[English] 日本語
Yorodumi
- PDB-6wr0: Human steroidogenic cytochrome P450 17A1 with 3-keto-delta4-abira... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wr0
TitleHuman steroidogenic cytochrome P450 17A1 with 3-keto-delta4-abiraterone analog
ComponentsSteroid 17-alpha-hydroxylase/17,20 lyase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / P450 / 17A1
Function / homology
Function and homology information


Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process ...Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process / sex differentiation / progesterone metabolic process / steroid biosynthetic process / steroid metabolic process / oxygen binding / iron ion binding / axon / neuronal cell body / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-U7P / Steroid 17-alpha-hydroxylase/17,20 lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPetrunak, E.M. / Bart, A.G. / Scott, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102505 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site.
Authors: Petrunak, E.M. / Bart, A.G. / Peng, H.M. / Auchus, R.J. / Scott, E.E.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Steroid 17-alpha-hydroxylase/17,20 lyase
B: Steroid 17-alpha-hydroxylase/17,20 lyase
C: Steroid 17-alpha-hydroxylase/17,20 lyase
D: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,92315
Polymers222,9614
Non-polymers3,96211
Water2,126118
1
A: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7043
Polymers55,7401
Non-polymers9642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7404
Polymers55,7401
Non-polymers9993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7404
Polymers55,7401
Non-polymers9993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Steroid 17-alpha-hydroxylase/17,20 lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7404
Polymers55,7401
Non-polymers9993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.347, 152.981, 168.499
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 31 through 503 or resid 600 through 601))A31 - 274
121(chain 'A' and (resid 31 through 503 or resid 600 through 601))A283 - 503
131(chain 'A' and (resid 31 through 503 or resid 600 through 601))A600 - 601
241chain 'B'B31 - 274
251chain 'B'B283 - 503
261chain 'B'B600 - 601
371(chain 'C' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))C31 - 274
381(chain 'C' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))C283 - 503
391(chain 'C' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))C600 - 601
4101(chain 'D' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))D31 - 274
4111(chain 'D' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))D283 - 503
4121(chain 'D' and (resid 31 through 274 or resid 283 through 503 or resid 600 through 601))D600 - 601

-
Components

#1: Protein
Steroid 17-alpha-hydroxylase/17,20 lyase / 17-alpha-hydroxyprogesterone aldolase / CYPXVII / Cytochrome P450 17A1 / Cytochrome P450-C17 / ...17-alpha-hydroxyprogesterone aldolase / CYPXVII / Cytochrome P450 17A1 / Cytochrome P450-C17 / Cytochrome P450c17 / Steroid 17-alpha-monooxygenase


Mass: 55740.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP17A1, CYP17, S17AH / Production host: Escherichia coli (E. coli)
References: UniProt: P05093, steroid 17alpha-monooxygenase, 17alpha-hydroxyprogesterone deacetylase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-U7P / (8alpha)-17-(pyridin-3-yl)androsta-4,16-dien-3-one / 3-keto-delta4-abiraterone analog / Δ4-Abiraterone


Mass: 347.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H29NO / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 175 mM Tris HCl, pH 8.5, 30% PEG-3350, 350 mM LiSO4, and 3% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→39.81 Å / Num. obs: 64672 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 53.1 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9236 / Rpim(I) all: 0.552 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SWZ

3swz


Resolution: 2.7→39.81 Å / SU ML: 0.3474 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 3264 5.06 %
Rwork0.209 61282 -
obs0.2109 64546 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.83 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14905 0 279 118 15302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016915547
X-RAY DIFFRACTIONf_angle_d1.390721132
X-RAY DIFFRACTIONf_chiral_restr0.0912369
X-RAY DIFFRACTIONf_plane_restr0.00832666
X-RAY DIFFRACTIONf_dihedral_angle_d20.21385776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3611330.31732518X-RAY DIFFRACTION94.07
2.74-2.780.36821400.30522614X-RAY DIFFRACTION99.64
2.78-2.830.31161360.29482636X-RAY DIFFRACTION99.53
2.83-2.880.34591430.27962623X-RAY DIFFRACTION99.71
2.88-2.930.29661570.28542621X-RAY DIFFRACTION99.68
2.93-2.990.31571410.26862650X-RAY DIFFRACTION99.86
2.99-3.050.33621470.29212622X-RAY DIFFRACTION99.93
3.05-3.110.27451340.2742679X-RAY DIFFRACTION100
3.11-3.190.31221270.26592648X-RAY DIFFRACTION99.75
3.19-3.270.32331370.2472640X-RAY DIFFRACTION99.93
3.27-3.350.33141580.24422656X-RAY DIFFRACTION99.68
3.35-3.450.26121520.2292614X-RAY DIFFRACTION99.68
3.45-3.560.27881570.22112634X-RAY DIFFRACTION99.89
3.56-3.690.24061400.22162661X-RAY DIFFRACTION99.82
3.69-3.840.24591610.19372659X-RAY DIFFRACTION99.96
3.84-4.010.21291260.18432701X-RAY DIFFRACTION99.96
4.01-4.220.21231430.18272668X-RAY DIFFRACTION99.96
4.22-4.490.21181420.17662680X-RAY DIFFRACTION99.82
4.49-4.830.21171280.16082698X-RAY DIFFRACTION99.68
4.84-5.320.19041370.17372726X-RAY DIFFRACTION99.93
5.32-6.090.24241360.2052717X-RAY DIFFRACTION99.79
6.09-7.660.23291410.18942764X-RAY DIFFRACTION99.59
7.66-39.810.18031480.16922853X-RAY DIFFRACTION99.34

+
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