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- EMDB-0140: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -

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Basic information

Entry
Database: EMDB / ID: EMD-0140
TitleSingle Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex.
Map dataMap at 3.9 A of the human CD71 receptor and human H-Ferritin
Sample
  • Complex: Complex of the ectodomain of human Transferrin Receptor 1 and H-chain Ferritin
    • Complex: C H-chain Ferritin
      • Protein or peptide: Ferritin heavy chain
    • Complex: Ectodomain of human Transferrin Receptor 1
      • Protein or peptide: Transferrin receptor protein 1
KeywordsTransferrin Receptor 1 / Ferritin / Complex / Single Particle Cryo-EM / METAL BINDING PROTEIN
Function / homology
Function and homology information


transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / response to manganese ion ...transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / response to manganese ion / iron ion sequestering activity / RND1 GTPase cycle / ferritin complex / RND2 GTPase cycle / negative regulation of ferroptosis / Scavenging by Class A Receptors / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / ferroxidase / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / autolysosome / ferroxidase activity / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of bone resorption / regulation of postsynaptic membrane neurotransmitter receptor levels / transport across blood-brain barrier / 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 / response to nutrient / Hsp70 protein binding / ferric iron binding / osteoclast differentiation / autophagosome / cellular response to leukemia inhibitory factor / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / HFE-transferrin receptor complex / ferrous iron binding / recycling endosome / receptor internalization / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / tertiary granule lumen / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / extracellular vesicle / double-stranded RNA binding / Clathrin-mediated endocytosis / iron ion transport / virus receptor activity / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / positive regulation of canonical NF-kappaB signal transduction / early endosome / response to hypoxia / endosome / endosome membrane / intracellular signal transduction / immune response / iron ion binding / external side of plasma membrane / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / 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: 3.9 Å
AuthorsTesti C / Montemiglio LC
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, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseMar 27, 2019-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h5i
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6h5i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0140.png

Downloads & links

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Map

FileDownload / File: emd_0140.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap at 3.9 A of the human CD71 receptor and human H-Ferritin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.33 Å/pix.
x 256 pix.
= 340.48 Å		1.33 Å/pix.
x 256 pix.
= 340.48 Å		1.33 Å/pix.
x 256 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8 / Movie #1: 2.5
Minimum - Maximum-11.31752 - 20.555223000000002
Average (Standard dev.)-0.000000000004483 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
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
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-11.31820.555-0.000

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Supplemental data

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Sample components

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Entire : Complex of the ectodomain of human Transferrin Receptor 1 and H-c...

EntireName: Complex of the ectodomain of human Transferrin Receptor 1 and H-chain Ferritin
Components
  • Complex: Complex of the ectodomain of human Transferrin Receptor 1 and H-chain Ferritin
    • Complex: C H-chain Ferritin
      • Protein or peptide: Ferritin heavy chain
    • Complex: Ectodomain of human Transferrin Receptor 1
      • Protein or peptide: Transferrin receptor protein 1

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Supramolecule #1: Complex of the ectodomain of human Transferrin Receptor 1 and H-c...

SupramoleculeName: Complex of the ectodomain of human Transferrin Receptor 1 and H-chain Ferritin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: C H-chain Ferritin

SupramoleculeName: C H-chain Ferritin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Ectodomain of human Transferrin Receptor 1

SupramoleculeName: Ectodomain of human Transferrin Receptor 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.116547 KDa
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

UniProtKB: Ferritin heavy chain

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Macromolecule #2: Transferrin receptor protein 1

MacromoleculeName: Transferrin receptor protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.807258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RLYWDDLKRK LSEKLDSTDF TSTIKLLNEN SYVPREAGSQ KDENLALYVE NQFREFKLSK VWRDQHFVKI QVKDSAQNSV IIVDKNGRL VYLVENPGGY VAYSKAATVT GKLVHANFGT KKDFEDLYTP VNGSIVIVRA GKITFAEKVA NAESLNAIGV L IYMDQTKF ...String:
RLYWDDLKRK LSEKLDSTDF TSTIKLLNEN SYVPREAGSQ KDENLALYVE NQFREFKLSK VWRDQHFVKI QVKDSAQNSV IIVDKNGRL VYLVENPGGY VAYSKAATVT GKLVHANFGT KKDFEDLYTP VNGSIVIVRA GKITFAEKVA NAESLNAIGV L IYMDQTKF PIVNAELSFF GHAHLGTGDP YTPGFPSFNH TQFPPSRSSG LPNIPVQTIS RAAAEKLFGN MEGDCPSDWK TD STCRMVT SESKNVKLTV SNVLKEIKIL NIFGVIKGFV EPDHYVVVGA QRDAWGPGAA KSGVGTALLL KLAQMFSDMV LKD GFQPSR SIIFASWSAG DFGSVGATEW LEGYLSSLHL KAFTYINLDK AVLGTSNFKV SASPLLYTLI EKTMQNVKHP VTGQ FLYQD SNWASKVEKL TLDNAAFPFL AYSGIPAVSF CFCEDTDYPY LGTTMDTYKE LIERIPELNK VARAAAEVAG QFVIK LTHD VELNLDYERY NSQLLSFVRD LNQYRADIKE MGLSLQWLYS ARGDFFRATS RLTTDFGNAE KTDRFVMKKL NDRVMR VEY HFLSPYVSPK ESPFRHVFWG SGSHTLPALL ENLKLRKQNN GAFNETLFRN QLALATWTIQ GAANALSGDV WDIDNEF

UniProtKB: Transferrin receptor protein 1

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

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Image processing

Particle selectionNumber selected: 73700
Startup modelType of model: EMDB MAP
EMDB ID:

2788

Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 53878
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 8 / Software - Name: RELION

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Atomic model buiding 1

Initial model
PDB IDChain

3ajo

source_name: PDB, initial_model_type: experimental model

3kas

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: OTHER
Output model

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

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