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- PDB-7aew: 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, C... -

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Basic information

Entry
Database: PDB / ID: 7aew
Title14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and non-canonical binding motifs
Components
  • 14-3-3 protein sigma
  • Aminopeptidase NAlanine aminopeptidase
KeywordsPEPTIDE BINDING PROTEIN / extracellular 14-3-3 / phosphorylation / aminopeptidase N / CD13 / protein binding
Function / homology
Function and homology information


membrane alanyl aminopeptidase / peptide catabolic process / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / metalloaminopeptidase activity / Regulation of localization of FOXO transcription factors / keratinocyte proliferation ...membrane alanyl aminopeptidase / peptide catabolic process / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / metalloaminopeptidase activity / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / endoplasmic reticulum-Golgi intermediate compartment / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / Metabolism of Angiotensinogen to Angiotensins / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / aminopeptidase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein kinase A signaling / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / secretory granule membrane / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / peptide binding / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / metallopeptidase activity / intrinsic apoptotic signaling pathway in response to DNA damage / virus receptor activity / signaling receptor activity / positive regulation of cell growth / angiogenesis / cell differentiation / regulation of cell cycle / cadherin binding / lysosomal membrane / external side of plasma membrane / Neutrophil degranulation / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / proteolysis / extracellular space / extracellular exosome / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / 14-3-3 protein sigma ...Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / 14-3-3 protein sigma / Peptidase M4/M1, CTD superfamily / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Aminopeptidase N / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKiehstaller, S. / Hennig, S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: MMP activation-associated aminopeptidase N reveals a bivalent 14-3-3 binding motif.
Authors: Kiehstaller, S. / Ottmann, C. / Hennig, S.
History
DepositionSep 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jun 8, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 14-3-3 protein sigma
CCC: Aminopeptidase N
BBB: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8098
Polymers34,6813
Non-polymers1275
Water7,674426
1
AAA: 14-3-3 protein sigma
CCC: Aminopeptidase N
BBB: Aminopeptidase N
hetero molecules

AAA: 14-3-3 protein sigma
CCC: Aminopeptidase N
BBB: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,61716
Polymers69,3626
Non-polymers25510
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.210, 112.060, 62.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-302-

NA

21AAA-795-

HOH

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Aminopeptidase N / Alanine aminopeptidase / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma ...hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma membrane glycoprotein CD13 / gp150


Mass: 4069.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15144, membrane alanyl aminopeptidase
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.7 0.19 M CaCl2 5% glycerol 27 % PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91165 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 1.2→45.52 Å / Num. obs: 86519 / % possible obs: 95.8 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 19.82
Reflection shellResolution: 1.2→1.3 Å / Num. unique obs: 16344 / CC1/2: 0.854

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0266refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mhr

3mhr


Resolution: 1.2→45.516 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.652 / SU ML: 0.029 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1836 4326 5 %
Rwork0.1618 82186 -
all0.163 --
obs-86512 95.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.766 Å2
Baniso -1Baniso -2Baniso -3
1-1.056 Å20 Å2-0 Å2
2---0.366 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.2→45.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 5 426 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132273
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172176
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.6493117
X-RAY DIFFRACTIONr_angle_other_deg1.5841.5885090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95823.065124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91115452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2151516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022683
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02501
X-RAY DIFFRACTIONr_nbd_refined0.260.2513
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.21927
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21043
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.2911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3440.21
X-RAY DIFFRACTIONr_metal_ion_refined0.10.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3140.243
X-RAY DIFFRACTIONr_nbd_other0.2540.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.340.250
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1610.24
X-RAY DIFFRACTIONr_mcbond_it1.5031.5881113
X-RAY DIFFRACTIONr_mcbond_other1.5031.5861112
X-RAY DIFFRACTIONr_mcangle_it2.362.3781417
X-RAY DIFFRACTIONr_mcangle_other2.3592.381418
X-RAY DIFFRACTIONr_scbond_it2.341.7971160
X-RAY DIFFRACTIONr_scbond_other2.3391.7991161
X-RAY DIFFRACTIONr_scangle_it3.5292.6081669
X-RAY DIFFRACTIONr_scangle_other3.5292.6081669
X-RAY DIFFRACTIONr_lrange_it5.55720.4162832
X-RAY DIFFRACTIONr_lrange_other5.53820.4532817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.2-1.2310.3242370.31245090.31365820.7750.79172.10570.293
1.231-1.2650.2962900.28155100.28264640.8520.84689.72770.26
1.265-1.3010.2323020.24257320.24162520.9010.89296.51310.219
1.301-1.3410.2372950.21256010.21360740.9030.91697.06950.187
1.341-1.3850.2232880.20654880.20759280.9290.92897.43590.18
1.385-1.4340.2342800.1953020.19257190.9240.93797.60450.167
1.434-1.4880.192700.17351450.17355380.9470.95297.7790.152
1.488-1.5490.1892610.16549540.16653090.9490.95798.22940.148
1.549-1.6180.1722530.15548000.15651400.960.96698.30740.139
1.618-1.6960.1722410.15445780.15548990.9610.96398.3670.141
1.696-1.7880.1952290.15343620.15546500.9560.96598.73120.14
1.788-1.8960.1692180.15641340.15743950.9660.96699.02160.145
1.896-2.0270.1752070.15239380.15341760.9620.96999.25770.143
2.027-2.1890.1631930.14336580.14438710.970.97599.48330.139
2.189-2.3970.1591790.13534080.13636030.9690.97599.55590.135
2.397-2.680.1611620.14130700.14232430.970.97399.66080.144
2.68-3.0920.1721430.15227220.15328690.9650.96699.86060.162
3.092-3.7830.1651230.13823470.13924720.9690.97699.91910.152
3.783-5.3310.182980.15818550.15919540.9670.97399.94880.188
5.331-45.5160.232570.23210730.23211370.9570.95499.38430.279

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