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- PDB-1suv: Structure of Human Transferrin Receptor-Transferrin Complex -

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Basic information

Entry
Database: PDB / ID: 1suv
TitleStructure of Human Transferrin Receptor-Transferrin Complex
Components
  • Serotransferrin, C-lobe
  • Serotransferrin, N-lobe
  • Transferrin receptor protein 1
KeywordsMETAL TRANSPORT / Protein Complex
Function / homology
Function and homology information


transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / iron chaperone activity / positive regulation of isotype switching / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / response to manganese ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin ...transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / iron chaperone activity / positive regulation of isotype switching / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / response to manganese ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / response to copper ion / multicellular organismal-level iron ion homeostasis / RHOC GTPase cycle / RHOJ GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / RHOH GTPase cycle / RAC3 GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of B cell proliferation / response to retinoic acid / endocytic vesicle / osteoclast differentiation / regulation of postsynaptic membrane neurotransmitter receptor levels / transport across blood-brain barrier / RAC1 GTPase cycle / positive regulation of T cell proliferation / response to nutrient / clathrin-coated pit / ferric iron binding / receptor-mediated endocytosis / Hsp70 protein binding / basal plasma membrane / acute-phase response / cellular response to xenobiotic stimulus / Post-translational protein phosphorylation / regulation of protein stability / clathrin-coated endocytic vesicle membrane / iron ion transport / HFE-transferrin receptor complex / receptor internalization / transferrin transport / cellular response to iron ion / positive regulation of protein-containing complex assembly / positive regulation of protein localization to nucleus / Iron uptake and transport / ferrous iron binding / positive regulation of receptor-mediated endocytosis / recycling endosome / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / recycling endosome membrane / melanosome / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / double-stranded RNA binding / Clathrin-mediated endocytosis / extracellular vesicle / virus receptor activity / cytoplasmic vesicle / secretory granule lumen / blood microparticle / antibacterial humoral response / response to hypoxia / vesicle / basolateral plasma membrane / early endosome / intracellular iron ion homeostasis / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / lysosome / endosome / apical plasma membrane / endosome membrane / intracellular signal transduction / endoplasmic reticulum lumen / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / cell surface / protein homodimerization activity / : / RNA binding / extracellular exosome / extracellular region / membrane
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Serotransferrin, mammalian / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain / PA domain superfamily / PA domain / Transferrin-like domain signature 2. ...Transferrin receptor protein 1/2, PA domain / Serotransferrin, mammalian / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain / PA domain superfamily / PA domain / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
CARBONATE ION / : / Transferrin receptor protein 1 / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsCheng, Y. / Zak, O. / Aisen, P. / Harrison, S.C. / Walz, T.
CitationJournal: Cell / Year: 2004
Title: Structure of the human transferrin receptor-transferrin complex.
Authors: Yifan Cheng / Olga Zak / Philip Aisen / Stephen C Harrison / Thomas Walz /
Abstract: Iron, insoluble as free Fe(3+) and toxic as free Fe(2+), is distributed through the body as Fe(3+) bound to transferrin (Tf) for delivery to cells by endocytosis of its complex with transferrin ...Iron, insoluble as free Fe(3+) and toxic as free Fe(2+), is distributed through the body as Fe(3+) bound to transferrin (Tf) for delivery to cells by endocytosis of its complex with transferrin receptor (TfR). Although much is understood of the transferrin endocytotic cycle, little has been uncovered of the molecular details underlying the formation of the receptor-transferrin complex. Using cryo-electron microscopy, we have produced a density map of the TfR-Tf complex at subnanometer resolution. An atomic model, obtained by fitting crystal structures of diferric Tf and the receptor ectodomain into the map, shows that the Tf N-lobe is sandwiched between the membrane and the TfR ectodomain and that the C-lobe abuts the receptor helical domain. When Tf binds receptor, its N-lobe moves by about 9 A with respect to its C-lobe. The structure of TfR-Tf complex helps account for known differences in the iron-release properties of free and receptor bound Tf.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_image_scans / pdbx_database_remark / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE NOT ALL THE CHAINS IN THE MODEL ARE HUMAN, ALTHOUGH THE PROTEINS USED TO DETERMINE THE 7.5 ...SEQUENCE NOT ALL THE CHAINS IN THE MODEL ARE HUMAN, ALTHOUGH THE PROTEINS USED TO DETERMINE THE 7.5 A STRUCTURE OF THE TFR-TF COMPLEX WERE ALL HUMAN. THE AUTHORS CREATED THE MODEL BY FITTING X-RAY CRYSTAL STRUCTURES INTO THEIR 7.5 A EM DENSITY MAP. SINCE THERE IS NO STRUCTURE FOR THE HUMAN TRANSFERRIN C-LOBE, THE AUTHORS OPTED TO USE THE C-LOBE FROM RABBIT TF (1JNF). THE OTHER TWO CHAINS ARE HUMAN (1CX8 - HUMAN TFR AND 1A8E - HUMAN TF N-LOBE). THE CHAINS E AND F MATCH SWS P19134, A RABBIT SOURCE. REGARDING THE CONFLICTS: BOTH SEQUENCE AND COORDINATES ARE FROM THE ORIGINAL PDB-FILES AND THE AUTHORS DID NOT MAKE ANY MODIFICATIONS TO IT.

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Assembly

Deposited unit
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1
C: Serotransferrin, N-lobe
D: Serotransferrin, N-lobe
E: Serotransferrin, C-lobe
F: Serotransferrin, C-lobe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,12714
Polymers292,6646
Non-polymers4638
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02786
#2: Protein Serotransferrin, N-lobe / Transferrin / Siderophilin / Beta-1-metal binding globulin / PRO1400


Mass: 36408.414 Da / Num. of mol.: 2 / Fragment: repeat 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF / Cell (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02787
#3: Protein Serotransferrin, C-lobe / Transferrin / Siderophilin / Beta-1-metal binding globulin


Mass: 38300.445 Da / Num. of mol.: 2 / Fragment: repeat 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF / Cell (production host): kidney / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
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: Human Transferrin Receptor - Transferrin Complex / Type: COMPLEX
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Oct 15, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51160 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: CTF correction for each particle
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: Fourier Space reconstruction / Resolution: 7.5 Å / Nominal pixel size: 2.8 Å / Actual pixel size: 2.74 Å / Details: using program FREALIGN / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: visual fit using program O followed by rigid body refinement using program MAVE
Details: REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11CX8

1cx8

11CX81PDBexperimental model
21A8E

1a8e

11A8E2PDBexperimental model
31JNF

1jnf

11JNF3PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms20584 0 28 0 20612

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