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- PDB-6sz5: Human calmodulin bound to a peptide of human NADPH oxidase 5 -

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Basic information

Entry
Database: PDB / ID: 6sz5
TitleHuman calmodulin bound to a peptide of human NADPH oxidase 5
Components
  • Calmodulin-2
  • NADPH oxidase 5
KeywordsOXIDOREDUCTASE / NOX5 / calmodulin
Function / homology
Function and homology information


regulation of fusion of sperm to egg plasma membrane / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / superoxide-generating NAD(P)H oxidase activity / negative regulation of calcium ion transmembrane transporter activity / cytoskeleton-dependent cytokinesis / NADPH oxidase complex / proton channel activity / superoxide anion generation / endothelial cell proliferation ...regulation of fusion of sperm to egg plasma membrane / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / superoxide-generating NAD(P)H oxidase activity / negative regulation of calcium ion transmembrane transporter activity / cytoskeleton-dependent cytokinesis / NADPH oxidase complex / proton channel activity / superoxide anion generation / endothelial cell proliferation / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Detoxification of Reactive Oxygen Species / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / : / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / voltage-gated potassium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / proton transmembrane transport / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of cytokine production / spindle microtubule / positive regulation of protein serine/threonine kinase activity / defense response / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / positive regulation of reactive oxygen species metabolic process / flavin adenine dinucleotide binding / myelin sheath / NADP binding / angiogenesis / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / centrosome / calcium ion binding / heme binding / endoplasmic reticulum membrane / apoptotic process / protein kinase binding / endoplasmic reticulum / protein-containing complex / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / EF-hand domain / EF hand / : ...Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / EF-hand domain / EF hand / : / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-2 / NADPH oxidase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMillana, E. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG19808 Italy
CitationJournal: Febs J. / Year: 2020
Title: On the mechanism of calcium-dependent activation of NADPH oxidase 5 (NOX5).
Authors: Millana Fananas, E. / Todesca, S. / Sicorello, A. / Masino, L. / Pompach, P. / Magnani, F. / Pastore, A. / Mattevi, A.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-2
B: NADPH oxidase 5
C: NADPH oxidase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,2517
Polymers181,0913
Non-polymers1604
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-72 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.759, 60.840, 102.444
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin-2


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2, CAM2, CAMB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DP24
#2: Protein NADPH oxidase 5


Mass: 82118.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96PH1, Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 30 mM Tris-HCl at pH 7.4, 2.5 mM CaCl2 and 2.5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.23→39.21 Å / Num. obs: 8098 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.088 / Rrim(I) all: 0.22 / Net I/σ(I): 6.5
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
2.23-2.316.31.46947387540.5290.6281.61.1100
8.64-39.185.10.0639091770.9950.030.0719.599.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.3data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k8q

5k8q


Resolution: 2.23→39.21 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.204 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.281
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2937 403 5 %RANDOM
Rwork0.219 ---
obs0.2227 7653 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.03 Å2 / Biso mean: 40.282 Å2 / Biso min: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å2-0 Å2
2--0.34 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 2.23→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 4 32 1347
Biso mean--35.98 37.83 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181191
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6581807
X-RAY DIFFRACTIONr_angle_other_deg0.9281.6542801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40724.63482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65615253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.503157
X-RAY DIFFRACTIONr_chiral_restr0.0670.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
LS refinement shellResolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 43 -
Rwork0.308 532 -
all-575 -
obs--99.83 %

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