[English] 日本語
Yorodumi
- PDB-7aew: 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, C... -

+
Open data


ID or keywords:

Loading...

-
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 N
KeywordsPEPTIDE BINDING PROTEIN / extracellular 14-3-3 / phosphorylation / aminopeptidase N / CD13 / protein binding
Function / homology
Function and homology information


alanyl aminopeptidase activity / 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 / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity ...alanyl aminopeptidase activity / 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 / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / aminopeptidase activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Metabolism of Angiotensinogen to Angiotensins / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / angiotensin maturation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / peptide binding / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / secretory granule membrane / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage / metallopeptidase activity / intracellular protein localization / signaling receptor activity / regulation of protein localization / virus 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 / cytoplasm / cytosol
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy ...Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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