[English] 日本語
Yorodumi
- PDB-9j48: GFP bound to 24-mer DARPin-apoferritin model 6c -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j48
TitleGFP bound to 24-mer DARPin-apoferritin model 6c
Components
  • Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
  • Green fluorescent protein
KeywordsMETAL BINDING PROTEIN/LUMINESCENT PROTEIN / GFP / DARPin / apoferritin / scaffold / METAL BINDING PROTEIN-LUMINESCENT PROTEIN complex
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / bioluminescence / generation of precursor metabolites and energy / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Green fluorescent protein, GFP ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ferritin-like superfamily
Similarity search - Domain/homology
Green fluorescent protein / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsLu, X. / Yan, M. / Zhang, H.M. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0906004 China
CitationJournal: IUCrJ / Year: 2025
Title: A large, general and modular DARPin-apoferritin scaffold enables the visualization of small proteins by cryo-EM.
Authors: Xin Lu / Ming Yan / Yang Cai / Xi Song / Huan Chen / Mengtan Du / Zhenyi Wang / Jia'an Li / Liwen Niu / Fuxing Zeng / Quan Hao / Hongmin Zhang /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has emerged as an indispensable technique in structural biology that is pivotal for deciphering protein architectures. However, the medium-sized ...Single-particle cryo-electron microscopy (cryo-EM) has emerged as an indispensable technique in structural biology that is pivotal for deciphering protein architectures. However, the medium-sized proteins (30-40 kDa) that are prevalent in both eukaryotic and prokaryotic organisms often elude the resolving capabilities of contemporary cryo-EM methods. To address this challenge, we engineered a scaffold strategy that securely anchors proteins of interest to a robust, symmetric base via a selective adapter. Our most efficacious constructs, namely models 4 and 6c, feature a designed ankyrin-repeat protein (DARPin) rigidly linked to an octahedral human apoferritin via a helical linker. By utilizing these large, highly symmetric scaffolds (∼1 MDa), we achieved near-atomic-resolution cryo-EM structures of green fluorescent protein (GFP) and maltose-binding protein (MBP), revealing nearly all side-chain densities of GFP and the distinct structural features of MBP. The modular design of our scaffold allows the adaptation of new DARPins through minor amino-acid-sequence modifications, enabling the binding and visualization of a diverse array of proteins. The high symmetry and near-spherical shape of the scaffold not only mitigates the prevalent challenge of preferred particle orientation in cryo-EM but also significantly reduces the demands of image collection and data processing. This approach presents a versatile solution, breaking through the size constraints that have traditionally limited single-particle cryo-EM.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
a: Green fluorescent protein
B: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
b: Green fluorescent protein
C: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
c: Green fluorescent protein
D: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
d: Green fluorescent protein
E: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
e: Green fluorescent protein
F: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
f: Green fluorescent protein
G: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
g: Green fluorescent protein
H: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
h: Green fluorescent protein
I: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
i: Green fluorescent protein
J: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
j: Green fluorescent protein
K: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
k: Green fluorescent protein
L: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
l: Green fluorescent protein
M: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
m: Green fluorescent protein
N: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
n: Green fluorescent protein
O: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
o: Green fluorescent protein
P: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
p: Green fluorescent protein
Q: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
q: Green fluorescent protein
R: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
r: Green fluorescent protein
S: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
s: Green fluorescent protein
T: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
t: Green fluorescent protein
V: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
v: Green fluorescent protein
W: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
w: Green fluorescent protein
X: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
x: Green fluorescent protein
Y: Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed
y: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)1,677,42048
Polymers1,677,42048
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
Designed ankyrin repeat proteins,Ferritin heavy chain, N-terminally processed


Mass: 43268.602 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794
#2: Protein ...
Green fluorescent protein


Mass: 26623.918 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: GFP bound with the 24-mer DARPin-apoferritin scaffold / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
250 mMsodium chlorideNacl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.28 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 39

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC9.01particle selection
2SerialEMimage acquisition
4cryoSPARC9.01CTF correction
7PHENIX1.16model fitting
9PHENIX1.16model refinement
10Coot0.9model refinement
11cryoSPARC9.01initial Euler assignment
12cryoSPARC9.01final Euler assignment
13cryoSPARC9.01classification
14cryoSPARC9.013D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 750123
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17397 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3AJO

3ajo


Accession code: 3AJO / Source name: PDB / Type: experimental model

+
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