[English] 日本語
Yorodumi
- PDB-3n57: Crystal Structure of human Insulin-degrading enzyme (IDE) in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n57
TitleCrystal Structure of human Insulin-degrading enzyme (IDE) in complex with human atrial natriuretic peptide (ANP)
Components
  • Atrial natriuretic factor
  • Insulin-degrading enzyme
KeywordsHYDROLASE/HORMONE / INSULYSIN / INSULINASE / A-BETA DEGRADING ENZYME / CRYPTIDASE / HYDROLASE / HORMONE / DISEASE MUTATION / DIABETES MELLITUS / INSULIN / CARDIAC / SECRETED / PROTEASE / DISULFIDE BOND / METALLOPROTEASE / HUMAN INSULIN-DEGRADNG ENZYME / METAL-BINDING / NATRIURETIC PEPTIDE / NATRIURETIC FACTOR / CARDIOVASCULAR REGULATION / HYDROLASE-HORMONE complex
Function / homology
Function and homology information


positive regulation of delayed rectifier potassium channel activity / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / neuropeptide receptor binding / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / insulysin / hormone receptor binding / insulin catabolic process ...positive regulation of delayed rectifier potassium channel activity / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / neuropeptide receptor binding / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / insulysin / hormone receptor binding / insulin catabolic process / ubiquitin recycling / ubiquitin-dependent protein binding / insulin metabolic process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / regulation of high voltage-gated calcium channel activity / hormone catabolic process / bradykinin catabolic process / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / cardiac conduction system development / amyloid-beta clearance by cellular catabolic process / negative regulation of JUN kinase activity / neuropeptide hormone activity / positive regulation of heart rate / protein catabolic process => GO:0030163 / cardiac muscle hypertrophy in response to stress / negative regulation of systemic arterial blood pressure / aortic valve morphogenesis / regulation of aerobic respiration / positive regulation of cardiac muscle contraction / insulin binding / amyloid-beta clearance / peptide catabolic process / negative regulation of epidermal growth factor receptor signaling pathway / cGMP-mediated signaling / peroxisomal matrix / neuropeptide signaling pathway / protein catabolic process / determination of adult lifespan / amyloid-beta metabolic process / response to muscle stretch / proteolysis involved in protein catabolic process / peptide binding / cell projection / female pregnancy / Peroxisomal protein import / positive regulation of protein catabolic process / peroxisome / hormone activity / vasodilation / insulin receptor signaling pathway / metalloendopeptidase activity / regulation of blood pressure / antigen processing and presentation of endogenous peptide antigen via MHC class I / negative regulation of canonical Wnt signaling pathway / basolateral plasma membrane / virus receptor activity / protein folding / perikaryon / collagen-containing extracellular matrix / positive regulation of protein binding / endopeptidase activity / Ub-specific processing proteases / Amyloid fiber formation / external side of plasma membrane / proteolysis / signaling receptor binding / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Natriuretic peptide, atrial type / Natriuretic peptide / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Middle or third domain of peptidase_M16 / Peptidase M16, middle/third domain / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome Bc1 Complex; Chain A, domain 1 ...Natriuretic peptide, atrial type / Natriuretic peptide / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Middle or third domain of peptidase_M16 / Peptidase M16, middle/third domain / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome Bc1 Complex; Chain A, domain 1 / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Insulinase (Peptidase family M16) / Peptidase M16, N-terminal / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Natriuretic peptides A / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.03 Å
AuthorsFunke, T. / Guo, Q. / Tang, W.-J.
CitationJournal: To be Published
Title: Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human atrial natriuretic peptide (ANP)
Authors: Ralat, L.A. / Funke, T. / Ren, M. / Guo, Q. / Dickey, D.M. / Potter, L.R. / Tang, W.-J.
History
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Database references / Refinement description / Source and taxonomy
Category: citation_author / entity_src_gen / software
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
C: Atrial natriuretic factor
D: Atrial natriuretic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,4276
Polymers235,2964
Non-polymers1312
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)264.101, 264.101, 91.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Insulin-degrading enzyme / / Insulin protease / Insulinase / Insulysin / Abeta-degrading protease


Mass: 114560.578 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019
Mutation: C110L, E111Q, C171S, C178S, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDE / Plasmid: PPROEX-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: P14735, insulysin
#2: Protein/peptide Atrial natriuretic factor / ANF / Atrial natriuretic peptide / ANP / Prepronatriodilatin / CDD-ANF / Cardiodilatin-related peptide / CDP


Mass: 3087.505 Da / Num. of mol.: 2 / Fragment: UNP residues 124-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPPA, ANP, PND / Production host: Escherichia coli (E. coli) / References: UniProt: P01160
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEGMME-5000, 10% TACSIMATE, 10% DIOXANE, 100 mM Na-HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: Si(111) AND Si(220) - SAGITALLY FOCUSED DOUBLE CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.026→50 Å / Num. obs: 65889 / % possible obs: 92.63 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.20693 / Rsym value: 0.144 / Net I/σ(I): 20.7
Reflection shellResolution: 3.026→3.104 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.562 / % possible all: 93.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 3.03→29.96 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.749 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 2.081 / ESU R Free: 0.373
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24154 1542 2.3 %RANDOM
Rwork0.2061 ---
obs0.20693 -96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 3.03→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15652 0 2 64 15718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02216019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.96621668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68451907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37324.51796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.674152876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5241583
X-RAY DIFFRACTIONr_chiral_restr0.0910.22333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112200
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3651.59574
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.715215494
X-RAY DIFFRACTIONr_scbond_it0.99236445
X-RAY DIFFRACTIONr_scangle_it1.7984.56174
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.03→3.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 108 -
Rwork0.263 4757 -
obs--93.2 %

+
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