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- PDB-8wie: Peptide 10-1/FTH1-1 Complex -

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Basic information

Entry
Database: PDB / ID: 8wie
TitlePeptide 10-1/FTH1-1 Complex
ComponentsPeptide 10-1,Ferritin heavy chain
KeywordsMETAL BINDING PROTEIN / Nano-delivery platform / De novo Design / Ferritin / Rabies virus Glycoprotein domain III (RABV-GDIII) / GDIII-Ferritin Nano-vaccine / stabilized / Strong immune response
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 / 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 / Ferritin-like superfamily
Similarity search - Domain/homology
: / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFu, D. / Wang, M. / Guo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFE0200400 China
CitationJournal: Nat Commun / Year: 2024
Title: Self-assembling nanoparticle engineered from the ferritinophagy complex as a rabies virus vaccine candidate.
Authors: Dan Fu / Wenming Wang / Yan Zhang / Fan Zhang / Pinyi Yang / Chun Yang / Yufei Tian / Renqi Yao / Jingwu Jian / Zixian Sun / Nan Zhang / Zhiyu Ni / Zihe Rao / Lei Zhao / Yu Guo /
Abstract: Over the past decade, there has been a growing interest in ferritin-based vaccines due to their enhanced antigen immunogenicity and favorable safety profiles, with several vaccine candidates ...Over the past decade, there has been a growing interest in ferritin-based vaccines due to their enhanced antigen immunogenicity and favorable safety profiles, with several vaccine candidates targeting various pathogens advancing to phase I clinical trials. Nevertheless, challenges associated with particle heterogeneity, improper assembly and unanticipated immunogenicity due to the bulky protein adaptor have impeded further advancement. To overcome these challenges, we devise a universal ferritin-adaptor delivery platform based on structural insights derived from the natural ferritinophagy complex of the human ferritin heavy chain (FTH1) and the nuclear receptor coactivator 4 (NCOA4). The engineered ferritinophagy (Fagy)-tag peptide demonstrate significantly enhanced binding affinity to the 24-mer ferritin nanoparticle, enabling efficient antigen presentation. Subsequently, we construct a self-assembling rabies virus (RABV) vaccine candidate by noncovalently conjugating the Fagy-tagged glycoprotein domain III (G) of RABV to the ferritin nanoparticle, maintaining superior homogeneity, stability and immunogenicity. This vaccine candidate induces potent, rapid, and durable immune responses, and protects female mice against the authentic RABV challenge after single-dose administration. Furthermore, this universal, ferritin-based antigen conjugating strategy offers significant potential for developing vaccine against diverse pathogens and diseases.
History
DepositionSep 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Peptide 10-1,Ferritin heavy chain
D: Peptide 10-1,Ferritin heavy chain
E: Peptide 10-1,Ferritin heavy chain
F: Peptide 10-1,Ferritin heavy chain
A: Peptide 10-1,Ferritin heavy chain
B: Peptide 10-1,Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8198
Polymers137,7236
Non-polymers962
Water8,467470
1
C: Peptide 10-1,Ferritin heavy chain
D: Peptide 10-1,Ferritin heavy chain
E: Peptide 10-1,Ferritin heavy chain
F: Peptide 10-1,Ferritin heavy chain
A: Peptide 10-1,Ferritin heavy chain
B: Peptide 10-1,Ferritin heavy chain
hetero molecules

C: Peptide 10-1,Ferritin heavy chain
D: Peptide 10-1,Ferritin heavy chain
E: Peptide 10-1,Ferritin heavy chain
F: Peptide 10-1,Ferritin heavy chain
A: Peptide 10-1,Ferritin heavy chain
B: Peptide 10-1,Ferritin heavy chain
hetero molecules

C: Peptide 10-1,Ferritin heavy chain
D: Peptide 10-1,Ferritin heavy chain
E: Peptide 10-1,Ferritin heavy chain
F: Peptide 10-1,Ferritin heavy chain
A: Peptide 10-1,Ferritin heavy chain
B: Peptide 10-1,Ferritin heavy chain
hetero molecules

C: Peptide 10-1,Ferritin heavy chain
D: Peptide 10-1,Ferritin heavy chain
E: Peptide 10-1,Ferritin heavy chain
F: Peptide 10-1,Ferritin heavy chain
A: Peptide 10-1,Ferritin heavy chain
B: Peptide 10-1,Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,27432
Polymers550,89124
Non-polymers3848
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area94040 Å2
ΔGint-366 kcal/mol
Surface area147300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.831, 142.831, 183.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-265-

HOH

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Components

#1: Protein
Peptide 10-1,Ferritin heavy chain


Mass: 22953.783 Da / Num. of mol.: 6 / Mutation: Q15R,R23K,N26T,K87Q,N110E,S114E,E117N
Source method: isolated from a genetically manipulated source
Details: 1-16 : peptide 17-23 : linker / Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Colibacter (bacteria) / References: UniProt: P02794
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M Sodium chloride , 15% Ethanol and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 81240 / % possible obs: 99.59 % / Redundancy: 12.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.049 / Rrim(I) all: 0.171 / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 8054 / CC1/2: 0.887 / CC star: 0.97 / Rpim(I) all: 0.267 / Rrim(I) all: 0.896 / Rsym value: 1.048 / Χ2: 0.518

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CEI

2cei


Resolution: 2.3→33.67 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1990 2.45 %
Rwork0.1936 --
obs0.1941 81240 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9287 0 2 470 9759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039467
X-RAY DIFFRACTIONf_angle_d0.53212740
X-RAY DIFFRACTIONf_dihedral_angle_d4.941216
X-RAY DIFFRACTIONf_chiral_restr0.0341361
X-RAY DIFFRACTIONf_plane_restr0.0041666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.24751390.22515595X-RAY DIFFRACTION99
2.36-2.420.2921400.20445659X-RAY DIFFRACTION100
2.42-2.490.27661440.21425681X-RAY DIFFRACTION100
2.49-2.570.23051450.25656X-RAY DIFFRACTION100
2.57-2.660.22171440.21745664X-RAY DIFFRACTION100
2.66-2.770.23631410.20685690X-RAY DIFFRACTION100
2.77-2.90.24211400.20325654X-RAY DIFFRACTION100
2.9-3.050.22811420.19735684X-RAY DIFFRACTION100
3.05-3.240.23111420.1965682X-RAY DIFFRACTION100
3.24-3.490.22561410.19525678X-RAY DIFFRACTION100
3.49-3.840.17261420.17915642X-RAY DIFFRACTION100
3.84-4.390.1921440.17255705X-RAY DIFFRACTION100
4.4-5.530.17461430.18025689X-RAY DIFFRACTION100
5.53-33.670.20391430.20215571X-RAY DIFFRACTION97

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