[English] 日本語
Yorodumi
- EMDB-45359: Assimilatory NADPH-dependent sulfite reductase minimal dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45359
TitleAssimilatory NADPH-dependent sulfite reductase minimal dimer
Map datamain map
Sample
  • Complex: sulfite reductase minimal dimer
    • Protein or peptide: Sulfite reductase [NADPH] flavoprotein alpha-component
    • Protein or peptide: Sulfite reductase [NADPH] hemoprotein beta-component
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: PHOSPHATE ION
  • Ligand: POTASSIUM ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: SIROHEME
Keywordssulfite reductase / hemoflavoprotein / oxidoreductase / cryo-EM / FLAVOPROTEIN
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
Sulfite reductase [NADPH] hemoprotein beta-component / Sulfite reductase [NADPH] flavoprotein alpha-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsGhazi Esfahani B / Walia N / Neselu K / Aragon M / Askenasy I / Wei A / Mendez JH / Stroupe ME
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45359.png

Downloads & links

-
Map

FileDownload / File: emd_45359.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 360 pix.
= 275.4 Å		0.77 Å/pix.
x 360 pix.
= 275.4 Å		0.77 Å/pix.
x 360 pix.
= 275.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.765 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.342
Minimum - Maximum-1.8226016 - 3.46245
Average (Standard dev.)0.0015131062 (±0.06590137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 244.79999 Å
α=β=γ: 90.0 °

-
Supplemental data

+
Additional map: map with the linker

Fileemd_45359_additional_1.map
Annotationmap with the linker
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 7 gauss z.mrc

Fileemd_45359_additional_10.map
Annotationvol_7_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 8 gauss z.mrc

Fileemd_45359_additional_11.map
Annotationvol_8_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 9 gauss z.mrc

Fileemd_45359_additional_12.map
Annotationvol_9_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: dimer obtained from the SiRFPdelta-SiRHP dataset

Fileemd_45359_additional_2.map
Annotationdimer obtained from the SiRFPdelta-SiRHP dataset
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 0 gauss z.mrc

Fileemd_45359_additional_3.map
Annotationvol_0_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 1 gauss z.mrc

Fileemd_45359_additional_4.map
Annotationvol_1_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 2 gauss z.mrc

Fileemd_45359_additional_5.map
Annotationvol_2_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 3 gauss z.mrc

Fileemd_45359_additional_6.map
Annotationvol_3_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 4 gauss z.mrc

Fileemd_45359_additional_7.map
Annotationvol_4_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 5 gauss z.mrc

Fileemd_45359_additional_8.map
Annotationvol_5_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: vol 6 gauss z.mrc

Fileemd_45359_additional_9.map
Annotationvol_6_gauss_z.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: half map A

Fileemd_45359_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: half map B

Fileemd_45359_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : sulfite reductase minimal dimer

EntireName: sulfite reductase minimal dimer
Components
  • Complex: sulfite reductase minimal dimer
    • Protein or peptide: Sulfite reductase [NADPH] flavoprotein alpha-component
    • Protein or peptide: Sulfite reductase [NADPH] hemoprotein beta-component
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: PHOSPHATE ION
  • Ligand: POTASSIUM ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: SIROHEME

-
Supramolecule #1: sulfite reductase minimal dimer

SupramoleculeName: sulfite reductase minimal dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 124 KDa

-
Macromolecule #1: Sulfite reductase [NADPH] flavoprotein alpha-component

MacromoleculeName: Sulfite reductase [NADPH] flavoprotein alpha-component
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: assimilatory sulfite reductase (NADPH)
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64.093684 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGGSHHHHHH GMASMTGGNN MGRDLYDDDD KDRWGSELEI TIISASQTGN ARRVAEALRD DLLAAKLNVK LVNAGDYKFK QIASEKLLI VVTSTQGCGE PPEEAVALHK FLFSKKAPKL ENTAFAVFSL GDSSYEFFTQ SGKDFDSKLA ELGGERLLDR V DADVEYQA ...String:
MGGSHHHHHH GMASMTGGNN MGRDLYDDDD KDRWGSELEI TIISASQTGN ARRVAEALRD DLLAAKLNVK LVNAGDYKFK QIASEKLLI VVTSTQGCGE PPEEAVALHK FLFSKKAPKL ENTAFAVFSL GDSSYEFFTQ SGKDFDSKLA ELGGERLLDR V DADVEYQA AASEWRARVV DALKSRAPVA APSQSVATGA VNEIHTSPYS KDAPLVASLS VNQKITGRNS EKDVRHIEID LG DSGLRYQ PGDALGVWYQ NDPALVKELV ELLWLKGDEP VTVEGKTLPL NEALQWHFEL TVNTANIVEN YATLTRSETL LPL VGDKAK LQHYAATTPI VDMVRFSPAQ LDAEALINLL RPLTPRLYSI ASSQAEVENE VHVTVGVVRY DVEGRARAGG ASSF LADRV EEEGEVRVFI EHNDNFRLPA NPETPVIMIG PGTGIAPFRA FMQQRAADEA PGKNWLFFGN PHFTEDFLYQ VEWQR YVKE GVLTRIDLAW SRDQKEKVYV QDKLREQGAE LWRWINDGAH IYVSGDACRM AKDVEQALLE VIAEFGGMDT EAADEF LSE LRVERRYQRD VY

UniProtKB: Sulfite reductase [NADPH] flavoprotein alpha-component

-
Macromolecule #2: Sulfite reductase [NADPH] hemoprotein beta-component

MacromoleculeName: Sulfite reductase [NADPH] hemoprotein beta-component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: assimilatory sulfite reductase (NADPH)
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64.091102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEKHPGPLV VEGKLTDAER MKHESNYLRG TIAEDLNDGL TGGFKGDNFL LIRFHGMYQQ DDRDIRAERA EQKLEPRHAM LLRCRLPGG VITTKQWQAI DKFAGENTIY GSIRLTNRQT FQFHGILKKN VKPVHQMLHS VGLDALATAN DMNRNVLCTS N PYESQLHA ...String:
MSEKHPGPLV VEGKLTDAER MKHESNYLRG TIAEDLNDGL TGGFKGDNFL LIRFHGMYQQ DDRDIRAERA EQKLEPRHAM LLRCRLPGG VITTKQWQAI DKFAGENTIY GSIRLTNRQT FQFHGILKKN VKPVHQMLHS VGLDALATAN DMNRNVLCTS N PYESQLHA EAYEWAKKIS EHLLPRTRAY AEIWLDQEKV ATTDEEPILG QTYLPRKFKT TVVIPPQNDI DLHANDMNFV AI AENGKLV GFNLLVGGGL SIEHGNKKTY ARTASEFGYL PLEHTLAVAE AVVTTQRDWG NRTDRKNAKT KYTLERVGVE TFK AEVERR AGIKFEPIRP YEFTGRGDRI GWVKGIDDNW HLTLFIENGR ILDYPARPLK TGLLEIAKIH KGDFRITANQ NLII AGVPE SEKAKIEKIA KESGLMNAVT PQRENSMACV SFPTCPLAMA EAERFLPSFI DNIDNLMAKH GVSDEHIVMR VTGCP NGCG RAMLAEVGLV GKAPGRYNLH LGGNRIGTRI PRMYKENITE PEILASLDEL IGRWAKEREA GEGFGDFTVR AGIIRP VLD PARDLWD

UniProtKB: Sulfite reductase [NADPH] hemoprotein beta-component

-
Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Macromolecule #4: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

-
Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

-
Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Macromolecule #8: SIROHEME

MacromoleculeName: SIROHEME / type: ligand / ID: 8 / Number of copies: 1 / Formula: SRM
Molecular weightTheoretical: 916.661 Da
Chemical component information

ChemComp-SRM:
SIROHEME

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 6.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more