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- PDB-2nsu: Crystal structure of the ectodomain of human transferrin receptor... -

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Basic information

Entry
Database: PDB / ID: 2nsu
TitleCrystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex
ComponentsTransferrin receptor protein 1
KeywordsMETAL TRANSPORT / transferrin receptor / virus-receptor complex
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 / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / 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 / response to retinoic acid / transport across blood-brain barrier / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / response to nutrient / Hsp70 protein binding / osteoclast differentiation / cellular response to leukemia inhibitory factor / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / recycling endosome / receptor internalization / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / 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 / intracellular iron ion homeostasis / positive regulation of canonical NF-kappaB signal transduction / early endosome / response to hypoxia / endosome / endosome membrane / intracellular signal transduction / external side of plasma membrane / intracellular membrane-bounded organelle / 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 / membrane / plasma membrane
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
Similarity search - Domain/homology
Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 27 Å
AuthorsHafenstein, S. / Kostyuchenko, V.A. / Rossmann, M.G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2007
Title: Asymmetric binding of transferrin receptor to parvovirus capsids.
Authors: Susan Hafenstein / Laura M Palermo / Victor A Kostyuchenko / Chuan Xiao / Marc C Morais / Christian D S Nelson / Valorie D Bowman / Anthony J Battisti / Paul R Chipman / Colin R Parrish / Michael G Rossmann /
Abstract: Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry ...Although many viruses are icosahedral when they initially bind to one or more receptor molecules on the cell surface, such an interaction is asymmetric, probably causing a breakdown in the symmetry and conformation of the original infecting virion in preparation for membrane penetration and release of the viral genome. Cryoelectron microscopy and biochemical analyses show that transferrin receptor, the cellular receptor for canine parvovirus, can bind to only one or a few of the 60 icosahedrally equivalent sites on the virion, indicating that either canine parvovirus has inherent asymmetry or binding of receptor induces asymmetry. The asymmetry of receptor binding to canine parvovirus is reminiscent of the special portal in tailed bacteriophages and some large, icosahedral viruses. Asymmetric interactions of icosahedral viruses with their hosts might be a more common phenomenon than previously thought and may have been obscured by averaging in previous crystallographic and electron microscopic structure determinations.
History
DepositionNov 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE AUTHORS STATE THAT PDB ENTRY 1CX8 WAS USED FOR FITTING IN THIS ENTRY. THE SEQUENCE ... SEQUENCE AUTHORS STATE THAT PDB ENTRY 1CX8 WAS USED FOR FITTING IN THIS ENTRY. THE SEQUENCE DIFFERENCES EXIST IN THE STRUCTURE 1CX8. THE UNIPROT ENTRY P02786 IS A RESULT OF DNA SEQUENCING, WHILE 1CX8 SEQUENCE IS APPARENTLY BASED ON MRNA SEQUENCE.

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Assembly

Deposited unit
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1


Theoretical massNumber of molelcules
Total (without water)143,2462
Polymers143,2462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Transferrin receptor protein 1 / TfR1 / TR / TfR / Trfr / CD71 antigen / T9 / p90


Mass: 71622.961 Da / Num. of mol.: 2 / Fragment: THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Plasmid: PCMVTFR / Organ (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / 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

ComponentName: MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS
Type: VIRUS / Details: Based on PDB entry 1CX8
Buffer solutionName: 0.02M TRIS-HCL / pH: 7.5 / Details: 0.02M TRIS-HCL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL 200
VitrificationCryogen name: ETHANE / Details: PLUNGED IN LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Jan 22, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 54000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 1700 nm / Cs: 2 mm
Image recordingElectron dose: 25.96 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 115
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2SPIDER3D reconstruction
3Xmipp3D reconstruction
CTF correctionDetails: CTF correction of each particle
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: projection matching / Resolution: 27 Å / Num. of particles: 8566 / Nominal pixel size: 2.6 Å / Actual pixel size: 2.6 Å / Details: a modified version of XMIPP software was used / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: BEST VISUAL FIT USING THE PROGRAM O
Details: METHOD--MANUAL FITTING USING THE PROGRAM O REFINEMENT PROTOCOL--RIGID BODY
Atomic model buildingPDB-ID: 1CX8

1cx8


Accession code: 1CX8 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 27 Å
Refinement stepCycle: LAST / Highest resolution: 27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10112 0 0 0 10112

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