[English] 日本語
Yorodumi
- EMDB-0046: Single Particle Cryo-EM map of human Transferrin receptor 1 - H-F... -

+
Open data


ID or keywords:

Loading...

-
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 / postsynaptic recycling endosome membrane / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / iron ion sequestering activity / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion ...transferrin receptor activity / postsynaptic recycling endosome membrane / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / iron ion sequestering activity / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / response to manganese ion / 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 / regulation of postsynaptic membrane neurotransmitter receptor levels / RAC3 GTPase cycle / positive regulation of bone resorption / 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 / ferrous iron binding / HFE-transferrin receptor complex / recycling endosome / receptor internalization / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / tertiary granule lumen / cellular response to xenobiotic stimulus / melanosome / 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 / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / 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 / positive regulation of gene expression / Neutrophil degranulation / 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: 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

-
Structure visualization

Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0046.png

Downloads & links

-
Map

FileDownload / File: emd_0046.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (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: 0.128 / Movie #1: 0
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 °

-
Supplemental data

-
Mask #1

Fileemd_0046_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

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

2788

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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
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.

+
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