7XX3 | pdb_00007xx3

Crystal structure of human Superoxide Dismutase (SOD1) in complex with a fungal metabolite molecule, Phialomustin B (PB)

PDB DOI: https://doi.org/10.2210/pdb7XX3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-28 Released: 2023-12-13
Deposition Author(s): Padmanabhan, B., Unni, S.
Funding Organization(s): Indian Council of Medical Research, Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.230 (Depositor), 0.215 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural insights into the modulation Of SOD1 aggregation By a fungal metabolite Phialomustin-B: Therapeutic potential in ALS.

Unni, S., Kommu, P., Aouti, S., Nalli, Y., Bharath, M.M.S., Ali, A., Padmanabhan, B.

(2024) PLoS One 19: e0298196-e0298196

PubMed: 38446760 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0298196
Primary Citation Related Structures:
7XX3

PubMed Abstract:
Amyotrophic lateral sclerosis (ALS) is a fatal human motor neuron disease leading to muscle atrophy and paralysis. Mutations in superoxide dismutase 1 (SOD1) are associated with familial ALS (fALS). The SOD1 mutants in ALS have a toxic-gain of function by destabilizing the functional SOD1 homodimer, consequently inducing fibril-like aggregation with a cytotoxic non-native trimer intermediate. Therefore, reducing SOD1 oligomerization via chemical modulators is an optimal therapy in ALS. Here, we report the discovery of Phialomustin-B, an unsaturated secondary metabolite from the endophytic fungus Phialophora mustea, as a modulator of SOD1 aggregation. The crystal structure of the SOD1-Phialomustin complex refined to 1.90 Å resolution demonstrated for the first time that the ligand binds to the dimer interface and the lateral region near the electrostatic loop. The aggregation analyses of SOD1WT and the disease mutant SOD1A4V revealed that Phialomustin-B reduces cytotoxic trimerization. We propose that Phialomustin-B is a potent lead molecule with therapeutic potential in fALS.

Organizational Affiliation

Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India.

Macromolecule Content

Total Structure Weight: 192.83 kDa
Atom Count: 12,385
Modeled Residue Count: 1,506
Deposited Residue Count: 1,800
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A B C [auth D] D [auth C] E [auth H] A, B, C [auth D], D [auth C], E [auth H], F [auth E], G [auth F], H [auth G], I, J	180	Homo sapiens	Mutation(s): 0 Gene Names: SOD1 EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441 Go to UniProtKB: P00441
PHAROS: P00441 GTEx: ENSG00000142168
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00441
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I2G (Subject of Investigation/LOI) Query on I2G Download:Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain N [auth B] SDF format, chain S [auth D] SDF format, chain V [auth C] MOL2 format, chain CA [auth I] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth I] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D] mmCIF format, chain V [auth C]	CA [auth I], N [auth B], S [auth D], V [auth C]	(2~{E},4~{E},6~{S})-4,6-dimethyldeca-2,4-dienoic acid C₁₂ H₂₀ O₂ DZXNZBWYVLLUAX-IVONAZQTSA-N		Interactions Focus chain CA [auth I] Focus chain N [auth B] Focus chain S [auth D] Focus chain V [auth C] Interactions & Density Focus chain CA [auth I] Focus chain N [auth B] Focus chain S [auth D] Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth D]	L [auth A], O [auth B], P [auth B], Q [auth B], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth D] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain X [auth E] MOL2 format, chain X [auth E] mmCIF format, chain X [auth E]	X [auth E]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain X [auth E] Interactions & Density Focus chain X [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth I] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain U [auth C] SDF format, chain W [auth H] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain U [auth C] MOL2 format, chain W [auth H] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth I] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain U [auth C] mmCIF format, chain W [auth H] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F]	AA [auth G] BA [auth I] K [auth A] M [auth B] R [auth D] AA [auth G], BA [auth I], K [auth A], M [auth B], R [auth D], U [auth C], W [auth H], Y [auth E], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth C] Focus chain W [auth H] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth C] Focus chain W [auth H] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230 (Depositor), 0.215 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.445	α = 90
b = 242.445	β = 90
c = 144.491	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Padmanabhan, B.

Unni, S.

Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	Indian Council of Medical Research (ICMR),
Department of Science & Technology (DST, India)	India	DST-FIST: SR/FST/LS-I/2017(C)