[English] 日本語
Yorodumi
- EMDB-30750: Liganded EGFR averaged cluster 10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30750
TitleLiganded EGFR averaged cluster 10
Map data
Sample
  • Complex: Liganded EGFR averaged cluster 10
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 15.0 Å
AuthorsPurba ER / Saita EI / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN
CitationJournal: Front Endocrinol / Year: 2022
Title: Allosteric activation of preformed EGF receptor dimers by a single ligand binding event.
Authors: Purba ER / Saita EI / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN
History
DepositionDec 3, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30750.png

Downloads & links

-
Map

FileDownload / File: emd_30750.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 110 pix.
= 248.38 Å		2.26 Å/pix.
x 110 pix.
= 248.38 Å		2.26 Å/pix.
x 110 pix.
= 248.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.258 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.5
Minimum - Maximum0.16321436 - 0.7295924
Average (Standard dev.)0.41403377 (±0.06652731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 248.38002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2582.2582.258
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z248.380248.380248.380
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ558558558
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS110110110
D min/max/mean0.1630.7300.414

-
Supplemental data

-
Sample components

-
Entire : Liganded EGFR averaged cluster 10

EntireName: Liganded EGFR averaged cluster 10
Components
  • Complex: Liganded EGFR averaged cluster 10

-
Supramolecule #1: Liganded EGFR averaged cluster 10

SupramoleculeName: Liganded EGFR averaged cluster 10 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Location in cell: membrane cell
Molecular weightTheoretical: 300 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMTris-HCL
200.0 mMSodium chloride
0.2 mMDodecyl maltocide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277.0 K / Instrument: FEI VITROBOT MARK IV
Detailsthe sample was monodisperse
Cryo protectantNo
SectioningOther: NO SECTIONING

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 135 / Average exposure time: 1.8 sec. / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 37000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Number images used: 141

-
Atomic model buiding 1

Initial model
PDB IDChain

3njp

chain_id: A, residue_range: 1-614

3njp

chain_id: B, residue_range: 1-614

2m20

chain_id: A, residue_range: 1-60

2m20

chain_id: B, residue_range: 61-120

2gs6

chain_id: A, residue_range: 669-995

2gs6

chain_id: B, residue_range: 669-995
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient

+
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