9LTV | pdb_00009ltv

Cryo-EM structure of the Dinoroseobacter shibae RC-LH1 supercomplex with incomplete LH1 ring(State 2)

PDB DOI: https://doi.org/10.2210/pdb9LTV/pdb
EM Map EMD-63382: 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: 2.75 Å
Resolution: 2.75 Å
Resolution: 2.75 Å
Resolution: 2.75 Å
Resolution: 2.75 Å
Resolution: 2.75 Å
Resolution: 2.75 Å
Resolution: 2.75 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 2)

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

To be published.

Macromolecule Content

Total Structure Weight: 350.66 kDa
Atom Count: 24,857
Modeled Residue Count: 2,616
Deposited Residue Count: 2,616
Unique protein chains: 7

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein beta chain	A [auth 0] AA [auth l] C [auth 2] CA [auth n] E [auth 4] A [auth 0], AA [auth l], C [auth 2], CA [auth n], E [auth 4], EA [auth p], G [auth 6], GA [auth x], I [auth 8], Q [auth b], S [auth d], U [auth f], W [auth h], Y [auth j]	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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein alpha chain	B [auth 1] BA [auth m] D [auth 3] DA [auth o] F [auth 5] B [auth 1], BA [auth m], D [auth 3], DA [auth o], F [auth 5], FA [auth w], H [auth 7], J [auth 9], P [auth a], R [auth c], T [auth e], V [auth g], X [auth i], Z [auth k]	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

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LRC	K [auth A]	76	Dinoroseobacter shibae DFL 12 = DSM 16493	Mutation(s): 0
UniProt
Find proteins for A8LIU2 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LIU2 Go to UniProtKB: A8LIU2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8LIU2
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	L [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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	M [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
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	N [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
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	O [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 AB [auth 9] SDF format, chain CC [auth g] SDF format, chain EB [auth L] SDF format, chain FC [auth h] SDF format, chain GB [auth L] SDF format, chain HA [auth 0] SDF format, chain HC [auth i] SDF format, chain JA [auth 1] SDF format, chain JC [auth j] SDF format, chain KB [auth M] SDF format, chain MA [auth 2] SDF format, chain MC [auth l] SDF format, chain NA [auth 3] SDF format, chain OC [auth m] SDF format, chain PA [auth 4] SDF format, chain PC [auth n] SDF format, chain RA [auth 5] SDF format, chain SC [auth o] SDF format, chain TC [auth p] SDF format, chain UA [auth 6] SDF format, chain UB [auth c] SDF format, chain VA [auth 7] SDF format, chain VC [auth w] SDF format, chain WB [auth d] SDF format, chain XA [auth 8] SDF format, chain XC [auth x] SDF format, chain YB [auth e] SDF format, chain ZB [auth f] SDF format, chain SB [auth b] SDF format, chain QB [auth a] SDF format, chain NB [auth M] SDF format, chain KC [auth k] MOL2 format, chain AB [auth 9] MOL2 format, chain CC [auth g] MOL2 format, chain EB [auth L] MOL2 format, chain FC [auth h] MOL2 format, chain GB [auth L] MOL2 format, chain HA [auth 0] MOL2 format, chain HC [auth i] MOL2 format, chain JA [auth 1] MOL2 format, chain JC [auth j] MOL2 format, chain KB [auth M] MOL2 format, chain MA [auth 2] MOL2 format, chain MC [auth l] MOL2 format, chain NA [auth 3] MOL2 format, chain OC [auth m] MOL2 format, chain PA [auth 4] MOL2 format, chain PC [auth n] MOL2 format, chain RA [auth 5] MOL2 format, chain SC [auth o] MOL2 format, chain TC [auth p] MOL2 format, chain UA [auth 6] MOL2 format, chain UB [auth c] MOL2 format, chain VA [auth 7] MOL2 format, chain VC [auth w] MOL2 format, chain WB [auth d] MOL2 format, chain XA [auth 8] MOL2 format, chain XC [auth x] MOL2 format, chain YB [auth e] MOL2 format, chain ZB [auth f] MOL2 format, chain SB [auth b] MOL2 format, chain QB [auth a] MOL2 format, chain NB [auth M] MOL2 format, chain KC [auth k] mmCIF format, chain AB [auth 9] mmCIF format, chain CC [auth g] mmCIF format, chain EB [auth L] mmCIF format, chain FC [auth h] mmCIF format, chain GB [auth L] mmCIF format, chain HA [auth 0] mmCIF format, chain HC [auth i] mmCIF format, chain JA [auth 1] mmCIF format, chain JC [auth j] mmCIF format, chain KB [auth M] mmCIF format, chain MA [auth 2] mmCIF format, chain MC [auth l] mmCIF format, chain NA [auth 3] mmCIF format, chain OC [auth m] mmCIF format, chain PA [auth 4] mmCIF format, chain PC [auth n] mmCIF format, chain RA [auth 5] mmCIF format, chain SC [auth o] mmCIF format, chain TC [auth p] mmCIF format, chain UA [auth 6] mmCIF format, chain UB [auth c] mmCIF format, chain VA [auth 7] mmCIF format, chain VC [auth w] mmCIF format, chain WB [auth d] mmCIF format, chain XA [auth 8] mmCIF format, chain XC [auth x] mmCIF format, chain YB [auth e] mmCIF format, chain ZB [auth f] mmCIF format, chain SB [auth b] mmCIF format, chain QB [auth a] mmCIF format, chain NB [auth M] mmCIF format, chain KC [auth k]	AB [auth 9] CC [auth g] EB [auth L] FC [auth h] GB [auth L] AB [auth 9], CC [auth g], EB [auth L], FC [auth h], GB [auth L], HA [auth 0], HC [auth i], JA [auth 1], JC [auth j], KB [auth M], KC [auth k], MA [auth 2], MC [auth l], NA [auth 3], NB [auth M], OC [auth m], PA [auth 4], PC [auth n], QB [auth a], RA [auth 5], SB [auth b], SC [auth o], TC [auth p], UA [auth 6], UB [auth c], VA [auth 7], VC [auth w], WB [auth d], XA [auth 8], XC [auth x], YB [auth e], ZB [auth f]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AB [auth 9] Focus chain CC [auth g] Focus chain EB [auth L] Focus chain FC [auth h] Focus chain GB [auth L] Focus chain HA [auth 0] Focus chain HC [auth i] Focus chain JA [auth 1] Focus chain JC [auth j] Focus chain KB [auth M] Focus chain KC [auth k] Focus chain MA [auth 2] Focus chain MC [auth l] Focus chain NA [auth 3] Focus chain NB [auth M] Focus chain OC [auth m] Focus chain PA [auth 4] Focus chain PC [auth n] Focus chain QB [auth a] Focus chain RA [auth 5] Focus chain SB [auth b] Focus chain SC [auth o] Focus chain TC [auth p] Focus chain UA [auth 6] Focus chain UB [auth c] Focus chain VA [auth 7] Focus chain VC [auth w] Focus chain WB [auth d] Focus chain XA [auth 8] Focus chain XC [auth x] Focus chain YB [auth e] Focus chain ZB [auth f] Interactions & Density Focus chain AB [auth 9] Focus chain CC [auth g] Focus chain EB [auth L] Focus chain FC [auth h] Focus chain GB [auth L] Focus chain HA [auth 0] Focus chain HC [auth i] Focus chain JA [auth 1] Focus chain JC [auth j] Focus chain KB [auth M] Focus chain KC [auth k] Focus chain MA [auth 2] Focus chain MC [auth l] Focus chain NA [auth 3] Focus chain NB [auth M] Focus chain OC [auth m] Focus chain PA [auth 4] Focus chain PC [auth n] Focus chain QB [auth a] Focus chain RA [auth 5] Focus chain SB [auth b] Focus chain SC [auth o] Focus chain TC [auth p] Focus chain UA [auth 6] Focus chain UB [auth c] Focus chain VA [auth 7] Focus chain VC [auth w] Focus chain WB [auth d] Focus chain XA [auth 8] Focus chain XC [auth x] Focus chain YB [auth e] Focus chain ZB [auth f]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain IB [auth L] SDF format, chain MB [auth M] SDF format, chain OB [auth M] MOL2 format, chain IB [auth L] MOL2 format, chain MB [auth M] MOL2 format, chain OB [auth M] mmCIF format, chain IB [auth L] mmCIF format, chain MB [auth M] mmCIF format, chain OB [auth M]	IB [auth L], MB [auth M], OB [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain IB [auth L] Focus chain MB [auth M] Focus chain OB [auth M] Interactions & Density Focus chain IB [auth L] Focus chain MB [auth M] Focus chain OB [auth M]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain FB [auth L] SDF format, chain LB [auth M] SDF format, chain HB [auth L] MOL2 format, chain FB [auth L] MOL2 format, chain LB [auth M] MOL2 format, chain HB [auth L] mmCIF format, chain FB [auth L] mmCIF format, chain LB [auth M] mmCIF format, chain HB [auth L]	FB [auth L], HB [auth L], LB [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain FB [auth L] Focus chain HB [auth L] Focus chain LB [auth M] Interactions & Density Focus chain FB [auth L] Focus chain HB [auth L] Focus chain LB [auth M]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain DB [auth C] SDF format, chain CB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain CB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain CB [auth C]	BB [auth C], CB [auth C], DB [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Interactions & Density Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C]
SPN (Subject of Investigation/LOI) Query on SPN Download Ideal Coordinates CCD File SDF format, chain AC [auth f] SDF format, chain EC [auth g] SDF format, chain GC [auth h] SDF format, chain IA [auth 0] SDF format, chain IC [auth i] SDF format, chain LA [auth 1] SDF format, chain LC [auth k] SDF format, chain NC [auth l] SDF format, chain OA [auth 3] SDF format, chain PB [auth M] SDF format, chain QA [auth 4] SDF format, chain QC [auth n] SDF format, chain RC [auth n] SDF format, chain TA [auth 5] SDF format, chain TB [auth b] SDF format, chain UC [auth p] SDF format, chain WA [auth 7] SDF format, chain WC [auth w] SDF format, chain XB [auth d] SDF format, chain ZA [auth 9] SDF format, chain YA [auth 8] SDF format, chain VB [auth c] SDF format, chain SA [auth 5] SDF format, chain RB [auth a] SDF format, chain KA [auth 1] SDF format, chain DC [auth g] SDF format, chain BC [auth f] MOL2 format, chain AC [auth f] MOL2 format, chain EC [auth g] MOL2 format, chain GC [auth h] MOL2 format, chain IA [auth 0] MOL2 format, chain IC [auth i] MOL2 format, chain LA [auth 1] MOL2 format, chain LC [auth k] MOL2 format, chain NC [auth l] MOL2 format, chain OA [auth 3] MOL2 format, chain PB [auth M] MOL2 format, chain QA [auth 4] MOL2 format, chain QC [auth n] MOL2 format, chain RC [auth n] MOL2 format, chain TA [auth 5] MOL2 format, chain TB [auth b] MOL2 format, chain UC [auth p] MOL2 format, chain WA [auth 7] MOL2 format, chain WC [auth w] MOL2 format, chain XB [auth d] MOL2 format, chain ZA [auth 9] MOL2 format, chain YA [auth 8] MOL2 format, chain VB [auth c] MOL2 format, chain SA [auth 5] MOL2 format, chain RB [auth a] MOL2 format, chain KA [auth 1] MOL2 format, chain DC [auth g] MOL2 format, chain BC [auth f] mmCIF format, chain AC [auth f] mmCIF format, chain EC [auth g] mmCIF format, chain GC [auth h] mmCIF format, chain IA [auth 0] mmCIF format, chain IC [auth i] mmCIF format, chain LA [auth 1] mmCIF format, chain LC [auth k] mmCIF format, chain NC [auth l] mmCIF format, chain OA [auth 3] mmCIF format, chain PB [auth M] mmCIF format, chain QA [auth 4] mmCIF format, chain QC [auth n] mmCIF format, chain RC [auth n] mmCIF format, chain TA [auth 5] mmCIF format, chain TB [auth b] mmCIF format, chain UC [auth p] mmCIF format, chain WA [auth 7] mmCIF format, chain WC [auth w] mmCIF format, chain XB [auth d] mmCIF format, chain ZA [auth 9] mmCIF format, chain YA [auth 8] mmCIF format, chain VB [auth c] mmCIF format, chain SA [auth 5] mmCIF format, chain RB [auth a] mmCIF format, chain KA [auth 1] mmCIF format, chain DC [auth g] mmCIF format, chain BC [auth f]	AC [auth f] BC [auth f] DC [auth g] EC [auth g] GC [auth h] AC [auth f], BC [auth f], DC [auth g], EC [auth g], GC [auth h], IA [auth 0], IC [auth i], KA [auth 1], LA [auth 1], LC [auth k], NC [auth l], OA [auth 3], PB [auth M], QA [auth 4], QC [auth n], RB [auth a], RC [auth n], SA [auth 5], TA [auth 5], TB [auth b], UC [auth p], VB [auth c], WA [auth 7], WC [auth w], XB [auth d], YA [auth 8], ZA [auth 9]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain AC [auth f] Focus chain BC [auth f] Focus chain DC [auth g] Focus chain EC [auth g] Focus chain GC [auth h] Focus chain IA [auth 0] Focus chain IC [auth i] Focus chain KA [auth 1] Focus chain LA [auth 1] Focus chain LC [auth k] Focus chain NC [auth l] Focus chain OA [auth 3] Focus chain PB [auth M] Focus chain QA [auth 4] Focus chain QC [auth n] Focus chain RB [auth a] Focus chain RC [auth n] Focus chain SA [auth 5] Focus chain TA [auth 5] Focus chain TB [auth b] Focus chain UC [auth p] Focus chain VB [auth c] Focus chain WA [auth 7] Focus chain WC [auth w] Focus chain XB [auth d] Focus chain YA [auth 8] Focus chain ZA [auth 9] Interactions & Density Focus chain AC [auth f] Focus chain BC [auth f] Focus chain DC [auth g] Focus chain EC [auth g] Focus chain GC [auth h] Focus chain IA [auth 0] Focus chain IC [auth i] Focus chain KA [auth 1] Focus chain LA [auth 1] Focus chain LC [auth k] Focus chain NC [auth l] Focus chain OA [auth 3] Focus chain PB [auth M] Focus chain QA [auth 4] Focus chain QC [auth n] Focus chain RB [auth a] Focus chain RC [auth n] Focus chain SA [auth 5] Focus chain TA [auth 5] Focus chain TB [auth b] Focus chain UC [auth p] Focus chain VB [auth c] Focus chain WA [auth 7] Focus chain WC [auth w] Focus chain XB [auth d] Focus chain YA [auth 8] Focus chain ZA [auth 9]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain JB [auth M] MOL2 format, chain JB [auth M] mmCIF format, chain JB [auth M]	JB [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain JB [auth M] Interactions & Density Focus chain JB [auth M]