[English] 日本語
Yorodumi
- EMDB-27664: Cryo-electron tomography of P10BP10 synthetic collagen fibers -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27664
TitleCryo-electron tomography of P10BP10 synthetic collagen fibers
Map dataCryo-electron tomography of P10BP10 synthetic collagen fibers
Sample
  • Organelle or cellular component: P10BP10 synthetic collagen fibers
Biological speciessynthetic construct (others)
Methodelectron tomography / cryo EM
AuthorsJiang J / Dai W / Hu J / Nanda V / Xu F
Funding support United States, China, 3 items
OrganizationGrant numberCountry
National Aeronautic Space Administration (NASA, United States)NAI 80NSSC18M0093 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM136431 United States
National Natural Science Foundation of China (NSFC)22078129 China
CitationJournal: Nat Commun / Year: 2022
Title: Design of synthetic collagens that assemble into supramolecular banded fibers as a functional biomaterial testbed.
Authors: Jinyuan Hu / Junhui Li / Jennifer Jiang / Lingling Wang / Jonathan Roth / Kenneth N McGuinness / Jean Baum / Wei Dai / Yao Sun / Vikas Nanda / Fei Xu /
Abstract: Collagens are the most abundant proteins of the extracellular matrix, and the hierarchical folding and supramolecular assembly of collagens into banded fibers is essential for mediating cell-matrix ...Collagens are the most abundant proteins of the extracellular matrix, and the hierarchical folding and supramolecular assembly of collagens into banded fibers is essential for mediating cell-matrix interactions and tissue mechanics. Collagen extracted from animal tissues is a valuable commodity, but suffers from safety and purity issues, limiting its biomaterials applications. Synthetic collagen biomaterials could address these issues, but their construction requires molecular-level control of folding and supramolecular assembly into ordered banded fibers, comparable to those of natural collagens. Here, we show an innovative class of banded fiber-forming synthetic collagens that recapitulate the morphology and some biological properties of natural collagens. The synthetic collagens comprise a functional-driver module that is flanked by adhesive modules that effectively promote their supramolecular assembly. Multiscale simulations support a plausible molecular-level mechanism of supramolecular assembly, allowing precise design of banded fiber morphology. We also experimentally demonstrate that synthetic fibers stimulate osteoblast differentiation at levels comparable to natural collagen. This work thus deepens understanding of collagen biology and disease by providing a ready source of safe, functional biomaterials that bridge the current gap between the simplicity of peptide biophysical models and the complexity of in vivo animal systems.
History
DepositionJul 20, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27664.png

Downloads & links

-
Map

FileDownload / File: emd_27664.map.gz / Format: CCP4 / Size: 163.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomography of P10BP10 synthetic collagen fibers
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
17.2 Å/pix.
x 151 pix.
= 2597.199 Å		17.2 Å/pix.
x 492 pix.
= 8462.396 Å		17.2 Å/pix.
x 578 pix.
= 9941.595 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 17.19999 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-35.063435 - 9.93754
Average (Standard dev.)-0.092197224 (±1.078785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-279-348-74
Dimensions492578151
Spacing578492151
CellA: 9941.595 Å / B: 8462.3955 Å / C: 2597.1987 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : P10BP10 synthetic collagen fibers

EntireName: P10BP10 synthetic collagen fibers
Components
  • Organelle or cellular component: P10BP10 synthetic collagen fibers

-
Supramolecule #1: P10BP10 synthetic collagen fibers

SupramoleculeName: P10BP10 synthetic collagen fibers / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP / Details: Blot time: 3 seconds.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 6 nm

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 41 / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 31000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: EMAN2 / Number images used: 41

+
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