[English] 日本語
Yorodumi
- EMDB-78781: CYP3A4 bound to ritonavir -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-78781
TitleCYP3A4 bound to ritonavir
Map data
Sample
  • Complex: homotrimeric complex of CYP3A4 bound to ritonavir
    • Protein or peptide: Cytochrome P450 3A4
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: RITONAVIR
Keywordsinhibited complex / cytochrome p450 / OXIDOREDUCTASE
Function / homology
Function and homology information


quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity ...quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / testosterone 6-beta-hydroxylase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / estrogen 2-hydroxylase activity / steroid catabolic process / oxidative demethylation / androgen metabolic process / vitamin D metabolic process / Atorvastatin ADME / steroid hydroxylase activity / Xenobiotics / retinoic acid metabolic process / Phase I - Functionalization of compounds / estrogen metabolic process / long-chain fatty acid biosynthetic process / retinol metabolic process / unspecific monooxygenase / Prednisone ADME / steroid metabolic process / Aspirin ADME / cholesterol metabolic process / intracellular membrane-bounded organelle / xenobiotic catabolic process / steroid binding / xenobiotic metabolic process / lipid metabolic process / monooxygenase activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / : / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsOrta AK / Fraser JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government1AY1AX000035-01 United States
CitationJournal: To Be Published
Title: Structural analysis of CYP3A4 inhibition by Cryo-EM
Authors: Orta AK / Fraser JS
History
DepositionAug 24, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_78781.png

Downloads & links

-
Map

FileDownload / File: emd_78781.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 233.92 Å		0.73 Å/pix.
x 320 pix.
= 233.92 Å		0.73 Å/pix.
x 320 pix.
= 233.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0852
Minimum - Maximum-0.5906701 - 0.8116714
Average (Standard dev.)-0.00017141152 (±0.021159774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_78781_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_78781_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : homotrimeric complex of CYP3A4 bound to ritonavir

EntireName: homotrimeric complex of CYP3A4 bound to ritonavir
Components
  • Complex: homotrimeric complex of CYP3A4 bound to ritonavir
    • Protein or peptide: Cytochrome P450 3A4
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: RITONAVIR

-
Supramolecule #1: homotrimeric complex of CYP3A4 bound to ritonavir

SupramoleculeName: homotrimeric complex of CYP3A4 bound to ritonavir / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cytochrome P450 3A4

MacromoleculeName: Cytochrome P450 3A4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: unspecific monooxygenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.757812 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAYLYGTHSH GLFKKLGIPG PTPLPFLGNI LSYHKGFCMF DMECHKKYGK VWGFYDGQQP VLAITDPDMI KTVLVKECYS VFTNRRPFG PVGFMKSAIS IAEDEEWKRL RSLLSPTFTS GKLKEMVPII AQYGDVLVRN LRREAETGKP VTLKDVFGAY S MDVITSTS ...String:
MAYLYGTHSH GLFKKLGIPG PTPLPFLGNI LSYHKGFCMF DMECHKKYGK VWGFYDGQQP VLAITDPDMI KTVLVKECYS VFTNRRPFG PVGFMKSAIS IAEDEEWKRL RSLLSPTFTS GKLKEMVPII AQYGDVLVRN LRREAETGKP VTLKDVFGAY S MDVITSTS FGVNIDSLNN PQDPFVENTK KLLRFDFLDP FFLSITVFPF LIPILEVLNI CVFPREVTNF LRKSVKRMKE SR LEDTQKH RVDFLQLMID SQNSKETESH KALSDLELVA QSIIFIFAGY ETTSSVLSFI MYELATHPDV QQKLQEEIDA VLP NKAPPT YDTVLQMEYL DMVVNETLRL FPIAMRLERV CKKDVEINGM FIPKGVVVMI PSYALHRDPK YWTEPEKFLP ERFS KKNKD NIDPYIYTPF GSGPRNCIGM RFALMNMKLA LIRVLQNFSF KPCKETQIPL KLSLGGLLQP EKPVVLKVES RDGTV SGAH HHH

UniProtKB: Cytochrome P450 3A4

-
Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 3 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Macromolecule #3: RITONAVIR

MacromoleculeName: RITONAVIR / type: ligand / ID: 3 / Number of copies: 3 / Formula: RIT
Molecular weightTheoretical: 720.944 Da
Chemical component information


ChemComp, No image

ChemComp-PRD_001001:
Unknown entry / medication, antiretroviral*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 19000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3nxu

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 67638
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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