9EYQ | pdb_00009eyq

The structure of nonameric pore of RN1 variant of actinoporin Fav

PDB DOI: https://doi.org/10.2210/pdb9EYQ/pdb
EM Map EMD-50062: EMDB EMDataResource

Classification: TOXIN
Organism(s): Orbicella faveolata
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-09 Released: 2025-04-23
Deposition Author(s): Solinc, G., Srnko, M., Anderluh, G., Crnkovic, A., Podobnik, M.
Funding Organization(s): Slovenian Research Agency, Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9EYQ

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

Literature

The structure of nonameric pore of RN1 variant of actinoporin Fav

Solinc, G., Srnko, M., Anderluh, G., Crnkovic, A., Podobnik, M.

To be published.

Macromolecule Content

Total Structure Weight: 224.71 kDa
Atom Count: 13,815
Modeled Residue Count: 1,629
Deposited Residue Count: 1,737
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actinoporin	A, B, C, D, E A, B, C, D, E, F, G, H, I	193	Orbicella faveolata	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H8M Query on A1H8M Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain J [auth A] SDF format, chain LA [auth F] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain ZA [auth I] SDF format, chain Z [auth D] SDF format, chain YA [auth I] SDF format, chain Y [auth D] SDF format, chain XA [auth I] SDF format, chain X [auth C] SDF format, chain WA [auth H] SDF format, chain W [auth C] SDF format, chain VA [auth H] SDF format, chain V [auth C] SDF format, chain UA [auth H] SDF format, chain TA [auth H] SDF format, chain T [auth C] SDF format, chain SA [auth H] SDF format, chain S [auth B] SDF format, chain RA [auth G] SDF format, chain QA [auth G] SDF format, chain Q [auth B] SDF format, chain PA [auth G] SDF format, chain P [auth B] SDF format, chain OA [auth G] SDF format, chain O [auth B] SDF format, chain NA [auth G] SDF format, chain N [auth A] SDF format, chain MA [auth F] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth F] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain IA [auth F] SDF format, chain HA [auth E] SDF format, chain GA [auth E] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth D] SDF format, chain BB [auth I] SDF format, chain BA [auth D] SDF format, chain AB [auth I] SDF format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain ZA [auth I] MOL2 format, chain Z [auth D] MOL2 format, chain YA [auth I] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain UA [auth H] MOL2 format, chain TA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain QA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain AB [auth I] MOL2 format, chain AA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain ZA [auth I] mmCIF format, chain Z [auth D] mmCIF format, chain YA [auth I] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth I] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain UA [auth H] mmCIF format, chain TA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain QA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain AB [auth I] mmCIF format, chain AA [auth D]	AA [auth D] AB [auth I] BA [auth D] BB [auth I] CA [auth D] AA [auth D], AB [auth I], BA [auth D], BB [auth I], CA [auth D], DA [auth E], EA [auth E], FA [auth E], GA [auth E], HA [auth E], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth A], NA [auth G], O [auth B], OA [auth G], P [auth B], PA [auth G], Q [auth B], QA [auth G], R [auth B], RA [auth G], S [auth B], SA [auth H], T [auth C], TA [auth H], U [auth C], UA [auth H], V [auth C], VA [auth H], W [auth C], WA [auth H], X [auth C], XA [auth I], Y [auth D], YA [auth I], Z [auth D], ZA [auth I]	Sphingomyelin C18 C₄₁ H₈₄ N₂ O₆ P LKQLRGMMMAHREN-YJFXYUILSA-O		Interactions Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain U [auth C] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth I] Focus chain Y [auth D] Focus chain YA [auth I] Focus chain Z [auth D] Focus chain ZA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain U [auth C] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth I] Focus chain Y [auth D] Focus chain YA [auth I] Focus chain Z [auth D] Focus chain ZA [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.98
MODEL REFINEMENT	PHENIX	1.19
MODEL REFINEMENT	ISOLDE	1.6
RECONSTRUCTION	cryoSPARC	v4

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	J4-8225
Slovenian Research Agency	Slovenia	P1-0391
Other private		--

Revision History (Full details and data files)

Version 1.0: 2025-04-23
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.