[English] 日本語
Yorodumi
- PDB-1w70: SH3 domain of p40phox complexed with C-terminal polyProline regio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w70
TitleSH3 domain of p40phox complexed with C-terminal polyProline region of p47phox
Components
  • NEUTROPHIL CYTOSOL FACTOR 1
  • NEUTROPHIL CYTOSOL FACTOR 4
KeywordsSH3 DOMAIN / NADPH OXIDASE / P40PHOX / P47PHOX / POLYPROLINE
Function / homology
Function and homology information


reactive oxygen species biosynthetic process / regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / phagolysosome / superoxide-generating NAD(P)H oxidase activity / positive regulation of epidermal growth factor-activated receptor activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / cellular response to testosterone stimulus ...reactive oxygen species biosynthetic process / regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / phagolysosome / superoxide-generating NAD(P)H oxidase activity / positive regulation of epidermal growth factor-activated receptor activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / cellular response to testosterone stimulus / phosphatidylinositol-3-phosphate binding / ROS and RNS production in phagocytes / phosphatidylinositol-3,4-bisphosphate binding / superoxide anion generation / protein targeting to membrane / positive regulation of p38MAPK cascade / superoxide metabolic process / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / cellular defense response / phagocytosis / RAC1 GTPase cycle / cellular response to cadmium ion / phosphatidylinositol binding / cellular response to glucose stimulus / positive regulation of JNK cascade / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway / SH3 domain binding / cellular response to reactive oxygen species / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / innate immune response / neuronal cell body / dendrite / positive regulation of DNA-templated transcription / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Neutrophil cytosol factor P40 / Neutrophil cytosol factor P40, PB1 domain / Neutrophil cytosol factor 4, PX domain / Neutrophil cytosol factor P40, SH3 domain / 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 ...Neutrophil cytosol factor P40 / Neutrophil cytosol factor P40, PB1 domain / Neutrophil cytosol factor 4, PX domain / Neutrophil cytosol factor P40, SH3 domain / 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 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
trifluoroacetic acid / Neutrophil cytosol factor 1 / Neutrophil cytosol factor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsMassenet, C. / Chenavas, S. / Cohen-Addad, C. / Dagher, M.-C. / Brandolin, G. / Pebay-Peyroula, E. / Fieschi, F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Effects of P47Phox C-Terminus Phosphorylation on Binding Interactions with P40Phox and P67Phox: Structural and Functional Comparison of P40Phox P67Phox SH3 Domains
Authors: Massenet, C. / Chenavas, S. / Cohen-Addad, C. / Dagher, M.-C. / Brandolin, G. / Pebay-Peyroula, E. / Fieschi, F.
History
DepositionAug 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEUTROPHIL CYTOSOL FACTOR 4
B: NEUTROPHIL CYTOSOL FACTOR 4
C: NEUTROPHIL CYTOSOL FACTOR 1
D: NEUTROPHIL CYTOSOL FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,96910
Polymers16,3574
Non-polymers6126
Water4,089227
1
A: NEUTROPHIL CYTOSOL FACTOR 4
C: NEUTROPHIL CYTOSOL FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2753
Polymers8,1792
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NEUTROPHIL CYTOSOL FACTOR 4
D: NEUTROPHIL CYTOSOL FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6957
Polymers8,1792
Non-polymers5165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.640, 50.490, 68.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCHAINS A AND B ARE ISOLATED FRAGMENTS OF P40PHOXAND THERE IS NO BIOLOGICAL EVIDENCE OF THEIRDIMERIZATION. HOWEVER, SINCE EACH CHAIN IS INCOMPLEX WITH A PEPTIDE IN THIS ENTRY, THE BIOLOGICALUNIT IS CLASSIFIED AS DIMERIC.

-
Components

#1: Protein NEUTROPHIL CYTOSOL FACTOR 4 / NCF-4 / NEUTROPHIL NADPH OXIDASE FACTOR 4 / P40PHOX / P40-PHOX


Mass: 6791.013 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 174-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NEUTROPHIL / Plasmid: PIVEX2.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15080
#2: Protein/peptide NEUTROPHIL CYTOSOL FACTOR 1 / NCF-1 / NEUTROPHIL NADPH OXIDASE FACTOR 1 / 47 KDA NEUTROPHIL OXIDASE FACTOR / P47-PHOX


Mass: 1387.581 Da / Num. of mol.: 2 / Fragment: POLYPROLINE MOTIF, RESIDUES 360-372 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P14598
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2HF3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPONENT OF THE NADPH-OXIDASE, A MULTICOMPONENT ENZYME SYSTEM RESPONSIBLE FOR TRANSPORT OF ...COMPONENT OF THE NADPH-OXIDASE, A MULTICOMPONENT ENZYME SYSTEM RESPONSIBLE FOR TRANSPORT OF ELECTRONS FROM NADPH TO MOLECULAR OXYGEN, GENERATING REACTIVE OXIDANT INTERMEDIATES. P40-PHOX ASSOCIATES PRIMARILY WITH P67-PHOX TO FORM A COMPLEX WITH P47-PHOX. NCF2, NCF1, AND A MEMBRANE BOUND CYTOCHROME B558 ARE REQUIRED FOR ACTIVATION OF THE LATENT NADPH OXIDASE (NECESSARY FOR SUPEROXIDE PRODUCTION).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: VAPOR DIFFUSION AT 20 DEGRE C AT 14MG/ML OF P40PHOX SH3 WITH A1/5 RATIO WITH POLYPROLINE PEPTIDE, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 100 MM NA-CITRATE/CITRIC ACID PH5, 2.4 M SA

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.46→23.7 Å / Num. obs: 23121 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 13
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.1 / % possible all: 83.7

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W6X

1w6x


Resolution: 1.46→23.7 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1168 4.8 %RANDOM
Rwork0.1811 ---
obs0.1811 23121 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.2164 Å2 / ksol: 0.541566 e/Å3
Displacement parametersBiso mean: 16.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.939 Å20 Å20 Å2
2--1.29 Å20 Å2
3----3.229 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.46→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 34 227 1396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008391
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.49521
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.50055
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05772
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.46→1.51 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2602 108 4.51 %
Rwork0.2308 1820 -
obs--79.47 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4SULF.PARAM
X-RAY DIFFRACTION5TFA.PARAM

+
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