7VZR | pdb_00007vzr

Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the smaller form)

PDB DOI: https://doi.org/10.2210/pdb7VZR/pdb
EM Map EMD-32229: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Chloracidobacterium thermophilum B, Chloracidobacterium thermophilum
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2021-11-16 Released: 2022-12-28
Deposition Author(s): Huang, G.Q., Dong, S.S., Qin, X.C., Sui, S.F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c

Dong, S., Huang, G., Wang, C., Wang, J., Sui, S.F., Qin, X.

(2022) Nat Commun 13: 7745

DOI: https://doi.org/10.1038/s41467-022-35460-6

Macromolecule Content

Total Structure Weight: 324.52 kDa
Atom Count: 21,354
Modeled Residue Count: 2,304
Deposited Residue Count: 2,364
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center subunit M	A, G [auth a]	865	Chloracidobacterium thermophilum B	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G2LDR8 (Chloracidobacterium thermophilum (strain B)) Explore G2LDR8 Go to UniProtKB: G2LDR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2LDR8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c, mono-and diheme variants	B [auth C]	221	Chloracidobacterium thermophilum B	Mutation(s): 0
UniProt
Find proteins for G2LDR4 (Chloracidobacterium thermophilum (strain B)) Explore G2LDR4 Go to UniProtKB: G2LDR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2LDR4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PscE	C [auth E], I [auth e]	35	Chloracidobacterium thermophilum B	Mutation(s): 0
UniProt
Find proteins for G2LK98 (Chloracidobacterium thermophilum (strain B)) Explore G2LK98 Go to UniProtKB: G2LK98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2LK98
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PscF	D [auth F], J [auth f]	35	Chloracidobacterium thermophilum B	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G2LEN5 (Chloracidobacterium thermophilum (strain B)) Explore G2LEN5 Go to UniProtKB: G2LEN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2LEN5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PscG	E [auth G], K [auth g]	45	Chloracidobacterium thermophilum B	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G2LJ20 (Chloracidobacterium thermophilum (strain B)) Explore G2LJ20 Go to UniProtKB: G2LJ20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2LJ20
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
undefined polypeptide	F [auth H], L [auth h]	19	Chloracidobacterium thermophilum	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c domain-containing protein	H [auth c]	145	Chloracidobacterium thermophilum B	Mutation(s): 0
UniProt
Find proteins for G2LDR3 (Chloracidobacterium thermophilum (strain B)) Explore G2LDR3 Go to UniProtKB: G2LDR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2LDR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2GO (Subject of Investigation/LOI) Query on 2GO Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain BB [auth a] MOL2 format, chain M [auth A] MOL2 format, chain BB [auth a] mmCIF format, chain M [auth A] mmCIF format, chain BB [auth a]	BB [auth a], M [auth A]	[methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc C₅₅ H₇₀ N₄ O₆ Zn WIUVDOQKCIQUQM-HCIDKWDRSA-L		Interactions Focus chain BB [auth a] Focus chain M [auth A] Interactions & Density Focus chain BB [auth a] Focus chain M [auth A]
BCL (Subject of Investigation/LOI) Query on BCL Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain JB [auth a] SDF format, chain IB [auth a] SDF format, chain HB [auth a] SDF format, chain GB [auth a] SDF format, chain FB [auth a] SDF format, chain EB [auth a] SDF format, chain DB [auth a] SDF format, chain CB [auth a] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain JB [auth a] MOL2 format, chain IB [auth a] MOL2 format, chain HB [auth a] MOL2 format, chain GB [auth a] MOL2 format, chain FB [auth a] MOL2 format, chain EB [auth a] MOL2 format, chain DB [auth a] MOL2 format, chain CB [auth a] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain JB [auth a] mmCIF format, chain IB [auth a] mmCIF format, chain HB [auth a] mmCIF format, chain GB [auth a] mmCIF format, chain FB [auth a] mmCIF format, chain EB [auth a] mmCIF format, chain DB [auth a] mmCIF format, chain CB [auth a]	CB [auth a] DB [auth a] EB [auth a] FB [auth a] GB [auth a] CB [auth a], DB [auth a], EB [auth a], FB [auth a], GB [auth a], HB [auth a], IB [auth a], JB [auth a], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain CB [auth a] Focus chain DB [auth a] Focus chain EB [auth a] Focus chain FB [auth a] Focus chain GB [auth a] Focus chain HB [auth a] Focus chain IB [auth a] Focus chain JB [auth a] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain CB [auth a] Focus chain DB [auth a] Focus chain EB [auth a] Focus chain FB [auth a] Focus chain GB [auth a] Focus chain HB [auth a] Focus chain IB [auth a] Focus chain JB [auth a] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]
CLA (Subject of Investigation/LOI) Query on CLA Download:Ideal Coordinates CCD File SDF format, chain ZA [auth a] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain SA [auth A] SDF format, chain QA [auth A] SDF format, chain NB [auth a] SDF format, chain MB [auth a] SDF format, chain LB [auth a] SDF format, chain KB [auth a] MOL2 format, chain ZA [auth a] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain NB [auth a] MOL2 format, chain MB [auth a] MOL2 format, chain LB [auth a] MOL2 format, chain KB [auth a] mmCIF format, chain ZA [auth a] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain NB [auth a] mmCIF format, chain MB [auth a] mmCIF format, chain LB [auth a] mmCIF format, chain KB [auth a]	KB [auth a] LB [auth a] MB [auth a] NB [auth a] QA [auth A] KB [auth a], LB [auth a], MB [auth a], NB [auth a], QA [auth A], SA [auth A], V [auth A], W [auth A], X [auth A], ZA [auth a]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain KB [auth a] Focus chain LB [auth a] Focus chain MB [auth a] Focus chain NB [auth a] Focus chain QA [auth A] Focus chain SA [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain ZA [auth a] Interactions & Density Focus chain KB [auth a] Focus chain LB [auth a] Focus chain MB [auth a] Focus chain NB [auth a] Focus chain QA [auth A] Focus chain SA [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain ZA [auth a]
85N (Subject of Investigation/LOI) Query on 85N Download:Ideal Coordinates CCD File SDF format, chain YA [auth G] SDF format, chain RA [auth A] SDF format, chain MC [auth g] SDF format, chain AB [auth a] MOL2 format, chain YA [auth G] MOL2 format, chain RA [auth A] MOL2 format, chain MC [auth g] MOL2 format, chain AB [auth a] mmCIF format, chain YA [auth G] mmCIF format, chain RA [auth A] mmCIF format, chain MC [auth g] mmCIF format, chain AB [auth a]	AB [auth a], MC [auth g], RA [auth A], YA [auth G]	[(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium C₃₉ H₇₆ N O₇ HRFZWHLOBWLUBX-ZGAWMTGXSA-O		Interactions Focus chain AB [auth a] Focus chain MC [auth g] Focus chain RA [auth A] Focus chain YA [auth G] Interactions & Density Focus chain AB [auth a] Focus chain MC [auth g] Focus chain RA [auth A] Focus chain YA [auth G]
85I (Subject of Investigation/LOI) Query on 85I Download:Ideal Coordinates CCD File SDF format, chain SB [auth a] SDF format, chain RB [auth a] SDF format, chain QB [auth a] SDF format, chain CA [auth A] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain SB [auth a] MOL2 format, chain RB [auth a] MOL2 format, chain QB [auth a] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain SB [auth a] mmCIF format, chain RB [auth a] mmCIF format, chain QB [auth a] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth A] QB [auth a] RB [auth a] AA [auth A], BA [auth A], CA [auth A], QB [auth a], RB [auth a], SB [auth a]	[(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate C₃₅ H₇₀ N O₈ P JRBIDHJPLMRMHE-PGUFJCEWSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain QB [auth a] Focus chain RB [auth a] Focus chain SB [auth a] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain QB [auth a] Focus chain RB [auth a] Focus chain SB [auth a]
84Q (Subject of Investigation/LOI) Query on 84Q Download:Ideal Coordinates CCD File SDF format, chain VA [auth E] SDF format, chain TB [auth a] MOL2 format, chain VA [auth E] MOL2 format, chain TB [auth a] mmCIF format, chain VA [auth E] mmCIF format, chain TB [auth a]	TB [auth a], VA [auth E]	[(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate C₃₄ H₆₈ N O₈ P TWGQVFCVUIINRS-UMSFTDKQSA-N		Interactions Focus chain TB [auth a] Focus chain VA [auth E] Interactions & Density Focus chain TB [auth a] Focus chain VA [auth E]
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain TA [auth C] SDF format, chain IC [auth c] MOL2 format, chain TA [auth C] MOL2 format, chain IC [auth c] mmCIF format, chain TA [auth C] mmCIF format, chain IC [auth c]	IC [auth c], TA [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain IC [auth c] Focus chain TA [auth C] Interactions & Density Focus chain IC [auth c] Focus chain TA [auth C]
LYC Query on LYC Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain HC [auth c] MOL2 format, chain Y [auth A] MOL2 format, chain HC [auth c] mmCIF format, chain Y [auth A] mmCIF format, chain HC [auth c]	HC [auth c], Y [auth A]	LYCOPENE C₄₀ H₅₆ OAIJSZIZWZSQBC-GYZMGTAESA-N		Interactions Focus chain HC [auth c] Focus chain Y [auth A] Interactions & Density Focus chain HC [auth c] Focus chain Y [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain PB [auth a] MOL2 format, chain PB [auth a] mmCIF format, chain PB [auth a]	PB [auth a]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain PB [auth a] Interactions & Density Focus chain PB [auth a]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain OB [auth a] MOL2 format, chain Z [auth A] MOL2 format, chain OB [auth a] mmCIF format, chain Z [auth A] mmCIF format, chain OB [auth a]	OB [auth a], Z [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain OB [auth a] Focus chain Z [auth A] Interactions & Density Focus chain OB [auth a] Focus chain Z [auth A]
UNL( Subject of Investigation/LOI) Query on UNL Download:Ideal Coordinates CCD File	AC [auth a] BC [auth a] CC [auth a] DA [auth A] DC [auth a] AC [auth a], BC [auth a], CC [auth a], DA [auth A], DC [auth a], EA [auth A], EC [auth a], FA [auth A], FC [auth a], GA [auth A], GC [auth a], HA [auth A], IA [auth A], JA [auth A], JC [auth c], KA [auth A], KC [auth e], LA [auth A], LC [auth e], MA [auth A], NA [auth A], OA [auth A], PA [auth A], UA [auth C], UB [auth a], VB [auth a], WA [auth E], WB [auth a], XA [auth E], XB [auth a], YB [auth a], ZB [auth a]	Unknown ligand BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AC [auth a] Focus chain BC [auth a] Focus chain CC [auth a] Focus chain DA [auth A] Focus chain DC [auth a] Focus chain EA [auth A] Focus chain EC [auth a] Focus chain FA [auth A] Focus chain FC [auth a] Focus chain GA [auth A] Focus chain GC [auth a] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JC [auth c] Focus chain KA [auth A] Focus chain KC [auth e] Focus chain LA [auth A] Focus chain LC [auth e] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain UA [auth C] Focus chain UB [auth a] Focus chain VB [auth a] Focus chain WA [auth E] Focus chain WB [auth a] Focus chain XA [auth E] Focus chain XB [auth a] Focus chain YB [auth a] Focus chain ZB [auth a] Interactions & Density Focus chain AC [auth a] Focus chain BC [auth a] Focus chain CC [auth a] Focus chain DA [auth A] Focus chain DC [auth a] Focus chain EA [auth A] Focus chain EC [auth a] Focus chain FA [auth A] Focus chain FC [auth a] Focus chain GA [auth A] Focus chain GC [auth a] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JC [auth c] Focus chain KA [auth A] Focus chain KC [auth e] Focus chain LA [auth A] Focus chain LC [auth e] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain UA [auth C] Focus chain UB [auth a] Focus chain VB [auth a] Focus chain WA [auth E] Focus chain WB [auth a] Focus chain XA [auth E] Focus chain XB [auth a] Focus chain YB [auth a] Focus chain ZB [auth a]