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- PDB-6dwm: Structure of Human Cytochrome P450 1A1 with Bergamottin -

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Basic information

Entry
Database: PDB / ID: 6dwm
TitleStructure of Human Cytochrome P450 1A1 with Bergamottin
ComponentsCytochrome P450 1A1
KeywordsOXIDOREDUCTASE / ligand
Function / homology
Function and homology information


arachidonate monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / response to diphenyl ether / phenol-containing compound metabolic process / oxidoreductase activity, acting on diphenols and related substances as donors / response to Aroclor 1254 ...arachidonate monooxygenase activity / ethylene metabolic process / flavonoid 3'-monooxygenase activity / insecticide metabolic process / dibenzo-p-dioxin catabolic process / long-chain fatty acid omega-hydroxylase activity / response to diphenyl ether / phenol-containing compound metabolic process / oxidoreductase activity, acting on diphenols and related substances as donors / response to Aroclor 1254 / long-chain fatty acid omega-1 hydroxylase activity / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / 9-cis-retinoic acid biosynthetic process / omega-hydroxylase P450 pathway / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / coumarin metabolic process / response to 3-methylcholanthrene / flavonoid metabolic process / porphyrin-containing compound metabolic process / maternal process involved in parturition / response to iron(III) ion / long-chain fatty acid metabolic process / Biosynthesis of protectins / epoxygenase P450 pathway / tissue remodeling / response to 2,3,7,8-tetrachlorodibenzodioxine / response to genistein / vitamin D 24-hydroxylase activity / lipid hydroxylation / demethylase activity / estrogen 16-alpha-hydroxylase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / vitamin D metabolic process / estrogen 2-hydroxylase activity / steroid biosynthetic process / hepatocyte differentiation / amine metabolic process / Xenobiotics / camera-type eye development / response to arsenic-containing substance / response to nematode / hydrogen peroxide biosynthetic process / digestive tract development / response to herbicide / long-chain fatty acid biosynthetic process / response to vitamin A / retinol metabolic process / estrogen metabolic process / unspecific monooxygenase / response to food / steroid metabolic process / : / response to immobilization stress / response to hyperoxia / positive regulation of G1/S transition of mitotic cell cycle / nitric oxide metabolic process / cellular response to copper ion / Hsp70 protein binding / xenobiotic metabolic process / fatty acid metabolic process / Hsp90 protein binding / monooxygenase activity / PPARA activates gene expression / oxygen binding / response to lipopolysaccharide / response to hypoxia / mitochondrial inner membrane / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / mitochondrion
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-HJJ / Cytochrome P450 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsBart, A.G. / Scott, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM076343 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structures of human cytochrome P450 1A1 with bergamottin and erlotinib reveal active-site modifications for binding of diverse ligands.
Authors: Bart, A.G. / Scott, E.E.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)229,01016
Polymers223,7774
Non-polymers5,23312
Water82946
1
A: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5144
Polymers55,9441
Non-polymers1,5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9914
Polymers55,9441
Non-polymers1,0473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8993
Polymers55,9441
Non-polymers9552
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6065
Polymers55,9441
Non-polymers1,6624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.330, 194.758, 236.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLUGLU(chain 'A' and (resid 39 through 291 or resid 303 through 601))AA39 - 29112 - 264
12SERSERSERSER(chain 'A' and (resid 39 through 291 or resid 303 through 601))AA303 - 512276 - 485
13HEMHEMHEMHEM(chain 'A' and (resid 39 through 291 or resid 303 through 601))AE601
24ASNASNGLUGLU(chain 'B' and (resid 39 through 291 or resid 303 through 601))BB39 - 29112 - 264
25SERSERSERSER(chain 'B' and (resid 39 through 291 or resid 303 through 601))BB303 - 512276 - 485
26HEMHEMHEMHEM(chain 'B' and (resid 39 through 291 or resid 303 through 601))BH601
37ASNASNGLUGLU(chain 'C' and resid 39 through 601)CC39 - 29112 - 264
38SERSERSERSER(chain 'C' and resid 39 through 601)CC303 - 512276 - 485
39HEMHEMHEMHEM(chain 'C' and resid 39 through 601)CK601
410ASNASNGLUGLU(chain 'D' and (resid 39 through 291 or resid 303 through 601))DD39 - 29112 - 264
411SERSERSERSER(chain 'D' and (resid 39 through 291 or resid 303 through 601))DD303 - 512276 - 485
412HEMHEMHEMHEM(chain 'D' and (resid 39 through 291 or resid 303 through 601))DM601

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Components

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Protein , 1 types, 4 molecules ABCD

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P04798, unspecific monooxygenase

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Non-polymers , 5 types, 58 molecules

#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-HJJ / 4-{[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-7H-furo[3,2-g][1]benzopyran-7-one


Mass: 338.397 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22O4
#4: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium phosphate dibasic, 20% PEG3350, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→39.36 Å / Num. obs: 71615 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 70.84 Å2 / Net I/σ(I): 8.6
Reflection shellResolution: 2.85→2.91 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4361 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.6.3data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4I8V

4i8v


Resolution: 2.85→39.36 Å / SU ML: 0.369 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8746 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2399 2000 2.8 %
Rwork0.2042 69343 -
obs0.2052 71343 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.47 Å2
Refinement stepCycle: LAST / Resolution: 2.85→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15178 0 173 46 15397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004215768
X-RAY DIFFRACTIONf_angle_d0.654721433
X-RAY DIFFRACTIONf_chiral_restr0.0432314
X-RAY DIFFRACTIONf_plane_restr0.00472724
X-RAY DIFFRACTIONf_dihedral_angle_d11.0739305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.35041330.30854592X-RAY DIFFRACTION94.88
2.92-30.35251400.28374887X-RAY DIFFRACTION99.19
3-3.080.3161410.27694892X-RAY DIFFRACTION99.51
3.08-3.180.30691420.25824906X-RAY DIFFRACTION99.82
3.18-3.30.31081430.25184962X-RAY DIFFRACTION99.98
3.3-3.430.26081420.26394927X-RAY DIFFRACTION100
3.43-3.580.29091420.24414904X-RAY DIFFRACTION99.74
3.58-3.770.27071420.21774932X-RAY DIFFRACTION99.65
3.77-4.010.2271430.19524964X-RAY DIFFRACTION99.8
4.01-4.320.21311440.18394981X-RAY DIFFRACTION99.77
4.32-4.750.1861430.16844986X-RAY DIFFRACTION99.88
4.75-5.440.22361460.17645038X-RAY DIFFRACTION99.85
5.44-6.850.25361450.19865063X-RAY DIFFRACTION99.9
6.85-39.360.19471540.17235309X-RAY DIFFRACTION99.78

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