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- PDB-6h5i: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -

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Basic information

Entry
Database: PDB / ID: 6h5i
TitleSingle Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex.
Components
  • Ferritin heavy chain
  • Transferrin receptor protein 1
KeywordsMETAL BINDING PROTEIN / Transferrin Receptor 1 / Ferritin / Complex / Single Particle Cryo-EM
Function / homology
Function and homology information


transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / ferritin complex / RND1 GTPase cycle / RND2 GTPase cycle / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / RHOB GTPase cycle / ferroxidase / autolysosome / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / ferroxidase activity / CDC42 GTPase cycle / RHOH GTPase cycle / intracellular sequestering of iron ion / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / RAC3 GTPase cycle / response to retinoic acid / positive regulation of T cell proliferation / negative regulation of fibroblast proliferation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / autophagosome / osteoclast differentiation / ferric iron binding / response to nutrient / cellular response to leukemia inhibitory factor / acute-phase response / Iron uptake and transport / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / ferrous iron binding / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / double-stranded RNA binding / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / tertiary granule lumen / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / blood microparticle / ficolin-1-rich granule lumen / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / immune response / iron ion binding / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / external side of plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28 ...Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28 / 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
Transferrin receptor protein 1 / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsTesti, C. / Montemiglio, L.C. / Vallone, B. / Des Georges, A. / Boffi, A. / Mancia, F. / Baiocco, P. / Savino, C.
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of the human ferritin-transferrin receptor 1 complex.
Authors: Linda Celeste Montemiglio / Claudia Testi / Pierpaolo Ceci / Elisabetta Falvo / Martina Pitea / Carmelinda Savino / Alessandro Arcovito / Giovanna Peruzzi / Paola Baiocco / Filippo Mancia / ...Authors: Linda Celeste Montemiglio / Claudia Testi / Pierpaolo Ceci / Elisabetta Falvo / Martina Pitea / Carmelinda Savino / Alessandro Arcovito / Giovanna Peruzzi / Paola Baiocco / Filippo Mancia / Alberto Boffi / Amédée des Georges / Beatrice Vallone /
Abstract: Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion ...Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion and epitopes on CD71 for interaction with transferrin and pathogenic hosts were identified. Here, we provide the molecular basis of the CD71 ectodomain-human ferritin interaction by determining the 3.9 Å resolution single-particle cryo-electron microscopy structure of their complex and by validating our structural findings in a cellular context. The contact surfaces between the heavy-chain ferritin and CD71 largely overlap with arenaviruses and Plasmodium vivax binding regions in the apical part of the receptor ectodomain. Our data account for transferrin-independent binding of ferritin to CD71 and suggest that select pathogens may have adapted to enter cells by mimicking the ferritin access gate.
History
DepositionJul 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
Aa: Ferritin heavy chain
Ab: Transferrin receptor protein 1
Ac: Ferritin heavy chain
Ad: Ferritin heavy chain
Ae: Ferritin heavy chain
Af: Ferritin heavy chain
Ag: Ferritin heavy chain
Ah: Ferritin heavy chain
Ai: Ferritin heavy chain
Aj: Ferritin heavy chain
Ak: Ferritin heavy chain
Al: Ferritin heavy chain
Am: Ferritin heavy chain
An: Ferritin heavy chain
Ao: Ferritin heavy chain
Ap: Ferritin heavy chain
Aq: Transferrin receptor protein 1
Ar: Ferritin heavy chain
As: Ferritin heavy chain
At: Ferritin heavy chain
Au: Ferritin heavy chain
Av: Ferritin heavy chain
Aw: Ferritin heavy chain
Ax: Ferritin heavy chain
Ay: Ferritin heavy chain
Az: Ferritin heavy chain


Theoretical massNumber of molelcules
Total (without water)626,41226
Polymers626,41226
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area95640 Å2
ΔGint-370 kcal/mol
Surface area207130 Å2
MethodPISA

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Components

#1: Protein ...
Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 20116.547 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, ferroxidase
#2: Protein Transferrin receptor protein 1 / Trfr / T9 / p90


Mass: 71807.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Production host: Homo sapiens (human) / References: UniProt: P02786
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of the ectodomain of human Transferrin Receptor 1 and H-chain FerritinCOMPLEXall0MULTIPLE SOURCES
2C H-chain FerritinCOMPLEX#11RECOMBINANT
3Ectodomain of human Transferrin Receptor 1COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Homo sapiens (human)9606
Buffer solutionpH: 7.2
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
9PHENIX1.13model refinement
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 73700
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53878 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13AJO

3ajo

13AJO1PDBexperimental model
23KAS

3kas

13KAS2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00644830
ELECTRON MICROSCOPYf_angle_d0.79960464
ELECTRON MICROSCOPYf_dihedral_angle_d4.35226989
ELECTRON MICROSCOPYf_chiral_restr0.0476432
ELECTRON MICROSCOPYf_plane_restr0.0067916

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