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- EMDB-0046: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -

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Basic information

Entry
Database: EMDB / ID: EMD-0046
TitleSingle Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex at 5.5 Angstrom resolution.
Map data
Sample
  • Complex: Complex of human Transferrin Receptor 1 and human H-chain Ferritin
    • Protein or peptide: Ferritin heavy chain
    • Protein or peptide: human Transferrin Receptor 1
Function / homology
Function and homology information


transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / response to iron ion / response to copper ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / autolysosome / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / ferroxidase / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / intracellular sequestering of iron ion / ferroxidase activity / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / positive regulation of B cell proliferation / negative regulation of fibroblast proliferation / clathrin-coated pit / Hsp70 protein binding / positive regulation of T cell proliferation / RAC1 GTPase cycle / cellular response to leukemia inhibitory factor / ferric iron binding / osteoclast differentiation / response to nutrient / acute-phase response / positive regulation of protein-containing complex assembly / ferrous iron binding / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / receptor internalization / HFE-transferrin receptor complex / recycling endosome / positive regulation of protein localization to nucleus / recycling endosome membrane / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / double-stranded RNA binding / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / tertiary granule lumen / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / immune response / positive regulation of protein phosphorylation / iron ion binding / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsTesti C / Montemiglio LC / Vallone B / Des Georges A / Boffi A / Mancia F / Baiocco P
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
DepositionJun 6, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseMar 27, 2019-
UpdateMar 27, 2019-
Current statusMar 27, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.128
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.128
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6gsr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0046.png

Downloads & links

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Map

FileDownload / File: emd_0046.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.33 Å
Density
Contour LevelBy AUTHOR: 0.128 / Movie #1: 0.128
Minimum - Maximum-0.08968253 - 0.3575655
Average (Standard dev.)0.0021613939 (±0.023968812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z340.480340.480340.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0900.3580.002

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Supplemental data

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Mask #1

Fileemd_0046_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human Transferrin Receptor 1 and human H-chain Ferritin

EntireName: Complex of human Transferrin Receptor 1 and human H-chain Ferritin
Components
  • Complex: Complex of human Transferrin Receptor 1 and human H-chain Ferritin
    • Protein or peptide: Ferritin heavy chain
    • Protein or peptide: human Transferrin Receptor 1

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Supramolecule #1: Complex of human Transferrin Receptor 1 and human H-chain Ferritin

SupramoleculeName: Complex of human Transferrin Receptor 1 and human H-chain Ferritin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 675 KDa

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TSQVRQNYHQ DSEAAINRQI NLELYASYVY LSMSYYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDCDDW ESGLNAMECA LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT NLRKMGAPES G LAEYLFDK HTLG

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Macromolecule #2: human Transferrin Receptor 1

MacromoleculeName: human Transferrin Receptor 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LYWDDLKRKL SEKLDSTDFT STIKLLNENS YVPREAGSQK DENLALYVEN EFREFKLSKV WRDQHFVKIQ VKDSAQNSVI IVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG KITFAEKVAN AESLNAIGVL I YMDQTKFP ...String:
LYWDDLKRKL SEKLDSTDFT STIKLLNENS YVPREAGSQK DENLALYVEN EFREFKLSKV WRDQHFVKIQ VKDSAQNSVI IVDKNGRLV YLVENPGGYV AYSKAATVTG KLVHANFGTK KDFEDLYTPV NGSIVIVRAG KITFAEKVAN AESLNAIGVL I YMDQTKFP IVNAELSFFG HAHLGTGDPY TPGFPSFNHT QFPPSRSSGL PNIPVQTISR AAAEKLFGNM EGDCPSDWKT DS TCRMVTS ESKNVKLTVS NVLKEIKILN IFGVIKGFVE PDHYVVVGAQ RDAWGPGAAK SGVGTALLLK LAQMFSDMVL KDG FQPSRS IIFASWSAGD FGSVGATEWL EGYLSSLHLK AFTYINLDKA VLGTSNFKVS ASPLLYTLIE KTMQNVKHPV TGQF LYQDS NWASKVEKLT LDNAAFPFLA YSGIPAVSFC FCEDTDYPYL GTTMDTYKEL IERIPELNKV ARAAAEVAGQ FVIKL THDV ELNLDYEEYN SQLLSFVRDL NQYRADIKEM GLSLQWLYSA RGDFFRATSR LTTDFGNAEK TDRFVMKKLN DRVMRV EYH FLSPYVSPKE SPFRHVFWGS GSHTLPALLE NLKLRKQNNG AFNETLFRNQ LALATWTIQG AANALSGDVW DIDNEF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

2788

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20958
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6gsr:
Single Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex at 5.5 Angstrom resolution.

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