[English] 日本語
Yorodumi
- PDB-4i8v: Human Cytochrome P450 1A1 in complex with alpha-naphthoflavone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i8v
TitleHuman Cytochrome P450 1A1 in complex with alpha-naphthoflavone
ComponentsCytochrome P450 1A1
KeywordsOXIDOREDUCTASE / monooxygenase / cytochrome P450 / P450 / CYP1A1 / P450 1A1 / heme / aryl hydrocarbon hydroxylase
Function / homology
Function and homology information


arachidonic acid monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / oxidoreductase activity, acting on diphenols and related substances as donors / long-chain fatty acid omega-1 hydroxylase activity / 9-cis-retinoic acid biosynthetic process / hydroperoxy icosatetraenoate dehydratase ...arachidonic acid monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / oxidoreductase activity, acting on diphenols and related substances as donors / long-chain fatty acid omega-1 hydroxylase activity / 9-cis-retinoic acid biosynthetic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / steroid 17-alpha-monooxygenase activity / : / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / coumarin metabolic process / response to 3-methylcholanthrene / maternal process involved in parturition / flavonoid metabolic process / porphyrin-containing compound metabolic process / response to iron(III) ion / hormone biosynthetic process / long-chain fatty acid metabolic process / Biosynthesis of protectins / epoxygenase P450 pathway / tissue remodeling / response to nematode / vitamin D 24-hydroxylase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / demethylase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / progesterone metabolic process / vitamin D metabolic process / hepatocyte differentiation / steroid biosynthetic process / Xenobiotics / amine metabolic process / response to arsenic-containing substance / camera-type eye development / digestive tract development / response to vitamin A / hydrogen peroxide biosynthetic process / long-chain fatty acid biosynthetic process / response to herbicide / estrogen metabolic process / retinol metabolic process / response to food / unspecific monooxygenase / aromatase activity / nitric oxide metabolic process / steroid metabolic process / cellular response to organic cyclic compound / response to immobilization stress / response to hyperoxia / positive regulation of G1/S transition of mitotic cell cycle / cellular response to copper ion / Hsp70 protein binding / monooxygenase activity / xenobiotic metabolic process / fatty acid metabolic process / Hsp90 protein binding / PPARA activates gene expression / oxygen binding / response to lipopolysaccharide / mitochondrial inner membrane / oxidoreductase activity / response to hypoxia / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding
Similarity search - Function
Cytochrome P450, E-class, group I, CYP1 / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / PROTOPORPHYRIN IX CONTAINING FE / NITRATE ION / Cytochrome P450 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWalsh, A.A. / Scott, E.E.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Human Cytochrome P450 1A1 Structure and Utility in Understanding Drug and Xenobiotic Metabolism.
Authors: Walsh, A.A. / Szklarz, G.D. / Scott, E.E.
History
DepositionDec 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 1A1
B: Cytochrome P450 1A1
C: Cytochrome P450 1A1
D: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,51815
Polymers223,7774
Non-polymers3,74111
Water3,261181
1
A: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9575
Polymers55,9441
Non-polymers1,0134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8954
Polymers55,9441
Non-polymers9513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8333
Polymers55,9441
Non-polymers8892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8333
Polymers55,9441
Non-polymers8892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.003, 195.491, 235.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Cytochrome P450 1A1 / CYPIA1 / Cytochrome P450 form 6 / Cytochrome P450-C / Cytochrome P450-P1


Mass: 55944.156 Da / Num. of mol.: 4 / Fragment: UNP residues 35-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP1A1 / Plasmid: pkk / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P04798, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-BHF / 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / 7,8-BENZOFLAVONE / ALPHA-NAPHTHOFLAVONE


Mass: 272.297 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H12O2
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 277.5 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 0.1 M bis-tris propane/HCl, 200 mM sodium malonate, 14% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.5K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97957 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 18, 2011 / Details: RH coated flat mirror, toroidal focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.6→38.24 Å / Num. obs: 93519 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 12.6
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 7 % / Mean I/σ(I) obs: 12.3 / Num. unique all: 6776 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HI4

2hi4


Resolution: 2.6→38.24 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.695 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24353 4687 5 %RANDOM
Rwork0.18842 ---
obs-88726 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.472 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15083 0 268 181 15532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01915765
X-RAY DIFFRACTIONr_bond_other_d0.0215002
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.97921417
X-RAY DIFFRACTIONr_angle_other_deg334450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg51877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.343709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg152676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15112
X-RAY DIFFRACTIONr_chiral_restr0.22313
X-RAY DIFFRACTIONr_gen_planes_refined0.02117701
X-RAY DIFFRACTIONr_gen_planes_other0.023827
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 349 -
Rwork0.292 6417 -
obs--99.91 %

+
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://pdbjlvh1.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