[English] 日本語
Yorodumi
- PDB-9q2v: Structure of peptide segment KLVFFA from amyloid-beta determined ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9q2v
TitleStructure of peptide segment KLVFFA from amyloid-beta determined by liquid cell MicroED at room temperature
ComponentsLYS-LEU-VAL-PHE-PHE-ALA
KeywordsPROTEIN FIBRIL / amyloid / liquid cell / room-temperature MicroED
Function / homologyACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsVlahakis, N.W. / Rodriguez, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Department of Energy (DOE, United States) United States
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Structures of solvated organic molecules enabled by liquid cell MicroED
Authors: Vlahakis, N.W. / Konieczny, K. / Flowers, C.W. / Garcia-Garibay, M.A. / Rodriguez, J.A.
History
DepositionAug 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LYS-LEU-VAL-PHE-PHE-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7842
Polymers7251
Non-polymers591
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)9.680, 12.940, 41.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide LYS-LEU-VAL-PHE-PHE-ALA


Mass: 724.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: Hexapeptide segment KLVFFA from amyloid-beta / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: synthetic construct (others)
EM crystal formationDetails: 95% pure peptide was dissolved at 5 mg/mL and crystals were grown in batch in a solution of 40% isopropanol, 0.3 M ammonium acetate, 0.1 M Tris pH 8.5. Crystals were mounted in a liquid cell ...Details: 95% pure peptide was dissolved at 5 mg/mL and crystals were grown in batch in a solution of 40% isopropanol, 0.3 M ammonium acetate, 0.1 M Tris pH 8.5. Crystals were mounted in a liquid cell for electron diffraction measurements.
Temperature: 293 K / Time: 24 HOUR
Buffer solutionpH: 8.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Details: 95% pure peptide was dissolved at 5 mg/mL and crystals were grown in batch in a solution of 40% isopropanol, 0.3 M ammonium acetate, 0.1 M Tris pH 8.5.

-
Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 50 µm
Specimen holderTemperature (max): 293 K / Temperature (min): 293 K
Image recordingElectron dose: 0.01 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
EM diffraction shellResolution: 1→1.1 Å / Fourier space coverage: 79.1 % / Multiplicity: 16.7 / Num. of structure factors: 592 / Phase residual: 42 °
EM diffraction statsFourier space coverage: 78.1 % / High resolution: 1 Å / Num. of intensities measured: 39087 / Num. of structure factors: 2452 / Phase error rejection criteria: Not applicable / Rmerge: 28.8

-
Processing

EM softwareName: PHENIX / Category: 3D reconstruction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 9.68 Å / B: 12.94 Å / C: 41.82 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingPDB-ID: 2Y29

2y29


Accession code: 2Y29 / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→11 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3183 245 10.03 %
Rwork0.2757 --
obs0.2799 2442 77.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00556
ELECTRON CRYSTALLOGRAPHYf_angle_d0.59573
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d6.3676
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0728
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.260.41731180.36921064ELECTRON CRYSTALLOGRAPHY78
1.26-110.29161270.24821133ELECTRON CRYSTALLOGRAPHY78

+
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