2 format, chain OA [auth M] MOL2 format, chain NB [auth j] MOL2 format, chain KB [auth i] MOL2 format, chain KA [auth L] MOL2 format, chain IB [auth h] MOL2 format, chain IA [auth L] MOL2 format, chain FB [auth g] MOL2 format, chain EA [auth 9] MOL2 format, chain DB [auth f] MOL2 format, chain BA [auth 8] MOL2 format, chain AB [auth e] MOL2 format, chain AA [auth 7] mmCIF format, chain ZA [auth d] mmCIF format, chain YA [auth c] mmCIF format, chain Y [auth 0] mmCIF format, chain XA [auth b] mmCIF format, chain WB [auth p] mmCIF format, chain VB [auth o] mmCIF format, chain TB [auth n] mmCIF format, chain TA [auth a] mmCIF format, chain RB [auth m] mmCIF format, chain RA [auth M] mmCIF format, chain PB [auth l] mmCIF format, chain OB [auth k] mmCIF format, chain OA [auth M] mmCIF format, chain NB [auth j] mmCIF format, chain KB [auth i] mmCIF format, chain KA [auth L] mmCIF format, chain IB [auth h] mmCIF format, chain IA [auth L] mmCIF format, chain FB [auth g] mmCIF format, chain EA [auth 9] mmCIF format, chain DB [auth f] mmCIF format, chain BA [auth 8] mmCIF format, chain AB [auth e] mmCIF format, chain AA [auth 7]	AA [auth 7] AB [auth e] BA [auth 8] DB [auth f] EA [auth 9] AA [auth 7], AB [auth e], BA [auth 8], DB [auth f], EA [auth 9], FB [auth g], IA [auth L], IB [auth h], KA [auth L], KB [auth i], NB [auth j], OA [auth M], OB [auth k], PB [auth l], RA [auth M], RB [auth m], TA [auth a], TB [auth n], VB [auth o], WB [auth p], XA [auth b], Y [auth 0], YA [auth c], ZA [auth d]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AA [auth 7] Focus chain AB [auth e] Focus chain BA [auth 8] Focus chain DB [auth f] Focus chain EA [auth 9] Focus chain FB [auth g] Focus chain IA [auth L] Focus chain IB [auth h] Focus chain KA [auth L] Focus chain KB [auth i] Focus chain NB [auth j] Focus chain OA [auth M] Focus chain OB [auth k] Focus chain PB [auth l] Focus chain RA [auth M] Focus chain RB [auth m] Focus chain TA [auth a] Focus chain TB [auth n] Focus chain VB [auth o] Focus chain WB [auth p] Focus chain XA [auth b] Focus chain Y [auth 0] Focus chain YA [auth c] Focus chain ZA [auth d] Interactions & Density Focus chain AA [auth 7] Focus chain AB [auth e] Focus chain BA [auth 8] Focus chain DB [auth f] Focus chain EA [auth 9] Focus chain FB [auth g] Focus chain IA [auth L] Focus chain IB [auth h] Focus chain KA [auth L] Focus chain KB [auth i] Focus chain NB [auth j] Focus chain OA [auth M] Focus chain OB [auth k] Focus chain PB [auth l] Focus chain RA [auth M] Focus chain RB [auth m] Focus chain TA [auth a] Focus chain TB [auth n] Focus chain VB [auth o] Focus chain WB [auth p] Focus chain XA [auth b] Focus chain Y [auth 0] Focus chain YA [auth c] Focus chain ZA [auth d]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain QA [auth M] SDF format, chain MA [auth L] SDF format, chain LA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain MA [auth L] MOL2 format, chain LA [auth L] mmCIF format, chain QA [auth M] mmCIF format, chain MA [auth L] mmCIF format, chain LA [auth L]	LA [auth L], MA [auth L], QA [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain LA [auth L] Focus chain MA [auth L] Focus chain QA [auth M] Interactions & Density Focus chain LA [auth L] Focus chain MA [auth L] Focus chain QA [auth M]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain PA [auth M] SDF format, chain JA [auth L] MOL2 format, chain PA [auth M] MOL2 format, chain JA [auth L] mmCIF format, chain PA [auth M] mmCIF format, chain JA [auth L]	JA [auth L], PA [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain JA [auth L] Focus chain PA [auth M] Interactions & Density Focus chain JA [auth L] Focus chain PA [auth M]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C]	FA [auth C], GA [auth C], HA [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C]
SPN (Subject of Investigation/LOI) Query on SPN Download Ideal Coordinates CCD File SDF format, chain Z [auth 0] SDF format, chain YB [auth p] SDF format, chain XB [auth p] SDF format, chain WA [auth a] SDF format, chain VA [auth a] SDF format, chain UB [auth n] SDF format, chain UA [auth a] SDF format, chain SB [auth m] SDF format, chain SA [auth M] SDF format, chain QB [auth l] SDF format, chain MB [auth i] SDF format, chain LB [auth i] SDF format, chain JB [auth h] SDF format, chain HB [auth g] SDF format, chain GB [auth g] SDF format, chain EB [auth f] SDF format, chain DA [auth 9] SDF format, chain CB [auth f] SDF format, chain CA [auth 8] SDF format, chain BB [auth e] MOL2 format, chain Z [auth 0] MOL2 format, chain YB [auth p] MOL2 format, chain XB [auth p] MOL2 format, chain WA [auth a] MOL2 format, chain VA [auth a] MOL2 format, chain UB [auth n] MOL2 format, chain UA [auth a] MOL2 format, chain SB [auth m] MOL2 format, chain SA [auth M] MOL2 format, chain QB [auth l] MOL2 format, chain MB [auth i] MOL2 format, chain LB [auth i] MOL2 format, chain JB [auth h] MOL2 format, chain HB [auth g] MOL2 format, chain GB [auth g] MOL2 format, chain EB [auth f] MOL2 format, chain DA [auth 9] MOL2 format, chain CB [auth f] MOL2 format, chain CA [auth 8] MOL2 format, chain BB [auth e] mmCIF format, chain Z [auth 0] mmCIF format, chain YB [auth p] mmCIF format, chain XB [auth p] mmCIF format, chain WA [auth a] mmCIF format, chain VA [auth a] mmCIF format, chain UB [auth n] mmCIF format, chain UA [auth a] mmCIF format, chain SB [auth m] mmCIF format, chain SA [auth M] mmCIF format, chain QB [auth l] mmCIF format, chain MB [auth i] mmCIF format, chain LB [auth i] mmCIF format, chain JB [auth h] mmCIF format, chain HB [auth g] mmCIF format, chain GB [auth g] mmCIF format, chain EB [auth f] mmCIF format, chain DA [auth 9] mmCIF format, chain CB [auth f] mmCIF format, chain CA [auth 8] mmCIF format, chain BB [auth e]	BB [auth e] CA [auth 8] CB [auth f] DA [auth 9] EB [auth f] BB [auth e], CA [auth 8], CB [auth f], DA [auth 9], EB [auth f], GB [auth g], HB [auth g], JB [auth h], LB [auth i], MB [auth i], QB [auth l], SA [auth M], SB [auth m], UA [auth a], UB [auth n], VA [auth a], WA [auth a], XB [auth p], YB [auth p], Z [auth 0]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain BB [auth e] Focus chain CA [auth 8] Focus chain CB [auth f] Focus chain DA [auth 9] Focus chain EB [auth f] Focus chain GB [auth g] Focus chain HB [auth g] Focus chain JB [auth h] Focus chain LB [auth i] Focus chain MB [auth i] Focus chain QB [auth l] Focus chain SA [auth M] Focus chain SB [auth m] Focus chain UA [auth a] Focus chain UB [auth n] Focus chain VA [auth a] Focus chain WA [auth a] Focus chain XB [auth p] Focus chain YB [auth p] Focus chain Z [auth 0] Interactions & Density Focus chain BB [auth e] Focus chain CA [auth 8] Focus chain CB [auth f] Focus chain DA [auth 9] Focus chain EB [auth f] Focus chain GB [auth g] Focus chain HB [auth g] Focus chain JB [auth h] Focus chain LB [auth i] Focus chain MB [auth i] Focus chain QB [auth l] Focus chain SA [auth M] Focus chain SB [auth m] Focus chain UA [auth a] Focus chain UB [auth n] Focus chain VA [auth a] Focus chain WA [auth a] Focus chain XB [auth p] Focus chain YB [auth p] Focus chain Z [auth 0]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain NA [auth M] MOL2 format, chain NA [auth M] mmCIF format, chain NA [auth M]	NA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain NA [auth M] Interactions & Density Focus chain NA [auth M]