9J2F | pdb_00009j2f

Structure of photosynthetic LH1-RC complex from the purple bacterium Blastochloris tepida

PDB DOI: https://doi.org/10.2210/pdb9J2F/pdb
EM Map EMD-61095: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Blastochloris tepida
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2024-08-06 Released: 2024-12-18
Deposition Author(s): Kimura, Y., Kanno, R., Mori, K., Matsuda, Y., Seto, R., Takenaka, S., Mino, H., Ohkubo, T., Honda, M., Sasaki, Y.C., Kishikawa, J., Mitsuoka, K., Mio, K., Hall, M., Purba, E.R., Mochizuki, T., Mizoguchi, A., Humbel, B.M., Madigan, M.T., Wang-Otomo, Z.-Y., Tani, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Thermal-Stable LH1-RC Complex of a Hot Spring Purple Bacterium Powers Photosynthesis with Extremely Low-Energy Near-Infrared Light.

Kimura, Y., Kanno, R., Mori, K., Matsuda, Y., Seto, R., Takenaka, S., Mino, H., Ohkubo, T., Honda, M., Sasaki, Y.C., Kishikawa, J.I., Mitsuoka, K., Mio, K., Hall, M., Purba, E.R., Mochizuki, T., Mizoguchi, A., Humbel, B.M., Madigan, M.T., Wang-Otomo, Z.Y., Tani, K.

(2025) Biochemistry 64: 170-179

PubMed: 39680849 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.4c00506
Primary Citation Related Structures:
9J2F

PubMed Abstract:
Blastochloris (Blc.) tepida is a hot spring purple nonsulfur phototrophic bacterium that contains bacteriochlorophyll (BChl) b . Here, we present a 2.21 Å cryo-EM structure of the thermostable light-harvesting 1-reaction center (LH1-RC) complex from Blc. tepida . The LH1 ring comprises 16 circularly arranged αβγ-subunits plus one αβ-subunit that surround the RC complex composed of C-, H-, L-, and M-subunits. In a comparative study, the Blc. tepida LH1-RC showed numerous electrostatic and hydrophobic interactions both within the LH1 complex itself and between the LH1 and the RC complexes that are absent from the LH1-RC complex of its mesophilic counterpart, Blc. viridis . These additional interactions result in a tightly packed LH1-RC architecture with a reduced accessible surface area per volume that enhances the thermal stability of the Blc. tepida complex and allows the light reactions of photosynthesis to proceed at hot spring temperatures. Moreover, based on high-resolution structural information combined with spectroscopic evidence, the unique photosynthetic property of the Blc. tepida LH1-RC─absorption of energy-poor near-infrared light beyond 1000 nm─can be attributed to strong hydrogen-bonding interactions between the C3-acetyl C═O of the LH1 BChl b and two LH1 α-Trp residues, structural rigidity of the LH1, and the enhanced exciton coupling of the LH1 BChls of this thermophile.

Organizational Affiliation

Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Kobe, Nada 657-8501, Japan.

Macromolecule Content

Total Structure Weight: 562.61 kDa
Atom Count: 32,918
Modeled Residue Count: 3,464
Deposited Residue Count: 4,477
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	354	Blastochloris tepida	Mutation(s): 0
UniProt
Find proteins for A0A348FW74 (Blastochloris tepida) Explore A0A348FW74 Go to UniProtKB: A0A348FW74
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UniProt Group	A0A348FW74
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	274	Blastochloris tepida	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A348FW72 (Blastochloris tepida) Explore A0A348FW72 Go to UniProtKB: A0A348FW72
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UniProt Group	A0A348FW72
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	332	Blastochloris tepida	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A348FW73 (Blastochloris tepida) Explore A0A348FW73 Go to UniProtKB: A0A348FW73
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UniProt Group	A0A348FW73
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center subunit H	D [auth H]	260	Blastochloris tepida	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A348FW44 (Blastochloris tepida) Explore A0A348FW44 Go to UniProtKB: A0A348FW44
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UniProt Group	A0A348FW44
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit domain-containing protein	AB [auth q] CA [auth 3] E [auth A] FA [auth 6] H [auth D] AB [auth q], CA [auth 3], E [auth A], FA [auth 6], H [auth D], IA [auth 9], K [auth I], LA [auth b], N, OA [auth e], Q, RA [auth h], T, UA [auth k], W, XA [auth n], Z	69	Blastochloris tepida	Mutation(s): 0 Membrane Entity: Yes
UniProt
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UniProt Group	A0A348FW71
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit domain-containing protein	AA [auth 1] BB [auth r] DA [auth 4] F [auth B] GA [auth 7] AA [auth 1], BB [auth r], DA [auth 4], F [auth B], GA [auth 7], I [auth E], JA [auth 0], L [auth J], MA [auth c], O, PA [auth f], R, SA [auth i], U, VA [auth l], X, YA [auth o]	69	Blastochloris tepida	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A348FW70 (Blastochloris tepida) Explore A0A348FW70 Go to UniProtKB: A0A348FW70
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UniProt Group	A0A348FW70
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein gamma1	G	56	Blastochloris tepida	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A348G0X9 (Blastochloris tepida) Explore A0A348G0X9 Go to UniProtKB: A0A348G0X9
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UniProt Group	A0A348G0X9
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-1015 gamma chain	BA [auth 2] EA [auth 5] HA [auth 8] J [auth F] KA [auth a] BA [auth 2], EA [auth 5], HA [auth 8], J [auth F], KA [auth a], M [auth K], NA [auth d], P, QA [auth g], S, TA [auth j], V, WA [auth m], Y, ZA [auth p]	57	Blastochloris tepida	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A348G0Y0 (Blastochloris tepida) Explore A0A348G0Y0 Go to UniProtKB: A0A348G0Y0
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A348G0Y0
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Reference Sequence

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain WB [auth M] SDF format, chain ZB [auth H] SDF format, chain NB [auth L] SDF format, chain ME [auth r] SDF format, chain AC [auth H] MOL2 format, chain WB [auth M] MOL2 format, chain ZB [auth H] MOL2 format, chain NB [auth L] MOL2 format, chain ME [auth r] MOL2 format, chain AC [auth H] mmCIF format, chain WB [auth M] mmCIF format, chain ZB [auth H] mmCIF format, chain NB [auth L] mmCIF format, chain ME [auth r] mmCIF format, chain AC [auth H]	AC [auth H], ME [auth r], NB [auth L], WB [auth M], ZB [auth H]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain AC [auth H] Focus chain ME [auth r] Focus chain NB [auth L] Focus chain WB [auth M] Focus chain ZB [auth H] Interactions & Density Focus chain AC [auth H] Focus chain ME [auth r] Focus chain NB [auth L] Focus chain WB [auth M] Focus chain ZB [auth H]
BCB (Subject of Investigation/LOI) Query on BCB Download:Ideal Coordinates CCD File SDF format, chain BE [auth k] SDF format, chain ED [auth Z] SDF format, chain FC [auth B] SDF format, chain FE [auth n] SDF format, chain JB [auth L] SDF format, chain JC [auth E] SDF format, chain JD [auth 6] SDF format, chain KB [auth L] SDF format, chain LE [auth r] SDF format, chain MD [auth 9] SDF format, chain PB [auth M] SDF format, chain PD [auth 0] SDF format, chain QB [auth M] SDF format, chain QC [auth O] SDF format, chain UC [auth R] SDF format, chain YC [auth U] SDF format, chain ZD [auth i] SDF format, chain XD [auth h] SDF format, chain VD [auth f] SDF format, chain VC [auth T] SDF format, chain UD [auth e] SDF format, chain TD [auth c] SDF format, chain SC [auth Q] SDF format, chain QD [auth b] SDF format, chain NC [auth N] SDF format, chain MC [auth J] SDF format, chain LD [auth 7] SDF format, chain KC [auth I] SDF format, chain JE [auth q] SDF format, chain IE [auth o] SDF format, chain ID [auth 4] SDF format, chain HD [auth 3] SDF format, chain GC [auth D] SDF format, chain FD [auth 1] SDF format, chain EE [auth l] SDF format, chain DD [auth X] SDF format, chain CC [auth A] SDF format, chain AD [auth W] MOL2 format, chain BE [auth k] MOL2 format, chain ED [auth Z] MOL2 format, chain FC [auth B] MOL2 format, chain FE [auth n] MOL2 format, chain JB [auth L] MOL2 format, chain JC [auth E] MOL2 format, chain JD [auth 6] MOL2 format, chain KB [auth L] MOL2 format, chain LE [auth r] MOL2 format, chain MD [auth 9] MOL2 format, chain PB [auth M] MOL2 format, chain PD [auth 0] MOL2 format, chain QB [auth M] MOL2 format, chain QC [auth O] MOL2 format, chain UC [auth R] MOL2 format, chain YC [auth U] MOL2 format, chain ZD [auth i] MOL2 format, chain XD [auth h] MOL2 format, chain VD [auth f] MOL2 format, chain VC [auth T] MOL2 format, chain UD [auth e] MOL2 format, chain TD [auth c] MOL2 format, chain SC [auth Q] MOL2 format, chain QD [auth b] MOL2 format, chain NC [auth N] MOL2 format, chain MC [auth J] MOL2 format, chain LD [auth 7] MOL2 format, chain KC [auth I] MOL2 format, chain JE [auth q] MOL2 format, chain IE [auth o] MOL2 format, chain ID [auth 4] MOL2 format, chain HD [auth 3] MOL2 format, chain GC [auth D] MOL2 format, chain FD [auth 1] MOL2 format, chain EE [auth l] MOL2 format, chain DD [auth X] MOL2 format, chain CC [auth A] MOL2 format, chain AD [auth W] mmCIF format, chain BE [auth k] mmCIF format, chain ED [auth Z] mmCIF format, chain FC [auth B] mmCIF format, chain FE [auth n] mmCIF format, chain JB [auth L] mmCIF format, chain JC [auth E] mmCIF format, chain JD [auth 6] mmCIF format, chain KB [auth L] mmCIF format, chain LE [auth r] mmCIF format, chain MD [auth 9] mmCIF format, chain PB [auth M] mmCIF format, chain PD [auth 0] mmCIF format, chain QB [auth M] mmCIF format, chain QC [auth O] mmCIF format, chain UC [auth R] mmCIF format, chain YC [auth U] mmCIF format, chain ZD [auth i] mmCIF format, chain XD [auth h] mmCIF format, chain VD [auth f] mmCIF format, chain VC [auth T] mmCIF format, chain UD [auth e] mmCIF format, chain TD [auth c] mmCIF format, chain SC [auth Q] mmCIF format, chain QD [auth b] mmCIF format, chain NC [auth N] mmCIF format, chain MC [auth J] mmCIF format, chain LD [auth 7] mmCIF format, chain KC [auth I] mmCIF format, chain JE [auth q] mmCIF format, chain IE [auth o] mmCIF format, chain ID [auth 4] mmCIF format, chain HD [auth 3] mmCIF format, chain GC [auth D] mmCIF format, chain FD [auth 1] mmCIF format, chain EE [auth l] mmCIF format, chain DD [auth X] mmCIF format, chain CC [auth A] mmCIF format, chain AD [auth W]	AD [auth W] BE [auth k] CC [auth A] DD [auth X] ED [auth Z] AD [auth W], BE [auth k], CC [auth A], DD [auth X], ED [auth Z], EE [auth l], FC [auth B], FD [auth 1], FE [auth n], GC [auth D], HD [auth 3], ID [auth 4], IE [auth o], JB [auth L], JC [auth E], JD [auth 6], JE [auth q], KB [auth L], KC [auth I], LD [auth 7], LE [auth r], MC [auth J], MD [auth 9], NC [auth N], PB [auth M], PD [auth 0], QB [auth M], QC [auth O], QD [auth b], SC [auth Q], TD [auth c], UC [auth R], UD [auth e], VC [auth T], VD [auth f], XD [auth h], YC [auth U], ZD [auth i]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain AD [auth W] Focus chain BE [auth k] Focus chain CC [auth A] Focus chain DD [auth X] Focus chain ED [auth Z] Focus chain EE [auth l] Focus chain FC [auth B] Focus chain FD [auth 1] Focus chain FE [auth n] Focus chain GC [auth D] Focus chain HD [auth 3] Focus chain ID [auth 4] Focus chain IE [auth o] Focus chain JB [auth L] Focus chain JC [auth E] Focus chain JD [auth 6] Focus chain JE [auth q] Focus chain KB [auth L] Focus chain KC [auth I] Focus chain LD [auth 7] Focus chain LE [auth r] Focus chain MC [auth J] Focus chain MD [auth 9] Focus chain NC [auth N] Focus chain PB [auth M] Focus chain PD [auth 0] Focus chain QB [auth M] Focus chain QC [auth O] Focus chain QD [auth b] Focus chain SC [auth Q] Focus chain TD [auth c] Focus chain UC [auth R] Focus chain UD [auth e] Focus chain VC [auth T] Focus chain VD [auth f] Focus chain XD [auth h] Focus chain YC [auth U] Focus chain ZD [auth i] Interactions & Density Focus chain AD [auth W] Focus chain BE [auth k] Focus chain CC [auth A] Focus chain DD [auth X] Focus chain ED [auth Z] Focus chain EE [auth l] Focus chain FC [auth B] Focus chain FD [auth 1] Focus chain FE [auth n] Focus chain GC [auth D] Focus chain HD [auth 3] Focus chain ID [auth 4] Focus chain IE [auth o] Focus chain JB [auth L] Focus chain JC [auth E] Focus chain JD [auth 6] Focus chain JE [auth q] Focus chain KB [auth L] Focus chain KC [auth I] Focus chain LD [auth 7] Focus chain LE [auth r] Focus chain MC [auth J] Focus chain MD [auth 9] Focus chain NC [auth N] Focus chain PB [auth M] Focus chain PD [auth 0] Focus chain QB [auth M] Focus chain QC [auth O] Focus chain QD [auth b] Focus chain SC [auth Q] Focus chain TD [auth c] Focus chain UC [auth R] Focus chain UD [auth e] Focus chain VC [auth T] Focus chain VD [auth f] Focus chain XD [auth h] Focus chain YC [auth U] Focus chain ZD [auth i]
BPB Query on BPB Download:Ideal Coordinates CCD File SDF format, chain LB [auth L] SDF format, chain RB [auth M] MOL2 format, chain LB [auth L] MOL2 format, chain RB [auth M] mmCIF format, chain LB [auth L] mmCIF format, chain RB [auth M]	LB [auth L], RB [auth M]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain LB [auth L] Focus chain RB [auth M] Interactions & Density Focus chain LB [auth L] Focus chain RB [auth M]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain HC [auth D] SDF format, chain OC [auth N] SDF format, chain RC [auth Q] SDF format, chain YB [auth M] SDF format, chain ZC [auth W] SDF format, chain LC [auth I] MOL2 format, chain HC [auth D] MOL2 format, chain OC [auth N] MOL2 format, chain RC [auth Q] MOL2 format, chain YB [auth M] MOL2 format, chain ZC [auth W] MOL2 format, chain LC [auth I] mmCIF format, chain HC [auth D] mmCIF format, chain OC [auth N] mmCIF format, chain RC [auth Q] mmCIF format, chain YB [auth M] mmCIF format, chain ZC [auth W] mmCIF format, chain LC [auth I]	HC [auth D] LC [auth I] OC [auth N] RC [auth Q] YB [auth M] HC [auth D], LC [auth I], OC [auth N], RC [auth Q], YB [auth M], ZC [auth W]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain HC [auth D] Focus chain LC [auth I] Focus chain OC [auth N] Focus chain RC [auth Q] Focus chain YB [auth M] Focus chain ZC [auth W] Interactions & Density Focus chain HC [auth D] Focus chain LC [auth I] Focus chain OC [auth N] Focus chain RC [auth Q] Focus chain YB [auth M] Focus chain ZC [auth W]
UQ8 Query on UQ8 Download:Ideal Coordinates CCD File SDF format, chain BC [auth A] SDF format, chain HB [auth C] SDF format, chain MB [auth L] SDF format, chain VB [auth M] SDF format, chain UB [auth M] MOL2 format, chain BC [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain MB [auth L] MOL2 format, chain VB [auth M] MOL2 format, chain UB [auth M] mmCIF format, chain BC [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain MB [auth L] mmCIF format, chain VB [auth M] mmCIF format, chain UB [auth M]	BC [auth A], HB [auth C], MB [auth L], UB [auth M], VB [auth M]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain BC [auth A] Focus chain HB [auth C] Focus chain MB [auth L] Focus chain UB [auth M] Focus chain VB [auth M] Interactions & Density Focus chain BC [auth A] Focus chain HB [auth C] Focus chain MB [auth L] Focus chain UB [auth M] Focus chain VB [auth M]
MQ7 Query on MQ7 Download:Ideal Coordinates CCD File SDF format, chain SB [auth M] MOL2 format, chain SB [auth M] mmCIF format, chain SB [auth M]	SB [auth M]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain SB [auth M] Interactions & Density Focus chain SB [auth M]
DGA Query on DGA Download:Ideal Coordinates CCD File SDF format, chain IB [auth L] MOL2 format, chain IB [auth L] mmCIF format, chain IB [auth L]	IB [auth L]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain IB [auth L] Interactions & Density Focus chain IB [auth L]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain DB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain DB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain DB [auth C]	CB [auth C], DB [auth C], EB [auth C], FB [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Interactions & Density Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C]
NS5 Query on NS5 Download:Ideal Coordinates CCD File SDF format, chain TB [auth M] MOL2 format, chain TB [auth M] mmCIF format, chain TB [auth M]	TB [auth M]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain TB [auth M] Interactions & Density Focus chain TB [auth M]
NS0 Query on NS0 Download:Ideal Coordinates CCD File SDF format, chain AE [auth k] SDF format, chain DE [auth l] SDF format, chain GD [auth 2] SDF format, chain HE [auth o] SDF format, chain IC [auth D] SDF format, chain KD [auth 7] SDF format, chain KE [auth q] SDF format, chain OD [auth 0] SDF format, chain TC [auth R] SDF format, chain WD [auth h] SDF format, chain XC [auth U] SDF format, chain PC [auth O] SDF format, chain ND [auth 9] SDF format, chain DC [auth A] SDF format, chain CD [auth X] SDF format, chain BD [auth W] MOL2 format, chain AE [auth k] MOL2 format, chain DE [auth l] MOL2 format, chain GD [auth 2] MOL2 format, chain HE [auth o] MOL2 format, chain IC [auth D] MOL2 format, chain KD [auth 7] MOL2 format, chain KE [auth q] MOL2 format, chain OD [auth 0] MOL2 format, chain TC [auth R] MOL2 format, chain WD [auth h] MOL2 format, chain XC [auth U] MOL2 format, chain PC [auth O] MOL2 format, chain ND [auth 9] MOL2 format, chain DC [auth A] MOL2 format, chain CD [auth X] MOL2 format, chain BD [auth W] mmCIF format, chain AE [auth k] mmCIF format, chain DE [auth l] mmCIF format, chain GD [auth 2] mmCIF format, chain HE [auth o] mmCIF format, chain IC [auth D] mmCIF format, chain KD [auth 7] mmCIF format, chain KE [auth q] mmCIF format, chain OD [auth 0] mmCIF format, chain TC [auth R] mmCIF format, chain WD [auth h] mmCIF format, chain XC [auth U] mmCIF format, chain PC [auth O] mmCIF format, chain ND [auth 9] mmCIF format, chain DC [auth A] mmCIF format, chain CD [auth X] mmCIF format, chain BD [auth W]	AE [auth k] BD [auth W] CD [auth X] DC [auth A] DE [auth l] AE [auth k], BD [auth W], CD [auth X], DC [auth A], DE [auth l], GD [auth 2], HE [auth o], IC [auth D], KD [auth 7], KE [auth q], ND [auth 9], OD [auth 0], PC [auth O], TC [auth R], WD [auth h], XC [auth U]	all-trans-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-XILUKMICSA-N		Interactions Focus chain AE [auth k] Focus chain BD [auth W] Focus chain CD [auth X] Focus chain DC [auth A] Focus chain DE [auth l] Focus chain GD [auth 2] Focus chain HE [auth o] Focus chain IC [auth D] Focus chain KD [auth 7] Focus chain KE [auth q] Focus chain ND [auth 9] Focus chain OD [auth 0] Focus chain PC [auth O] Focus chain TC [auth R] Focus chain WD [auth h] Focus chain XC [auth U] Interactions & Density Focus chain AE [auth k] Focus chain BD [auth W] Focus chain CD [auth X] Focus chain DC [auth A] Focus chain DE [auth l] Focus chain GD [auth 2] Focus chain HE [auth o] Focus chain IC [auth D] Focus chain KD [auth 7] Focus chain KE [auth q] Focus chain ND [auth 9] Focus chain OD [auth 0] Focus chain PC [auth O] Focus chain TC [auth R] Focus chain WD [auth h] Focus chain XC [auth U]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain CE [auth k] SDF format, chain EC [auth B] SDF format, chain GE [auth n] SDF format, chain RD [auth b] SDF format, chain SD [auth b] SDF format, chain YD [auth h] SDF format, chain XB [auth M] SDF format, chain WC [auth T] MOL2 format, chain CE [auth k] MOL2 format, chain EC [auth B] MOL2 format, chain GE [auth n] MOL2 format, chain RD [auth b] MOL2 format, chain SD [auth b] MOL2 format, chain YD [auth h] MOL2 format, chain XB [auth M] MOL2 format, chain WC [auth T] mmCIF format, chain CE [auth k] mmCIF format, chain EC [auth B] mmCIF format, chain GE [auth n] mmCIF format, chain RD [auth b] mmCIF format, chain SD [auth b] mmCIF format, chain YD [auth h] mmCIF format, chain XB [auth M] mmCIF format, chain WC [auth T]	CE [auth k] EC [auth B] GE [auth n] RD [auth b] SD [auth b] CE [auth k], EC [auth B], GE [auth n], RD [auth b], SD [auth b], WC [auth T], XB [auth M], YD [auth h]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain CE [auth k] Focus chain EC [auth B] Focus chain GE [auth n] Focus chain RD [auth b] Focus chain SD [auth b] Focus chain WC [auth T] Focus chain XB [auth M] Focus chain YD [auth h] Interactions & Density Focus chain CE [auth k] Focus chain EC [auth B] Focus chain GE [auth n] Focus chain RD [auth b] Focus chain SD [auth b] Focus chain WC [auth T] Focus chain XB [auth M] Focus chain YD [auth h]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain OB [auth M] MOL2 format, chain OB [auth M] mmCIF format, chain OB [auth M]	OB [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain OB [auth M] Interactions & Density Focus chain OB [auth M]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain GB [auth C] MOL2 format, chain GB [auth C] mmCIF format, chain GB [auth C]	GB [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GB [auth C] Interactions & Density Focus chain GB [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	D [auth H]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101118
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101116
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H04174
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05153
Japan Society for the Promotion of Science (JSPS)	Japan	20H05086
Japan Society for the Promotion of Science (JSPS)	Japan	20H02856