[English] 日本語
Yorodumi
- PDB-8anl: Structure of the amyloid-forming peptide LFIEWL from exendin-4, g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8anl
TitleStructure of the amyloid-forming peptide LFIEWL from exendin-4, grown from water
ComponentsPeptide LFIEWL from exendin-4
KeywordsPROTEIN FIBRIL / amyloid
Biological speciesHeloderma suspectum (Gila monster)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDurvanger, Z.
Funding support Hungary, European Union, 3items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 Hungary
European Regional Development FundVEKOP-2.3.2-16-2017-00014, VEKOP-2.3.3-15-2017-00018European Union
Hungarian National Research, Development and Innovation OfficeThematic Excellence Program Synth+ Hungary
CitationJournal: Nat Commun / Year: 2023
Title: Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation.
Authors: Horvath, D. / Durvanger, Z. / K Menyhard, D. / Sulyok-Eiler, M. / Bencs, F. / Gyulai, G. / Horvath, P. / Taricska, N. / Perczel, A.
History
DepositionAug 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptide LFIEWL from exendin-4
B: Peptide LFIEWL from exendin-4
C: Peptide LFIEWL from exendin-4
D: Peptide LFIEWL from exendin-4


Theoretical massNumber of molelcules
Total (without water)3,2804
Polymers3,2804
Non-polymers00
Water362
1
A: Peptide LFIEWL from exendin-4
B: Peptide LFIEWL from exendin-4


Theoretical massNumber of molelcules
Total (without water)1,6402
Polymers1,6402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peptide LFIEWL from exendin-4
D: Peptide LFIEWL from exendin-4


Theoretical massNumber of molelcules
Total (without water)1,6402
Polymers1,6402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)9.520, 14.292, 34.287
Angle α, β, γ (deg.)90.590, 93.300, 95.970
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein/peptide
Peptide LFIEWL from exendin-4


Mass: 819.986 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Heloderma suspectum (Gila monster)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 310 K / Method: evaporation, recrystallization
Details: Lyophilized peptide was dissolved in water (0.15 mg/ml concentration), followed by pH adjustment with NaOH to pH 5.50. Crystals appeared after incubation at 310K for several days.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.75→14.21 Å / Num. obs: 1803 / % possible obs: 99.28 % / Redundancy: 3.14 % / Biso Wilson estimate: 8.77 Å2 / CC1/2: 0.984 / Rrim(I) all: 0.144 / Net I/σ(I): 6.4
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 193 / CC1/2: 0.7 / Rrim(I) all: 0.799 / % possible all: 99.48

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: crystal structure of LYIQWL

Resolution: 1.75→14.21 Å / SU ML: 0.1872 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.4882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2125 178 10 %
Rwork0.1761 1602 -
obs0.18 1780 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.56 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms236 0 0 2 238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183250
X-RAY DIFFRACTIONf_angle_d1.7792342
X-RAY DIFFRACTIONf_chiral_restr0.072338
X-RAY DIFFRACTIONf_plane_restr0.008537
X-RAY DIFFRACTIONf_dihedral_angle_d13.753380
LS refinement shellResolution: 1.75→14.21 Å
RfactorNum. reflection% reflection
Rfree0.2125 178 -
Rwork0.1761 1602 -
obs--98.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.432060567190.308338496592-1.071681189966.82550478175-5.253480426817.150818075080.1212464853680.388248117328-0.05206762533840.00463320224633-0.1417236278690.0401487576061-0.2579814076510.340468432803-0.06261709621970.04227473231190.00402063793691-0.01901166224450.09787661286980.002005455620630.08908838375452.169802021970.696574779066-1.12085388817
23.05558495285-0.8080423376410.6436747356374.23045089935-0.1656387180924.30000796468-0.0184785938372-0.703586618793-0.3331455442540.285005555430.3229393264640.1055858479430.286834048352-0.3143232161720.06806121856720.06401418516860.00685071906186-0.03733527773990.1134591487810.06905204183320.0728808789513-2.87826255743-1.28548213771.97495971718
34.136450795760.2379286651170.1895065089679.07803872158-6.653186169237.647667248580.0526489026446-0.04665305943640.133107813108-0.256145050629-0.08524991936750.01803143262270.272649807904-0.0120454300425-0.05193035734910.1364208342630.0581926748156-0.02337212850710.1082833053260.03089530525570.119664505767-5.115766992750.918231292071-17.9006709772
45.337863391331.16466053453-0.95750395878.44776511338-7.052090108759.414222155410.0644920169479-0.17881460915-0.04012072903820.314619579383-0.1293205146580.0516423172273-0.2189180635430.06497405050160.2351949440790.1023635987640.02720585248140.02300777040510.1672680311880.007360819097250.11084571792-0.81432273862-1.3683610475-15.3344677175
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 6 / Label seq-ID: 1 - 6

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A' and (resid 1 through 6 )AA
22chain 'B' and (resid 1 through 6 )BB
33chain 'C' and (resid 1 through 6 )CC
44chain 'D' and (resid 1 through 6 )DD

+
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