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- PDB-9c91: Assimilatory NADPH-dependent sulfite reductase minimal dimer -

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Basic information

Entry
Database: PDB / ID: 9c91
TitleAssimilatory NADPH-dependent sulfite reductase minimal dimer
Components(Sulfite reductase [NADPH] ...) x 2
KeywordsFLAVOPROTEIN / sulfite reductase / hemoflavoprotein / oxidoreductase / cryo-EM
Function / homology
Function and homology information


sulfite reductase (ferredoxin) activity / assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase complex (NADPH) / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / FMN binding / NADP binding / flavin adenine dinucleotide binding ...sulfite reductase (ferredoxin) activity / assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase complex (NADPH) / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / FMN binding / NADP binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding / cytosol
Similarity search - Function
Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Sulphite reductase (NADPH) hemoprotein, beta subunit / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain ...Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Sulphite reductase (NADPH) hemoprotein, beta subunit / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / : / PHOSPHATE ION / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase [NADPH] hemoprotein beta-component / Sulfite reductase [NADPH] flavoprotein alpha-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsGhazi Esfahani, B. / Walia, N. / Neselu, K. / Aragon, M. / Askenasy, I. / Wei, A. / Mendez, J.H. / Stroupe, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1856502 United States
National Science Foundation (NSF, United States)CHE1904612 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding.
Authors: Behrouz Ghazi Esfahani / Nidhi Walia / Kasahun Neselu / Yashika Garg / Mahira Aragon / Isabel Askenasy / Hui Alex Wei / Joshua H Mendez / M Elizabeth Stroupe /
Abstract: Escherichia coli NADPH-dependent assimilatory sulfite reductase (SiR) reduces sulfite by six electrons to make sulfide for incorporation into sulfur-containing biomolecules. SiR has two subunits: an ...Escherichia coli NADPH-dependent assimilatory sulfite reductase (SiR) reduces sulfite by six electrons to make sulfide for incorporation into sulfur-containing biomolecules. SiR has two subunits: an NADPH, FMN, and FAD-binding diflavin flavoprotein and a siroheme/FeS cluster-containing hemoprotein. The molecular interactions that govern subunit binding have been unknown since the discovery of SiR over 50 years ago because SiR is flexible, thus has been intransigent for traditional high-resolution structural analysis. We use a combination of the chameleon® plunging system with a fluorinated lipid to overcome the challenges of preserving a flexible molecule to determine a 2.78 Å-resolution cryo-EM structure of a minimal heterodimer complex. Chameleon®, combined with the fluorinated lipid, overcomes persistent denaturation at the air-water interface. Using a previously characterized minimal heterodimer reduces the heterogeneity of a structurally heterogeneous complex to a level that we analyze using multi-conformer cryo-EM image analysis algorithms. Here, we report the near-atomic resolution structure of the flavoprotein/hemoprotein complex, revealing how they interact in a minimal interface. Further, we determine the structural elements that discriminate between pairing a hemoprotein with a diflavin reductase, as in the E. coli homolog, or a ferredoxin partner, as in maize (Zea mays).
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfite reductase [NADPH] flavoprotein alpha-component
B: Sulfite reductase [NADPH] hemoprotein beta-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8298
Polymers128,1852
Non-polymers2,6446
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Sulfite reductase [NADPH] ... , 2 types, 2 molecules AB

#1: Protein Sulfite reductase [NADPH] flavoprotein alpha-component / SiR-FP


Mass: 64093.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cysJ, HEP34_003108 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8S7Y2L5, assimilatory sulfite reductase (NADPH)
#2: Protein Sulfite reductase [NADPH] hemoprotein beta-component / SiR-HP / SiRHP


Mass: 64091.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: cysI, BANRA_01280, HMV95_03860, IH772_07600, P6223_002112
Production host: Escherichia coli (E. coli)
References: UniProt: A0A090HXE8, assimilatory sulfite reductase (NADPH)

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Non-polymers , 6 types, 6 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H44FeN4O16

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: sulfite reductase minimal dimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.124 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.8
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038985
ELECTRON MICROSCOPYf_angle_d0.62312214
ELECTRON MICROSCOPYf_dihedral_angle_d7.0381229
ELECTRON MICROSCOPYf_chiral_restr0.0431325
ELECTRON MICROSCOPYf_plane_restr0.0041591

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