[English] 日本語
Yorodumi
- PDB-7cfz: SH3 domain of NADPH oxidase activator 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cfz
TitleSH3 domain of NADPH oxidase activator 1
ComponentsNADPH oxidase activator 1
KeywordsCYTOSOLIC PROTEIN / SH3 / NOXA1 / NADPH oxidase activator 1
Function / homology
Function and homology information


superoxide-generating NADPH oxidase activator activity / regulation of respiratory burst / regulation of hydrogen peroxide metabolic process / NADPH oxidase complex / WNT5:FZD7-mediated leishmania damping / superoxide anion generation / superoxide metabolic process / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle / RAC1 GTPase cycle ...superoxide-generating NADPH oxidase activator activity / regulation of respiratory burst / regulation of hydrogen peroxide metabolic process / NADPH oxidase complex / WNT5:FZD7-mediated leishmania damping / superoxide anion generation / superoxide metabolic process / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle / RAC1 GTPase cycle / SH3 domain binding / small GTPase binding / enzyme binding / identical protein binding / cytosol
Similarity search - Function
: / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / SH3 domain ...: / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
NADPH oxidase activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKim, M. / Park, J.H. / Attri, P. / Lee, W.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study.
Authors: Attri, P. / Park, J.H. / De Backer, J. / Kim, M. / Yun, J.H. / Heo, Y. / Dewilde, S. / Shiratani, M. / Choi, E.H. / Lee, W. / Bogaerts, A.
History
DepositionJun 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: 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 1.2Nov 29, 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: NADPH oxidase activator 1
B: NADPH oxidase activator 1


Theoretical massNumber of molelcules
Total (without water)14,2222
Polymers14,2222
Non-polymers00
Water86548
1
A: NADPH oxidase activator 1


Theoretical massNumber of molelcules
Total (without water)7,1111
Polymers7,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH oxidase activator 1


Theoretical massNumber of molelcules
Total (without water)7,1111
Polymers7,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.596, 49.014, 72.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-121-

HOH

-
Components

#1: Protein NADPH oxidase activator 1 / NOX activator 1 / Antigen NY-CO-31 / NCF2-like protein / P67phox-like factor / p51-nox


Mass: 7111.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOXA1, P51NOX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86UR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M Magnesium chloride hexahydrate, 25% PEG 3,350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.885→50 Å / Num. obs: 9201 / % possible obs: 98.57 % / Redundancy: 5 % / Biso Wilson estimate: 33.09 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 27.2
Reflection shellResolution: 1.885→1.96 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 225 / % possible all: 98.22

-
Processing

Software
NameVersionClassification
HKL-20001.13_2998data scaling
PHASER1.13_2998phasing
Cootmodel building
PHENIX1.13-2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k28
Resolution: 1.89→40.68 Å / SU ML: 0.2188 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.303 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2555 920 10 %
Rwork0.227 8276 -
obs0.2298 9196 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.39 Å2
Refinement stepCycle: LAST / Resolution: 1.89→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 0 48 957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034933
X-RAY DIFFRACTIONf_angle_d0.69541270
X-RAY DIFFRACTIONf_chiral_restr0.0508135
X-RAY DIFFRACTIONf_plane_restr0.0042170
X-RAY DIFFRACTIONf_dihedral_angle_d3.0669539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.980.27981270.27141150X-RAY DIFFRACTION98.69
1.98-2.110.25251300.25341160X-RAY DIFFRACTION99.61
2.11-2.270.27981300.24331173X-RAY DIFFRACTION99.16
2.27-2.50.29931300.22951171X-RAY DIFFRACTION98.94
2.5-2.860.27581300.24681171X-RAY DIFFRACTION98.41
2.86-3.610.25781340.22281198X-RAY DIFFRACTION98.38
3.61-40.680.23331390.21221253X-RAY DIFFRACTION97

+
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