[English] 日本語
Yorodumi
- PDB-5k7n: MicroED structure of tau VQIVYK peptide at 1.1 A resolution -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5k7n
TitleMicroED structure of tau VQIVYK peptide at 1.1 A resolution
DescriptorVQIVYK
KeywordsPROTEIN FIBRIL / Amyloid
Specimen sourceHomo sapiens / human
MethodElectron crystallography (1.1 Å resolution / 3d array / Crystallography)
Authorsde la Cruz, M.J. / Hattne, J. / Shi, D. / Seidler, P. / Rodriguez, J. / Reyes, F.E. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Gonen, T.
CitationNat. Methods, 2017, 14, 399-402

Nat. Methods, 2017, 14, 399-402 StrPapers
Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 26, 2016 / Release: Apr 5, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 5, 2017Structure modelrepositoryInitial release
1.1Apr 12, 2017Structure modelDatabase references

-
Structure visualization

Movie
  • Biological unit as nonameric
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
Z: VQIVYK


Theoretical massNumber of molelcules
Total (without water)7501
Polyers7501
Non-polymers00
Water362
#1
Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK


Theoretical massNumber of molelcules
Total (without water)6,7499
Polyers6,7499
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
Unit cell
γ
α
β
Length a, b, c (Å)29.420, 4.990, 37.170
Angle α, β, γ (deg.)90.00, 111.55, 90.00
Int Tables number5
Space group name H-MC 1 2 1
DetailsThe biological unit is an extended pair of beta sheets comprising peptides at position X,Y,Z extended ad infinitum along the b crystal axis.

-
Components

#1: Polypeptide(L)VQIVYK / tau peptide


Mass: 749.917 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens / human

Cellular component

Molecular function

Biological process

#2: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / Reconstruction method: CRYSTALLOGRAPHY

-
Sample preparation

ComponentName: VQIVYK / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.000747 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 8.5
Buffer component
IDConc.UnitsNameBuffer ID
122.5%ethylene glycol1
2Tris1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Apr 26, 2016
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.1 sec. / Electron dose: 0.002 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number of diffraction images: 299 / Number of grids imaged: 1 / Number of real images: 299
Image scansSampling size: 0.0311999992 microns / Dimension width: 2048 / Dimension height: 2048
EM diffractionCamera length: 730 mm
EM diffraction shellFourier space coverage: 79.4 / High resolution: 1.1 Å / Low resolution: 1.23 Å / Multiplicity: 1.8 / Number of structure factors: 255 / Phase residual: 47.6 deg.
EM diffraction statsFourier space coverage: 83 / High resolution: 1.1 Å / Number of intensities measured: 6185 / Number of structure factors: 3319 / Overall phase error: 0 deg. / Overall phase residual: 39.4 deg. / Phase error rejection criteria: 0 / R merge: 12.9 / R sym: 12.9
ReflectionB iso Wilson estimate: 8.35 Å2 / D resolution high: 1.1 Å / D resolution low: 14.7 Å / Number all: 6185 / Number obs: 3319 / Rmerge I obs: 0.126 / Rsym value: 0.126 / NetI over sigmaI: 2.4 / Redundancy: 1.9 / Percent possible obs: 83
Reflection shellRmerge I obs: 0.472 / Highest resolution: 1.1 Å / Lowest resolution: 1.23 Å / Number unique all: 463 / Number unique obs: 255 / Rsym value: 0.472 / NetI over sigmaI obs: 1.1 / Redundancy: 1.8 / Percent possible all: 79.4

-
Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
EM software
IDNameVersionCategoryImaging IDDetailsImage processing IDFitting ID
1EM-Menu4.0.9.75IMAGE ACQUISITION1
5XDSMay 1, 2016DIFFRACTION INDEXING
7SHELXT2014/5OTHERphasing
11XDSMay 1, 2016CRYSTALLOGRAPHY MERGING1
13BUSTER2.10.0MODEL REFINEMENT1
EM 3D crystal entityAngle alpha: 90 deg. / Angle beta: 111.55 deg. / Angle gamma: 90 deg. / Length a: 29.42 Å / Length b: 4.99 Å / Length c: 37.17 Å / Space group name: C 1 2 1 / Space group num: 5
CTF correctionType: NONE
3D reconstructionResolution: 1.1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: RECIPROCAL
RefineCorrelation coeff Fo to Fc: 0.9486 / Correlation coeff Fo to Fc free: 0.9516 / Overall SU R Cruickshank DPI: 0.048 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall SU R Blow DPI: 0.046 / Overall SU R free Blow DPI: 0.046 / Overall SU R free Cruickshank DPI: 0.045
Displacement parametersB iso mean: 13.51 Å2 / Aniso B11: 1.6602 Å2 / Aniso B12: 0 Å2 / Aniso B13: 3.1898 Å2 / Aniso B22: 0.0678 Å2 / Aniso B23: 0 Å2 / Aniso B33: -1.728 Å2
Least-squares processR factor R free: 0.2228 / R factor R work: 0.2097 / R factor obs: 0.211 / Highest resolution: 1.1 Å / Lowest resolution: 14.7 Å / Number reflection R free: 190 / Number reflection obs: 1898 / Percent reflection R free: 10.01 / Percent reflection obs: 81.11
Refine analyzeLuzzati coordinate error obs: 0.203 Å
Refine LS restraints
Refine IDTypeDev idealNumberRestraint functionWeight
ELECTRON CRYSTALLOGRAPHYt_bond_d0.012111HARMONIC2.00
ELECTRON CRYSTALLOGRAPHYt_angle_deg0.77202HARMONIC2.00
ELECTRON CRYSTALLOGRAPHYt_dihedral_angle_d26SINUSOIDAL2.00
ELECTRON CRYSTALLOGRAPHYt_incorr_chiral_ct
ELECTRON CRYSTALLOGRAPHYt_pseud_angle
ELECTRON CRYSTALLOGRAPHYt_trig_c_planes2HARMONIC2.00
ELECTRON CRYSTALLOGRAPHYt_gen_planes12HARMONIC5.00
ELECTRON CRYSTALLOGRAPHYt_it111HARMONIC20.00
ELECTRON CRYSTALLOGRAPHYt_nbd0SEMIHARMONIC5.00
ELECTRON CRYSTALLOGRAPHYt_omega_torsion1.62
ELECTRON CRYSTALLOGRAPHYt_other_torsion9.65
ELECTRON CRYSTALLOGRAPHYt_improper_torsion
ELECTRON CRYSTALLOGRAPHYt_chiral_improper_torsion7SEMIHARMONIC5.00
ELECTRON CRYSTALLOGRAPHYt_sum_occupancies
ELECTRON CRYSTALLOGRAPHYt_utility_distance
ELECTRON CRYSTALLOGRAPHYt_utility_angle
ELECTRON CRYSTALLOGRAPHYt_utility_torsion
ELECTRON CRYSTALLOGRAPHYt_ideal_dist_contact68SEMIHARMONIC4.00
Refine LS shellHighest resolution: 1.1 Å / R factor R free: 0.2243 / R factor R work: 0.2104 / R factor all: 0.2117 / Lowest resolution: 1.23 Å / Number reflection R free: 54 / Number reflection R work: 489 / Number reflection all: 543 / Total number of bins used: 5 / Percent reflection R free: 9.94 / Percent reflection obs: 81.11
Refine TLSMethod: refined / L11: 0.4341 deg.2 / L12: 0.2835 deg.2 / L13: 0.124 deg.2 / L22: 0.6654 deg.2 / L23: 0.2447 deg.2 / L33: 0.0381 deg.2 / S11: -0.0138 Å deg. / S12: 0.0028 Å deg. / S13: 0.002 Å deg. / S21: -0.0426 Å deg. / S22: 0.0046 Å deg. / S23: 0.0052 Å deg. / S31: 0.028 Å deg. / S32: 0.0029 Å deg. / S33: 0.0092 Å deg. / T11: -0.0041 Å2 / T12: -0.0004 Å2 / T13: 0.0615 Å2 / T22: -0.0667 Å2 / T23: -0.0046 Å2 / T33: 0.0721 Å2 / Origin x: 10.8417 Å / Origin y: 1.956 Å / Origin z: 8.5763 Å
Refine TLS groupSelection details: { Z|* }

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more