[English] 日本語
Yorodumi
- EMDB-66267: Cryo-EM structure of full-length self-sufficient P450 in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66267
TitleCryo-EM structure of full-length self-sufficient P450 in complex with NADPH from Shimazuella soli
Map data
Sample
  • Complex: bifunctional cytochrome P450
    • Protein or peptide: bifunctional cytochrome P450/NADPH--P450 reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water
Keywordsself-sufficient P450 / heme / oxidoreductase
Biological speciesShimazuella soli (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsXie ZZ / Li SY / Liu ZW / Li QR / Huang J-W / Chen C-C / Guo R-T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of full-length self-sufficient P450 in complex with NADPH from Shimazuella soli
Authors: Xie ZZ / Li SY / Liu ZW / Li QR / Huang J-W / Chen C-C / Guo R-T
History
DepositionSep 18, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66267.png

Downloads & links

-
Map

FileDownload / File: emd_66267.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 237.056 Å		0.93 Å/pix.
x 256 pix.
= 237.056 Å		0.93 Å/pix.
x 256 pix.
= 237.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-1.4653814 - 2.317279
Average (Standard dev.)0.0003860453 (±0.05904527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 237.056 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_66267_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66267_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66267_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : bifunctional cytochrome P450

EntireName: bifunctional cytochrome P450
Components
  • Complex: bifunctional cytochrome P450
    • Protein or peptide: bifunctional cytochrome P450/NADPH--P450 reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water

-
Supramolecule #1: bifunctional cytochrome P450

SupramoleculeName: bifunctional cytochrome P450 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Shimazuella soli (bacteria)

-
Macromolecule #1: bifunctional cytochrome P450/NADPH--P450 reductase

MacromoleculeName: bifunctional cytochrome P450/NADPH--P450 reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shimazuella soli (bacteria)
Molecular weightTheoretical: 121.038234 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDEANIIPQP KTYGPLGNIP LIDKDKPILS FMKLAEEYGP IFRLQTPGDS TIVVSGHELV KEVCDESRFL KSAEGPLEKV RAFGGDGLF TSWTHEPNWR KAHNILMPTF SQRAMKDYHD MMVDIAVQLI QKWIRLNPDE TVDVPDDMTR LTLDTIGLCG F NYRFNSYY ...String:
MDEANIIPQP KTYGPLGNIP LIDKDKPILS FMKLAEEYGP IFRLQTPGDS TIVVSGHELV KEVCDESRFL KSAEGPLEKV RAFGGDGLF TSWTHEPNWR KAHNILMPTF SQRAMKDYHD MMVDIAVQLI QKWIRLNPDE TVDVPDDMTR LTLDTIGLCG F NYRFNSYY RETPHPFITS MVRALDEAMH QTQRLDLQDK LMIRTKRQFQ HDIQVMFSLV DSIIAERRAG KNQKENDLLS RM LNVSDPE TGEKLDDENI RYQIITFLIA GHETTSGLLS FALYFLLKNP DKLKKAYEEV DQVLTGSTPT YKQVLHLKYV RMI LNEALR LWPTAPAFSL YAKEDTIIGG KYPVKKEQER ITVLIPQLHR DKEAWGEDVE EFRPERFEDQ NKVPHHAYKP FGNG QRACI GMQFALHEAT LVLGMLLRHF EFIDYKDYQL DIKQTLTLKP GDFNIQVQPR NQPAFQQSVS VTEDVAAESK MEMKQ VKDH FDQKSTIQGL NNRPLLVLYG SDTGTAEGIA RELADTATLH GVHTEVATLN ERIGELPKEG AVLIVTSSYN GKPPSN AGQ FVQWLEAVQA GELSGVQYAV FGCGDHNWAS TYQDVPRFID KQLAEKGAVR FSARGEGDVS GDFEEQFDQW KEKMWSD AI EAFGLEISDD VKKDQNTLSL QFVKGTGGSP LARSYEAVYA KVVENRELQS PDSGRSTRHI EITLPKGVSY QEGDHLGV L PANSKENVHR VLQKYKLNEN DQVVLTASGR SMAHLPLAQE VSLRDLLLYS VELQDAATRA QIRELAAFTV CPPHKRELE ALLEEGIYQE QVLKKRISML DLLEKYEACE MPFERFLELL HPLKPRYYSI SSSPRLNSER ASITVAVVRG PAWSGLGEYR GVASNYLAD CKPGEDVMMF IRTPESNFQL PEESETPIIM VGPGTGLAPF RGFLQARDAM KQEGKTLGEA YLYFGCRNEA D FIYRKELE QYKKNGIMTL YIAFSRKEGI PKTYVQHVMA SNAESLIRIL DQGGRLYICG DGSRMAPEVE ATLKNSYQEV HG AGEQEAS QWLEKLQKDG QYAKDVWAGL

-
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 MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

-
Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

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

-
Macromolecule #5: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 5 / Number of copies: 2 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 25 mM HEPES,150 mM NaCl, pH 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm
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: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 139104
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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