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- EMDB-72110: Asymmetric syNOS -

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Basic information

Entry
Database: EMDB / ID: EMD-72110
TitleAsymmetric syNOS
Map data
Sample
  • Complex: Synechococcus Nitric Oxide Synthase(asymmetric state)
    • Protein or peptide: Ferredoxin--NADP reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE
KeywordsNOS / FAD / FMN / Heme / Electron Transfer / OXIDOREDUCTASE
Function / homology:
Function and homology information
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsNair D / Crane BR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 2129729 United States
CitationJournal: To Be Published
Title: Asymmetric syNOS
Authors: Nair D / Crane BR
History
DepositionAug 13, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72110.png

Downloads & links

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Map

FileDownload / File: emd_72110.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.844 Å
Density
Contour LevelBy AUTHOR: 0.0461
Minimum - Maximum-0.19766684 - 0.43087316
Average (Standard dev.)0.0001811613 (±0.007926323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 371.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72110_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72110_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72110_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Synechococcus Nitric Oxide Synthase(asymmetric state)

EntireName: Synechococcus Nitric Oxide Synthase(asymmetric state)
Components
  • Complex: Synechococcus Nitric Oxide Synthase(asymmetric state)
    • Protein or peptide: Ferredoxin--NADP reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Synechococcus Nitric Oxide Synthase(asymmetric state)

SupramoleculeName: Synechococcus Nitric Oxide Synthase(asymmetric state) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Ferredoxin--NADP reductase

MacromoleculeName: Ferredoxin--NADP reductase / type: protein_or_peptide / ID: 1
Details: Though density is present for hemes in chain B, mobility of the domain prevents refinement. Hemes can be placed in a composite structure deposited.
Number of copies: 2 / Enantiomer: LEVO / EC number: nitric oxide dioxygenase
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 166.440266 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLVNDSRPTV EAHVLSVVRL VELCASGIPS NNEFKYKANV RVTCSGTEQS NTQLMTRLQP SWLVDIAHPS NCLFTVTLFY RQGGLGQPW HEAGSIKVTT ADLFDKQRSV EISRPVATWP AAPELMLNAR FTCSDHTSQS GEAVSLSLAG TRANASRRPT S LALVSDDS ...String:
MLVNDSRPTV EAHVLSVVRL VELCASGIPS NNEFKYKANV RVTCSGTEQS NTQLMTRLQP SWLVDIAHPS NCLFTVTLFY RQGGLGQPW HEAGSIKVTT ADLFDKQRSV EISRPVATWP AAPELMLNAR FTCSDHTSQS GEAVSLSLAG TRANASRRPT S LALVSDDS IELPEAIPLT YSEAVIVKDV WNKLRAWKEL QMETFFKRLL LEVPELDYIF GEAFESIPDY FFEMFDCCVR EL CPHTENV VWEPMMGVPP EKGDAFDTVA DYGALFADIG MQPQHWLRAR QVWMWMLPQI PYLEEYDRED LAKGNKSALC KFF NTHVIG GMVAARDRYD SALPPALVQK MADSWQYFAP RKNEMGVEFY QTLFERYPQV LPIFGRADMD YLSTHLFQSL EFIF LCLAE GSTERLMKEL RHLGRLHGNA GVPSFAYGAI SEVMISMFEK YVPGFDEQLK EAWQVLIARV SNVIKLPKLN EERLL KKAR EYLDVIANEQ AWEESDRERR WQEIKAEVQA TGTYTHTYEE LAYGAQLAWR NTSKCIGRIQ WSNMVVRDRR HVTDPD EMF QELEEHLRLG TNGGNIQIVM TVFRPKLPKE RWGPRIWNPQ LIRYAAYEMP DGSIMGDAAN LELTHQIIEK MGWQPPE PR SPYDILPLVI EVPRHEPRLY SFAPEEILEV EIEHPTIPDF KTLGLRWYAV PAISNFRMDI GGVTYACLPF NGWYMGTE I ARDFLEGGRY GKMKAIANLL GLNTSSEQTL WRDRVALEMN IAVLHSFQKA KVTMVDHQSA AQQFLAHDLR EKRAGRECP ADYGWVVPPA GGSACPVWHH QMRDFYLEPA YHHAADRWAV EADIDLEQFV QTTHESDHQR DRILILFGSE TGTAEGFARR AARQLSAYH PKVMALDDYN VNTLDEEKLL LVVTSTFGNG EVPGNAQQFT QWLKQQPSDT LNGLNYSVLG IGSTVYEHFC A AGITLDKA LAKAGANSVV PLHKGDEIKG QADTFKRWLS LISRILGADS TSTTPTTSKL KVTYLADSES HALLNLEAEH SH SRVPVLT NQELLKAVTP GSRSTRYLLF DTAKTEIAYE TGDHVSVHPH NPEELVLRVC DRLSLSPDTA FSAKYVLPDG RQL EDEPPI AVPTTVGQAL TEDLDLAFKE PFGELLNVLH QAAENTEEKI RLETWLEILA LEDGHEENAA LRKMLRDNFM SVAD LFDEF PSAQITLEML LEVLPKEKPR LYSISSCPQL QPGKLQITVG VLQIQTDAGK TRQGLCSNYL AGLSEGDLVR IETHT SDFR PPNDPSAPLL MVGPGTGISP LIAFLQHREY LNSQGIPLGK ATLYTGCRNH DDFLYEDQLR VWLEQGTLTD LQVAFS RLT AQKVYVQNLM QDNARSLWQQ LSHSQCHYYV CGDAKMADNV FEVFMQIAKT EGGLTHLEAV DFFNRMKSEK RFSTDVW GV TLNFKQAIKQ VEKDNYARAE KWLANL

UniProtKB: UNIPROTKB: B4WU43

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 54000
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 7100
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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