[English] 日本語
Yorodumi
- PDB-4e0k: Crystal Structure of the amyloid-fibril forming peptide KDWSFY de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e0k
TitleCrystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2 Microglobulin (58-63)
ComponentsAmyloidogenic peptide segment KDWSFY
KeywordsPROTEIN FIBRIL / amyloid / out-of-register / fiber-forming
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 0.97 Å
AuthorsZhao, M. / Liu, C. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates.
Authors: Liu, C. / Zhao, M. / Jiang, L. / Cheng, P.N. / Park, J. / Sawaya, M.R. / Pensalfini, A. / Gou, D. / Berk, A.J. / Glabe, C.G. / Nowick, J. / Eisenberg, D.
History
DepositionMar 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amyloidogenic peptide segment KDWSFY
B: Amyloidogenic peptide segment KDWSFY
C: Amyloidogenic peptide segment KDWSFY
D: Amyloidogenic peptide segment KDWSFY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1167
Polymers3,3844
Non-polymers7323
Water88349
1
A: Amyloidogenic peptide segment KDWSFY
B: Amyloidogenic peptide segment KDWSFY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0694
Polymers1,6922
Non-polymers3772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-9 kcal/mol
Surface area2030 Å2
MethodPISA
2
C: Amyloidogenic peptide segment KDWSFY
D: Amyloidogenic peptide segment KDWSFY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0463
Polymers1,6922
Non-polymers3541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-5 kcal/mol
Surface area2120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.370, 62.370, 11.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein/peptide
Amyloidogenic peptide segment KDWSFY


Mass: 845.918 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P61769*PLUS
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BIS-TRIS PROPANE pH 6.5, 0.2 M SODIUM FLUORIDE, 20% (w/v) PEG 3350, vapor diffusion, hanging drop, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionNumber: 137939 / Rmerge(I) obs: 0.069 / D res high: 0.97 Å / Num. obs: 29973 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
3.074.3459998.210.046
2.513.0780699.810.06
2.172.5194910010.058
1.942.17103910010.062
1.771.94122410010.067
1.641.77128610010.071
1.531.64140010010.08
1.451.53143710010.088
1.371.45159910010.102
1.311.37158310010.12
1.251.31176910010.14
1.21.25178810010.144
1.161.2179598.510.11
1.121.16198199.310.122
1.081.12194410010.147
1.051.08201097.910.18
1.021.05209798.510.262
11.02217399.910.34
0.971216897.410.448
ReflectionResolution: 0.97→14.981 Å / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.162 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
0.97-10.4482.425383216897.4
1-1.020.343.085490217399.9
1.02-1.050.2623.825435209798.5
1.05-1.080.184.895364201097.9
1.08-1.120.1475.6951591944100
1.12-1.160.1226.685411198199.3
1.16-1.20.117.225033179598.5
1.2-1.250.1449.1790451788100
1.25-1.310.1411.09117641769100
1.31-1.370.1213.16106071583100
1.37-1.450.10215.66106761599100
1.45-1.530.08818.196801437100
1.53-1.640.0820.7992831400100
1.64-1.770.07123.7285101286100
1.77-1.940.06726.1280471224100
1.94-2.170.06229.0167121039100
2.17-2.510.05829.896277949100
2.51-3.070.0631.34516580699.8
3.07-4.340.04631.9333059998.2
4.340.04331.18156832695

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 0.97→14.981 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.9532 / SU ML: 0.06 / σ(F): 2.01 / Phase error: 9.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1311 1601 10.01 %
Rwork0.1119 --
obs0.1138 15997 99.84 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.541 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 48.94 Å2 / Biso mean: 10.9748 Å2 / Biso min: 1.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.2207 Å2-0 Å2-0 Å2
2--0.2207 Å2-0 Å2
3----0.4415 Å2
Refinement stepCycle: LAST / Resolution: 0.97→14.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms244 0 31 49 324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01369
X-RAY DIFFRACTIONf_angle_d1.417495
X-RAY DIFFRACTIONf_chiral_restr0.09537
X-RAY DIFFRACTIONf_plane_restr0.00958
X-RAY DIFFRACTIONf_dihedral_angle_d19.613163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9703-1.00160.17131400.14951251139199
1.0016-1.03740.15711440.134213031447100
1.0374-1.07890.11381450.107213011446100
1.0789-1.1280.10881420.090812781420100
1.128-1.18740.10481440.089112991443100
1.1874-1.26180.11981440.094112911435100
1.2618-1.35920.12381460.096113161462100
1.3592-1.49580.10291460.098213141460100
1.4958-1.7120.13251470.100313201467100
1.712-2.15590.13491470.107513301477100
2.1559-14.98260.14451560.13041393154999

+
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