[English] 日本語
Yorodumi
- EMDB-72087: syNOS monomer bound to NADPH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72087
TitlesyNOS monomer bound to NADPH
Map data
Sample
  • Complex: Monomeric syNOS bound to NADPH
    • Protein or peptide: Nitric oxide synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
KeywordsNOS / FAD / FMN / NADPH / C2 domain / Heme / OXIDOREDUCTASE
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsNair D / Crane B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 2129729 United States
CitationJournal: To Be Published
Title: Structure and dynamics of a muti-domain nitric oxide synthase regulated by a C2 domain.
Authors: Nair D / Crane B
History
DepositionAug 12, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72087.png

Downloads & links

-
Map

FileDownload / File: emd_72087.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.73 Å
Density
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-0.4013825 - 1.0066788
Average (Standard dev.)-0.000059805097 (±0.020646695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 365.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72087_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72087_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72087_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Monomeric syNOS bound to NADPH

EntireName: Monomeric syNOS bound to NADPH
Components
  • Complex: Monomeric syNOS bound to NADPH
    • Protein or peptide: Nitric oxide synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Supramolecule #1: Monomeric syNOS bound to NADPH

SupramoleculeName: Monomeric syNOS bound to NADPH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)

-
Macromolecule #1: Nitric oxide synthase

MacromoleculeName: Nitric oxide synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
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

-
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

-
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: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.4 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45964
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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