8K6Y | pdb_00008k6y

Serial femtosecond crystallography structure of photo dissociated CO from ba3- type cytochrome c oxidase determined by extrapolation method

PDB DOI: https://doi.org/10.2210/pdb8K6Y/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Thermus thermophilus HB8
Expression System: Thermus thermophilus HB8
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-07-25 Released: 2023-11-15
Deposition Author(s): Safari, C., Ghosh, S., Andersson, R., Johannesson, J., Donoso, A.V., Zoric, D., Sandelin, E., Iwata, S., Neutze, R., Branden, G.
Funding Organization(s): Swedish Research Council, Carl Trygger Foundation, European Research Council (ERC), European Commission, Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.435 (Depositor), 0.436 (DCC)
R-Value Work:
0.396 (Depositor), 0.405 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase.

Safari, C., Ghosh, S., Andersson, R., Johannesson, J., Bath, P., Uwangue, O., Dahl, P., Zoric, D., Sandelin, E., Vallejos, A., Nango, E., Tanaka, R., Bosman, R., Borjesson, P., Dunevall, E., Hammarin, G., Ortolani, G., Panman, M., Tanaka, T., Yamashita, A., Arima, T., Sugahara, M., Suzuki, M., Masuda, T., Takeda, H., Yamagiwa, R., Oda, K., Fukuda, M., Tosha, T., Naitow, H., Owada, S., Tono, K., Nureki, O., Iwata, S., Neutze, R., Branden, G.

(2023) Sci Adv 9: eadh4179-eadh4179

PubMed: 38064560 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adh4179
Primary Citation Related Structures:
8AJZ, 8K65, 8K6Y

PubMed Abstract:
Cytochrome c oxidase (C c O) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a ₃ of ba ₃-type C c O. In contrast with the aa ₃-type enzyme, our data show how CO is stabilized on Cu _B through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the Cu _B-CO complex in ba ₃-type C c O and, by extension, the extremely high oxygen affinity of the enzyme.

Organizational Affiliation

Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.

Macromolecule Content

Total Structure Weight: 93 kDa
Atom Count: 6,474
Modeled Residue Count: 752
Deposited Residue Count: 771
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A	569	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: cbaA, TTHA1135 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for Q5SJ79 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ79 Go to UniProtKB: Q5SJ79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJ79
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B	168	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: cbaB, ctaC, TTHA1134 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for Q5SJ80 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ80 Go to UniProtKB: Q5SJ80
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJ80
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide 2A	C	34	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: cbaD, TTHA1133 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P82543 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P82543 Go to UniProtKB: P82543
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82543
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HAS (Subject of Investigation/LOI) Query on HAS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	HEME-AS C₅₄ H₆₄ Fe N₄ O₆ PDYODZVCODUKFH-ZOMLSHGTSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain S [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 M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [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 M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [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 M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth A], U [auth B], V [auth B], W [auth C]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.435 (Depositor), 0.436 (DCC)
R-Value Work: 0.396 (Depositor), 0.405 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.85	α = 90
b = 100.32	β = 126.76
c = 96.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2017-06734 and 2021-05662
Carl Trygger Foundation	Sweden	CTS 16:79
European Research Council (ERC)	European Union	789030
Swedish Research Council	Sweden	2015-00560
European Commission	European Union	Marie Curie Training Network X-probe
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101070