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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 / flavin adenine dinucleotide binding / NADP 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 / flavin adenine dinucleotide binding / NADP 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: To Be Published
Title: Assimilatory NADPH-dependent sulfite reductase minimal dimer
Authors: Ghazi Esfahani, B. / Walia, N. / Neselu, K. / Aragon, M. / Askenasy, I. / Wei, A. / Mendez, J.H. / Stroupe, M.E.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
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Revision 1.1Feb 26, 2025Group: Data collection / Data processing / Category: em_3d_reconstruction / em_admin
Item: _em_3d_reconstruction.resolution / _em_admin.last_update
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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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