9VDJ | pdb_00009vdj

Serial synchrotron crystallography structure of a ba3-type cytochrome c oxidase using a goniometer-compatible chip-based platform

PDB DOI: https://doi.org/10.2210/pdb9VDJ/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Thermus thermophilus HB8
Expression System: Thermus thermophilus
Mutation(s): No

Deposited: 2025-06-08 Released: 2026-03-25
Deposition Author(s): Kabbinale, A., Branden, G., Neutze, R., Ghosh, S.
Funding Organization(s): European Research Council (ERC), Swedish Research Council, The Swedish Foundation for Strategic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.264 (Depositor), 0.263 (DCC)
R-Value Work:
0.209 (Depositor), 0.207 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons.

Ghosh, S., Banacore, A., Norder, P., Bjelcic, M., Kabbinale, A., Nileshwar, P., Wehlander, G., de Sanctis, D., Basu, S., Orlans, J., Vallejos, A., Chavas, L.M.G., Neutze, R., Branden, G.

(2026) J Appl Crystallogr 59: 303-315

PubMed: 41959872 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1600576725011513
Primary Citation Related Structures:
9S39, 9TBL, 9UYR, 9VDJ, 9VDX

PubMed Abstract:
Fixed-target platforms provide convenient support for microcrystals during serial X-ray crystallography studies using synchrotron radiation. Here, we describe a simple user-friendly 3D-printed support where the crystals are sandwiched between two layers of thin X-ray-transparent membrane resulting in very low scattering background. The platform is compatible with magnetic mounting onto the standard goniometer of macromolecular crystallography beamlines. Our design utilizes a 96-well frame that facilitates hanging-drop experiments directly on the membrane using conventional crystallization plates, thereby eliminating multiple pipetting and crystal handling steps. Crystals can be enclosed in a sandwich and packed into 'cassettes', preventing the risk of the sample drying out during room-temperature transportation to synchrotron sources. The versatility of the platform is demonstrated by five structures solved using different crystallization and data-collection strategies. Lysozyme single-crystal rotational crystallography at room temperature is shown, as well as microcrystal serial data collection under cryogenic conditions. On-chip microcrystallization is illustrated by use of a photosynthetic reaction center as an example. Finally, serial crystallography data collection at room temperature from microcrystals of the membrane protein cytochrome c oxidase crystallized in lipidic cubic phase is presented.

Organizational Affiliation

Department of Chemistry and Molecular Biology Gothenburg University Sweden.

Macromolecule Content

Total Structure Weight: 92.97 kDa
Atom Count: 6,426
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
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
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
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 5 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 (Subject of Investigation/LOI) 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 (Subject of Investigation/LOI) Query on OLC Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain V [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] 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 J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain V [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] 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 J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain V [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B] 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 J [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], R [auth B], T [auth B], U [auth B], V [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 R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [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 R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C]
CUA (Subject of Investigation/LOI) Query on CUA Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
CU (Subject of Investigation/LOI) 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.264 (Depositor), 0.263 (DCC)
R-Value Work: 0.209 (Depositor), 0.207 (DCC)
R-Value Observed: 0.212 (Depositor)

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
MxCuBE	data collection
CrystFEL	data reduction
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	789030 and 963936
Swedish Research Council	Sweden	2017-06734, 2021-05662 and 2021-05981
Swedish Research Council	Sweden	2015-00560
The Swedish Foundation for Strategic Research	Sweden	ID17-0060

Revision History (Full details and data files)

Version 1.0: 2026-03-25
Type: Initial release
Version 1.1: 2026-04-22
Changes: Database references
Version 1.2: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Derived calculations, Structure summary