9QG1 | pdb_00009qg1

Natively purified Rubrerythrin 16-mer from the anaerobic extremophile P. furiosus

PDB DOI: https://doi.org/10.2210/pdb9QG1/pdb
EM Map EMD-53127: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus furiosus
Mutation(s): No

Deposited: 2025-03-13 Released: 2025-07-16
Deposition Author(s): Skalidis, I., Song, W., Howes, S., Foerster, F.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9QG1

This is version 1.0 of the entry. See complete history.

Literature

Structure of an oxygen-induced tubular nanocompartment in Pyrococcus furiosus

Song, W., Fiala, J., Skalidis, I., Albanese, P., Patinios, C., Chaillet, M.L., Kengen, S.W., Scheltema, R.A., Howes, S.C., Heck, A.J., Forster, F.

(2025) Elife

DOI: https://doi.org/10.7554/elife.106890.1

Macromolecule Content

Total Structure Weight: 315.15 kDa
Atom Count: 21,968
Modeled Residue Count: 2,736
Deposited Residue Count: 2,736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubrerythrin	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	171	Pyrococcus furiosus	Mutation(s): 0
UniProt
Find proteins for E7FHI1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore E7FHI1 Go to UniProtKB: E7FHI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E7FHI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth M] SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain JB [auth P] SDF format, chain S [auth A] SDF format, chain TA [auth J] SDF format, chain U [auth B] SDF format, chain UA [auth K] SDF format, chain W [auth C] SDF format, chain ZA [auth L] SDF format, chain Z [auth D] SDF format, chain YA [auth L] SDF format, chain Y [auth D] SDF format, chain XA [auth L] SDF format, chain X [auth C] SDF format, chain WA [auth K] SDF format, chain VA [auth K] SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth J] SDF format, chain RA [auth J] SDF format, chain R [auth A] SDF format, chain QA [auth J] SDF format, chain Q [auth A] SDF format, chain PA [auth I] SDF format, chain OA [auth I] SDF format, chain NA [auth H] SDF format, chain MA [auth H] SDF format, chain LB [auth P] SDF format, chain LA [auth H] SDF format, chain KB [auth P] SDF format, chain KA [auth G] SDF format, chain JA [auth G] SDF format, chain IB [auth P] SDF format, chain IA [auth G] SDF format, chain HB [auth O] SDF format, chain HA [auth F] SDF format, chain GB [auth O] SDF format, chain GA [auth F] SDF format, chain FB [auth N] SDF format, chain FA [auth F] SDF format, chain EB [auth N] SDF format, chain DB [auth M] SDF format, chain DA [auth E] SDF format, chain CB [auth M] SDF format, chain CA [auth E] SDF format, chain BB [auth M] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth M] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain JB [auth P] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth J] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth K] MOL2 format, chain W [auth C] MOL2 format, chain ZA [auth L] MOL2 format, chain Z [auth D] MOL2 format, chain YA [auth L] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth K] MOL2 format, chain VA [auth K] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain RA [auth J] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth I] MOL2 format, chain OA [auth I] MOL2 format, chain NA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain LB [auth P] MOL2 format, chain LA [auth H] MOL2 format, chain KB [auth P] MOL2 format, chain KA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain IB [auth P] MOL2 format, chain IA [auth G] MOL2 format, chain HB [auth O] MOL2 format, chain HA [auth F] MOL2 format, chain GB [auth O] MOL2 format, chain GA [auth F] MOL2 format, chain FB [auth N] MOL2 format, chain FA [auth F] MOL2 format, chain EB [auth N] MOL2 format, chain DB [auth M] MOL2 format, chain DA [auth E] MOL2 format, chain CB [auth M] MOL2 format, chain CA [auth E] MOL2 format, chain BB [auth M] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth M] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain JB [auth P] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth J] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth K] mmCIF format, chain W [auth C] mmCIF format, chain ZA [auth L] mmCIF format, chain Z [auth D] mmCIF format, chain YA [auth L] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth L] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth K] mmCIF format, chain VA [auth K] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth J] mmCIF format, chain RA [auth J] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth I] mmCIF format, chain OA [auth I] mmCIF format, chain NA [auth H] mmCIF format, chain MA [auth H] mmCIF format, chain LB [auth P] mmCIF format, chain LA [auth H] mmCIF format, chain KB [auth P] mmCIF format, chain KA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain IB [auth P] mmCIF format, chain IA [auth G] mmCIF format, chain HB [auth O] mmCIF format, chain HA [auth F] mmCIF format, chain GB [auth O] mmCIF format, chain GA [auth F] mmCIF format, chain FB [auth N] mmCIF format, chain FA [auth F] mmCIF format, chain EB [auth N] mmCIF format, chain DB [auth M] mmCIF format, chain DA [auth E] mmCIF format, chain CB [auth M] mmCIF format, chain CA [auth E] mmCIF format, chain BB [auth M]	AA [auth D] AB [auth M] BA [auth D] BB [auth M] CA [auth E] AA [auth D], AB [auth M], BA [auth D], BB [auth M], CA [auth E], CB [auth M], DA [auth E], DB [auth M], EA [auth E], EB [auth N], FA [auth F], FB [auth N], GA [auth F], GB [auth O], HA [auth F], HB [auth O], IA [auth G], IB [auth P], JA [auth G], JB [auth P], KA [auth G], KB [auth P], LA [auth H], LB [auth P], MA [auth H], NA [auth H], OA [auth I], PA [auth I], Q [auth A], QA [auth J], R [auth A], RA [auth J], S [auth A], SA [auth J], T [auth B], TA [auth J], U [auth B], UA [auth K], V [auth B], VA [auth K], W [auth C], WA [auth K], X [auth C], XA [auth L], Y [auth D], YA [auth L], Z [auth D], ZA [auth L]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth M] Focus chain BA [auth D] Focus chain BB [auth M] Focus chain CA [auth E] Focus chain CB [auth M] Focus chain DA [auth E] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain EB [auth N] Focus chain FA [auth F] Focus chain FB [auth N] Focus chain GA [auth F] Focus chain GB [auth O] Focus chain HA [auth F] Focus chain HB [auth O] Focus chain IA [auth G] Focus chain IB [auth P] Focus chain JA [auth G] Focus chain JB [auth P] Focus chain KA [auth G] Focus chain KB [auth P] Focus chain LA [auth H] Focus chain LB [auth P] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain R [auth A] Focus chain RA [auth J] Focus chain S [auth A] Focus chain SA [auth J] Focus chain T [auth B] Focus chain TA [auth J] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth C] Focus chain WA [auth K] Focus chain X [auth C] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain YA [auth L] Focus chain Z [auth D] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth M] Focus chain BA [auth D] Focus chain BB [auth M] Focus chain CA [auth E] Focus chain CB [auth M] Focus chain DA [auth E] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain EB [auth N] Focus chain FA [auth F] Focus chain FB [auth N] Focus chain GA [auth F] Focus chain GB [auth O] Focus chain HA [auth F] Focus chain HB [auth O] Focus chain IA [auth G] Focus chain IB [auth P] Focus chain JA [auth G] Focus chain JB [auth P] Focus chain KA [auth G] Focus chain KB [auth P] Focus chain LA [auth H] Focus chain LB [auth P] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain R [auth A] Focus chain RA [auth J] Focus chain S [auth A] Focus chain SA [auth J] Focus chain T [auth B] Focus chain TA [auth J] Focus chain U [auth B] Focus chain UA [auth K] Focus chain V [auth B] Focus chain VA [auth K] Focus chain W [auth C] Focus chain WA [auth K] Focus chain X [auth C] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain YA [auth L] Focus chain Z [auth D] Focus chain ZA [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	2.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	741.018.201

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release