[English] 日本語
Yorodumi
- PDB-7yxw: Structure of the p22phox A200G mutant in complex with p47phox peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yxw
TitleStructure of the p22phox A200G mutant in complex with p47phox peptide
Components
  • Cytochrome b-245 light chain
  • Neutrophil cytosol factor 1
KeywordsOXIDOREDUCTASE / NADPH oxidase complex / oxidoreductase activator
Function / homology
Function and homology information


negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / regulation of respiratory burst involved in inflammatory response / neutrophil-mediated killing of gram-positive bacterium / superoxide-generating NADPH oxidase activator activity / cellular response to L-glutamine / neutrophil-mediated killing of fungus / phagolysosome / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium ...negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / regulation of respiratory burst involved in inflammatory response / neutrophil-mediated killing of gram-positive bacterium / superoxide-generating NADPH oxidase activator activity / cellular response to L-glutamine / neutrophil-mediated killing of fungus / phagolysosome / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion / perinuclear endoplasmic reticulum / superoxide-generating NAD(P)H oxidase activity / leukotriene metabolic process / response to yeast / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / cytochrome complex assembly / cellular response to testosterone stimulus / respiratory burst / WNT5:FZD7-mediated leishmania damping / respiratory burst involved in defense response / phosphatidylinositol-3,4-bisphosphate binding / ROS and RNS production in phagocytes / regulation of release of sequestered calcium ion into cytosol / hydrogen peroxide biosynthetic process / protein targeting to membrane / superoxide anion generation / positive regulation of mucus secretion / superoxide metabolic process / response to aldosterone / Detoxification of Reactive Oxygen Species / positive regulation of reactive oxygen species biosynthetic process / tertiary granule membrane / cellular response to angiotensin / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / cellular defense response / specific granule membrane / stress fiber / positive regulation of phagocytosis / positive regulation of endothelial cell proliferation / RAC1 GTPase cycle / phosphatidylinositol binding / response to interleukin-1 / secretory granule / positive regulation of superoxide anion generation / epithelial cell proliferation / response to activity / response to nutrient levels / positive regulation of smooth muscle cell proliferation / cellular response to glucose stimulus / establishment of localization in cell / cellular response to gamma radiation / SH3 domain binding / positive regulation of interleukin-6 production / VEGFA-VEGFR2 Pathway / cytoplasmic side of plasma membrane / cellular response to mechanical stimulus / phagocytic vesicle membrane / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of cell growth / response to hypoxia / electron transfer activity / endosome / apical plasma membrane / inflammatory response / response to xenobiotic stimulus / protein heterodimerization activity / innate immune response / focal adhesion / neuronal cell body / heme binding / dendrite / Neutrophil degranulation / endoplasmic reticulum membrane / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / Neutrophil cytosol factor 1 / Neutrophil cytosol factor 1, C-terminal / Neutrophil cytosol factor 1, PBR/AIR / Neutrophil cytosol factor 1, PX domain / Neutrophil cytosol factor 1, first SH3 domain / Neutrophil cytosol factor 1, second SH3 domain / NADPH oxidase subunit p47Phox, C terminal domain / Neutrophil cytosol factor 1, PBR/AIR ...Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / Neutrophil cytosol factor 1 / Neutrophil cytosol factor 1, C-terminal / Neutrophil cytosol factor 1, PBR/AIR / Neutrophil cytosol factor 1, PX domain / Neutrophil cytosol factor 1, first SH3 domain / Neutrophil cytosol factor 1, second SH3 domain / NADPH oxidase subunit p47Phox, C terminal domain / Neutrophil cytosol factor 1, PBR/AIR / : / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Cytochrome b-245 light chain / Neutrophil cytosol factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCukier, C.D. / Vuillard, L.M. / Komjati, B. / Szlavik, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Targeting NOX2 via p47/phox-p22/phox Inhibition with Novel Triproline Mimetics
Authors: Garsi, J.B. / Komjati, B. / Cullia, G. / Fejes, I. / Sipos, M. / Sipos, Z. / Fordos, E. / Markacz, P. / Balazs, B. / Lancelot, N. / Berger, S. / Raimbaud, E. / Brown, D. / Vuillard, L.M. / ...Authors: Garsi, J.B. / Komjati, B. / Cullia, G. / Fejes, I. / Sipos, M. / Sipos, Z. / Fordos, E. / Markacz, P. / Balazs, B. / Lancelot, N. / Berger, S. / Raimbaud, E. / Brown, D. / Vuillard, L.M. / Haberkorn, L. / Cukier, C. / Szlavik, Z. / Hanessian, S.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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
D: Cytochrome b-245 light chain
A: Neutrophil cytosol factor 1


Theoretical massNumber of molelcules
Total (without water)16,5822
Polymers16,5822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area7920 Å2
Unit cell
Length a, b, c (Å)102.444, 102.444, 56.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein/peptide Cytochrome b-245 light chain / Cytochrome b(558) alpha chain / Cytochrome b558 subunit alpha / Neutrophil cytochrome b 22 kDa ...Cytochrome b(558) alpha chain / Cytochrome b558 subunit alpha / Neutrophil cytochrome b 22 kDa polypeptide / Superoxide-generating NADPH oxidase light chain subunit / p22 phagocyte B-cytochrome / p22-phox / p22phox


Mass: 1927.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13498
#2: Protein Neutrophil cytosol factor 1 / NCF-1 / 47 kDa autosomal chronic granulomatous disease protein / 47 kDa neutrophil oxidase factor / ...NCF-1 / 47 kDa autosomal chronic granulomatous disease protein / 47 kDa neutrophil oxidase factor / NCF-47K / Neutrophil NADPH oxidase factor 1 / Nox organizer 2 / Nox-organizing protein 2 / SH3 and PX domain-containing protein 1A / p47-phox


Mass: 14654.306 Da / Num. of mol.: 1 / Mutation: A200G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCF1, NOXO2, SH3PXD1A / Production host: Escherichia coli (E. coli) / References: UniProt: P14598

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.2 M sodium citrate tribasic dihydrate, 1:1 protein:precipitant ratio

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→45.81 Å / Num. obs: 10811 / % possible obs: 99.9 % / Redundancy: 12 % / Biso Wilson estimate: 58.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.031 / Rrim(I) all: 0.104 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.612.91.1411525411810.9270.3381.1921.799.9
9.01-45.81100.04828442830.9990.0150.05126.898.7

-
Processing

Software
NameVersionClassification
XDSVERSION January 10, 2014data reduction
Aimless0.5.27data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ng2

1ng2


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.798 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 554 5.1 %RANDOM
Rwork0.2411 ---
obs0.2426 10220 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.26 Å2 / Biso mean: 91.471 Å2 / Biso min: 60.34 Å2
Baniso -1Baniso -2Baniso -3
1--9.77 Å20 Å20 Å2
2---9.77 Å20 Å2
3---19.55 Å2
Refinement stepCycle: final / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 0 1093
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021126
X-RAY DIFFRACTIONr_bond_other_d0.0020.021027
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.9721537
X-RAY DIFFRACTIONr_angle_other_deg1.05132395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6085137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.01325.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90515177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.307154
X-RAY DIFFRACTIONr_chiral_restr0.10.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02227
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 37 -
Rwork0.529 733 -
all-770 -
obs--99.87 %

+
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