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- PDB-6xwd: 14-3-3 sigma bound to canonical mono-phosphorylated aminopeptidas... -

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Basic information

Entry
Database: PDB / ID: 6xwd
Title14-3-3 sigma bound to canonical mono-phosphorylated aminopeptidase N (APN, CD13) binding motif
Components
  • 14-3-3 protein sigma
  • Amino peptidase N 38-46
KeywordsPROTEIN BINDING / extracellular 14-3-3 Phosphorylation Aminopeptidase N CD13
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 / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / aminopeptidase activity / 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 / secretory granule membrane / positive regulation of protein export from nucleus / 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: 1.60000193301 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
DepositionJan 23, 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 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Amino peptidase N 38-46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6897
Polymers27,5542
Non-polymers1355
Water7,548419
1
A: 14-3-3 protein sigma
P: Amino peptidase N 38-46
hetero molecules

A: 14-3-3 protein sigma
P: Amino peptidase N 38-46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,37714
Polymers55,1084
Non-polymers26910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5450 Å2
ΔGint-95 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.000, 111.600, 62.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-305-

MG

21A-794-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#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 Amino peptidase N 38-46


Mass: 1010.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15144*PLUS

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Non-polymers , 4 types, 424 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH7.3 0.19 M CaCl2 5% glycerol 28% 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: 1.6→45.369 Å / Num. obs: 38136 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.9717835273 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.111 / Net I/σ(I): 15.06
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2.66 / Num. unique obs: 6243 / CC1/2: 0.879 / Rrim(I) all: 0.784 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mhr

3mhr


Resolution: 1.60000193301→45.3686677903 Å / SU ML: 0.175496899688 / Cross valid method: FREE R-VALUE / σ(F): 1.36776067045 / Phase error: 19.4543244167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196211883185 1907 5.0035420985 %
Rwork0.166056682714 36206 -
obs0.167601021414 38113 99.9868828375 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.4319744705 Å2
Refinement stepCycle: LAST / Resolution: 1.60000193301→45.3686677903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 5 419 2326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005625356540092130
X-RAY DIFFRACTIONf_angle_d0.7776413759362915
X-RAY DIFFRACTIONf_chiral_restr0.0410118685598323
X-RAY DIFFRACTIONf_plane_restr0.00468534765003386
X-RAY DIFFRACTIONf_dihedral_angle_d1.926725595871779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.60000193301-1.640.2340699591841340.2260214917762554X-RAY DIFFRACTION99.9628114541
1.64-1.68440.2346054270441330.214904647862524X-RAY DIFFRACTION99.9247837533
1.6844-1.73390.2401192613881360.2106490044522578X-RAY DIFFRACTION100
1.7339-1.78990.2822849919651340.2550118476332551X-RAY DIFFRACTION100
1.7899-1.85390.2546393813591350.223528432342550X-RAY DIFFRACTION99.9627699181
1.8539-1.92810.2289076559481350.1872012843482568X-RAY DIFFRACTION100
1.9281-2.01580.217439201891350.1644723576692571X-RAY DIFFRACTION100
2.0158-2.12210.1714394262551350.1571449332392560X-RAY DIFFRACTION100
2.1221-2.25510.2024725416791350.155733972352576X-RAY DIFFRACTION100
2.2551-2.42920.1747749633071360.1604201615172582X-RAY DIFFRACTION100
2.4292-2.67360.216663646561380.1683450092032604X-RAY DIFFRACTION100
2.6736-3.06040.2114611674631360.1720374005972598X-RAY DIFFRACTION100
3.0604-3.85550.1691131467121400.1392482587192652X-RAY DIFFRACTION100
3.8555-45.36866779030.1700924380671450.1535024345992738X-RAY DIFFRACTION100

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