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- EMDB-66262: Cryo-EM structure of loop truncated self-sufficient P450 from Shi... -

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Basic information

Entry
Database: EMDB / ID: EMD-66262
TitleCryo-EM structure of loop truncated self-sufficient P450 from Shimazuella soli
Map data
Sample
  • Complex: bifunctional cytochrome P450/NADPH--P450 reductase
    • Protein or peptide: bifunctional cytochrome P450/NADPH--P450 reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: water
Keywordsself-sufficient P450 / heme / OXIDOREDUCTASE
Biological speciesShimazuella soli (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.34 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 loop truncated self-sufficient P450 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

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Structure visualization

Supplemental images

emd_66262.png

Downloads & links

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Map

FileDownload / File: emd_66262.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.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.6273952 - 3.488509
Average (Standard dev.)0.0008819308 (±0.06980032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66262_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66262_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66262_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 : bifunctional cytochrome P450/NADPH--P450 reductase

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

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

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

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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: 117.526359 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 NQPAFQGLNN RPLLVLYGSD TGTAE GIAR ELADTATLHG VHTEVATLNE RIGELPKEGA VLIVTSSYNG KPPSNAGQFV QWLEAVQAGE LSGVQYAVFG CGDHNW AST YQDVPRFIDK QLAEKGAVRF SARGEGDVSG DFEEQFDQWK EKMWSDAIEA FGLEISDDVK KDQNTLSLQF VKGTGGS PL ARSYEAVYAK VVENRELQSP DSGRSTRHIE ITLPKGVSYQ EGDHLGVLPA NSKENVHRVL QKYKLNENDQ VVLTASGR S MAHLPLAQEV SLRDLLLYSV ELQDAATRAQ IRELAAFTVC PPHKRELEAL LEEGIYQEQV LKKRISMLDL LEKYEACEM PFERFLELLH PLKPRYYSIS SSPRLNSERA SITVAVVRGP AWSGLGEYRG VASNYLADCK PGEDVMMFIR TPESNFQLPE ESETPIIMV GPGTGLAPFR GFLQARDAMK QEGKTLGEAY LYFGCRNEAD FIYRKELEQY KKNGIMTLYI AFSRKEGIPK T YVQHVMAS NAESLIRILD QGGRLYICGD GSRMAPEVEA TLKNSYQEVH GAGEQEASQW LEKLQKDGQY AKDVWAGL

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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 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

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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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1180657
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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