1cx8

CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR

Method: X-RAY DIFFRACTION D_max: 227.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRANSFERRIN RECEPTOR PROTEIN

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 122–760 Chain B； UniProt 122–760	Fragment：RESIDUES 122-760	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SM SAMARIUM (III) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；291 K；2.4 M KCl 10 mM KPi 1.5% PEG 20K, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 3.20 Å R-free 0.284
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 122–760 Chain D； UniProt 122–760	Fragment：RESIDUES 122-760	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SM SAMARIUM (III) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；291 K；2.4 M KCl 10 mM KPi 1.5% PEG 20K, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 3.20 Å R-free 0.284
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 122–760 Chain F； UniProt 122–760	Fragment：RESIDUES 122-760	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SM SAMARIUM (III) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；291 K；2.4 M KCl 10 mM KPi 1.5% PEG 20K, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 3.20 Å R-free 0.284
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 122–760 Chain H； UniProt 122–760	Fragment：RESIDUES 122-760	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SM SAMARIUM (III) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；291 K；2.4 M KCl 10 mM KPi 1.5% PEG 20K, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 3.20 Å R-free 0.284

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1CX8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11QC Human transferrin receptor ectodomain Deposited 2026-03-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 122–760（639 aa） Chain B 122–760（639 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
11RN Complex of B19V VP1u RBD and human transferrin receptor ectodomain Deposited 2026-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 122–758（637 aa） Chain B 122–758（637 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
1DE4 HEMOCHROMATOSIS PROTEIN HFE COMPLEXED WITH TRANSFERRIN RECEPTOR Deposited 1999-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 121–760（640 aa） Fragment：ECTODOMAIN Chain F 121–760（640 aa） Fragment：ECTODOMAIN	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 8000, TRIS, TRIMETHYLAMINE HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.265
1DE4 HEMOCHROMATOSIS PROTEIN HFE COMPLEXED WITH TRANSFERRIN RECEPTOR Deposited 1999-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 121–760（640 aa） Fragment：ECTODOMAIN	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 8000, TRIS, TRIMETHYLAMINE HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.265
1SUV Structure of Human Transferrin Receptor-Transferrin Complex Deposited 2004-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 122–760（639 aa） Chain B 122–760（639 aa）	Not recorded	CO3 CARBONATE ION × 4 FE FE (III) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 7.50 Å
2NSU Crystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex Deposited 2006-11-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 122–760（639 aa） Fragment：THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR Chain B 122–760（639 aa） Fragment：THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 0.02M TRIS-HCL；pH 7.5；0.02M TRIS-HCL cryo-EM vitrification conditions Cryogen ETHANE；PLUNGED IN LIQUID ETHANE	Resolution 27.00 Å
3KAS Machupo virus GP1 bound to human transferrin receptor 1 Deposited 2009-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 121–760（640 aa） Fragment：residues 121-760	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 PO4 PHOSPHATE ION × 12 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；1.6 M sodium potassium phosphate, 150 mM NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.238
3S9L Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe, cryocooled 2 Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 120–760（641 aa） Fragment：UNP residues 120-760	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 FE FE (III) ION × 2 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；5% PEG 3350, 0.2 M MgCl2, 10% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.22 Å R-free 0.314
3S9L Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe, cryocooled 2 Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 120–760（641 aa） Fragment：UNP residues 120-760	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 FE FE (III) ION × 2 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；5% PEG 3350, 0.2 M MgCl2, 10% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.22 Å R-free 0.314
3S9M Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe, cryocooled 1 Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 120–760（641 aa） Fragment：UNP residues 120-760	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 CO3 CARBONATE ION × 2 FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；5% PEG 3350, 0.2 M MgCl2, 20% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.32 Å R-free 0.332
3S9M Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe, cryocooled 1 Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 120–760（641 aa） Fragment：UNP residues 120-760	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 CO3 CARBONATE ION × 2 FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；5% PEG 3350, 0.2 M MgCl2, 20% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.32 Å R-free 0.332
3S9N Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe, room temperature Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 120–760（641 aa） Fragment：UNP residues 120-760	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 FE FE (III) ION × 2 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；5% PEG 3350, 0.2 M MgCl2, 10% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.25 Å R-free 0.289
3S9N Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe, room temperature Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 120–760（641 aa） Fragment：UNP residues 120-760	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 FE FE (III) ION × 2 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；5% PEG 3350, 0.2 M MgCl2, 10% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K	Resolution 3.25 Å R-free 0.289
6D03 Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; one molecule of parasite ligand. Deposited 2018-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 121–760（640 aa） Chain B 121–760（640 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 4 CO3 CARBONATE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
6D04 Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 1. Deposited 2018-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 121–760（640 aa） Chain B 121–760（640 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 4 CO3 CARBONATE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
6D05 Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2. Deposited 2018-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 121–760（640 aa） Chain B 121–760（640 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 4 CO3 CARBONATE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6GSR Single Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex at 5.5 Angstrom resolution. Deposited 2018-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric	Chain Ab 121–760（640 aa） Chain Aq 121–760（640 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.50 Å
6H5I Single Particle Cryo-EM map of human Transferrin receptor 1 - H-Ferritin complex. Deposited 2018-07-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric	Chain Ab 121–760（640 aa） Chain Aq 121–760（640 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6OKD Crystal Structure of human transferrin receptor in complex with a cystine-dense peptide Deposited 2019-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 121–760（640 aa） Fragment：ligand binding domain	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；PEG 6000, Mes	Resolution 1.85 Å R-free 0.187
6OKD Crystal Structure of human transferrin receptor in complex with a cystine-dense peptide Deposited 2019-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 121–760（640 aa） Fragment：ligand binding domain	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；PEG 6000, Mes	Resolution 1.85 Å R-free 0.187
6W3H Brain delivery of therapeutic proteins using an Fc fragment blood-brain barrier transport vehicle in mice and monkeys Deposited 2020-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 326–379（54 aa） Chain D 194–296（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297.15 K；20-25% PEG3350, 0.1M Bis-Tris pH6.5, and 0.2M LiSO4	Resolution 3.38 Å R-free 0.318
6W3H Brain delivery of therapeutic proteins using an Fc fragment blood-brain barrier transport vehicle in mice and monkeys Deposited 2020-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 326–379（54 aa） Chain C 194–296（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297.15 K；20-25% PEG3350, 0.1M Bis-Tris pH6.5, and 0.2M LiSO4	Resolution 3.38 Å R-free 0.318
6WRV Crystal structure of computationally designed protein 3DS18 in complex with the human Transferrin receptor ectodomain Deposited 2020-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 121–759（639 aa） Chain B 121–759（639 aa） Chain E 121–759（639 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.1M Sodium Malonate pH 7, 0.1M HEPES pH 7, 0.5% Jeffamine ED-2001 pH 7	Resolution 2.47 Å R-free 0.236
6WRW Crystal structure of computationally designed protein 2DS25.5 in complex with the human Transferrin receptor ectodomain Deposited 2020-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 121–760（640 aa） Chain B 121–760（640 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M BICINE pH 8.5, 12% (w/v) monomethyl ether 550	Resolution 2.84 Å R-free 0.235
6WRX Crystal structure of computationally designed protein 2DS25.1 in complex with the human Transferrin receptor ectodomain Deposited 2020-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 121–760（640 aa） Chain B 121–760（640 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES pH 7.5, 12% (w/v) polyethylene glycol 3350	Resolution 3.07 Å R-free 0.225
6Y76 AP01 - a redesigned transferrin receptor apical domain Deposited 2020-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 197–378（182 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium fluoride and 20% v/v PEG 3350	Resolution 1.98 Å R-free 0.275
6Y76 AP01 - a redesigned transferrin receptor apical domain Deposited 2020-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 197–378（182 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium fluoride and 20% v/v PEG 3350	Resolution 1.98 Å R-free 0.275
7ZQS Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer Deposited 2022-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain B 1–760（760 aa） Chain D 1–760（760 aa）	Not recorded	MG MAGNESIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
8P0Z AP01-S2.3 - a variant of a redesigned transferrin receptor apical domain Deposited 2023-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 197–299（103 aa） Chain A 332–377（46 aa）	Not recorded	NA SODIUM ION × 2 BO3 BORIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；11 mg/mL protein in 20 mM HEPES, pH 6.8, 150 mM NaCl mixed with 100 mM MIB buffer, pH 7.5, and 24 % PEG in a ratio 1:2	Resolution 1.88 Å R-free 0.236
9GH7 Complex of human TfR1 with a potent bicyclic peptide Deposited 2024-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 89–760（672 aa）	Not recorded	CA CALCIUM ION × 2 GOL GLYCEROL × 2 A1ILE 1-(3,5-diethanoyl-1,3,5-triazinan-1-yl)ethanone × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M ammonium tartrate dibasic pH 7.0, 12% (w/v) PEG 3350.	Resolution 2.08 Å R-free 0.235

23 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TFR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–639； UniProt 122–760 Author chain B； PDBConstruct 1–639； UniProt 122–760 Author chain C； PDBConstruct 1–639； UniProt 122–760 Author chain D； PDBConstruct 1–639； UniProt 122–760 Author chain E； PDBConstruct 1–639； UniProt 122–760 Author chain F； PDBConstruct 1–639； UniProt 122–760 Author chain G； PDBConstruct 1–639； UniProt 122–760 Author chain H； PDBConstruct 1–639； UniProt 122–760

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cx8
Deposition date deposition_date	1999-08-28
Structure title title	CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR
Keywords keywords	HUMAN TRANSFERRIN RECEPTOR, METAL TRANSPORT; METAL TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	63.20 Å
Radius of gyration Rg (electron density) rg_electron	63.17 Å
Forward intensity I(0) i0	4565360000.00
Molecular weight molecular_weight	580680.0 kDa
Excluded volume excluded_volume	728770 Å³
Envelope volume envelope_volume	992540 Å³
Hydration-shell volume shell_volume	128850 Å³
Envelope diameter envelope_diameter	212.7 Å
Shell Rg shell_rg	64.65 Å
Envelope Rg envelope_rg	62.62 Å
Shape Rg shape_rg	63.12 Å
Total Rg total_rg	63.38 Å
Total atoms total_atoms	40808
Residues n_residues	5112
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	227.6 Å
Rg (real space) rg_real	63.39 Å
Rg uncertainty (real space) rg_real_error	2.14 Å
I(0) (real space) i0_real	4.5650e+09
I(0) uncertainty (real space) i0_real_error	9.6930e+07
Rg (reciprocal space) rg_reciprocal	62.98 Å
I(0) (reciprocal space) i0_reciprocal	4562000000.0000
Solution quality estimate total_estimate	0.8600
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.7 Å
Skewness Skewness skewness	0.376
Kurtosis Kurtosis kurtosis	-0.483
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	639200000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.878

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	TRANSFERRIN RECEPTOR PROTEIN
Molecular weight formula_weight	71623.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	40808

LYWDDLKRKLSEKLDSTDFTSTIKLLNENSYVPREAGSQKDENLALYVENEFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIKLTHDVELNLDYEEYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetinae gen. sp.

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	24

Entity 3 Entity 3 non-polymer

Description description	SAMARIUM (III) ION
Molecular weight formula_weight	150.4 kDa
Source method src_method	syn
Copy count entity_count	24

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7. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d1cx8a1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

Domain ID domain_id	d1cx8b1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8b3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

Domain ID domain_id	d1cx8c1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8c3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

Domain ID domain_id	d1cx8d1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8d3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

Domain ID domain_id	d1cx8e1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8e2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8e3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

Domain ID domain_id	d1cx8f1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8f2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8f3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

Domain ID domain_id	d1cx8g1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8g2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8g3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

Domain ID domain_id	d1cx8h1
Class class	a — All alpha proteins
Fold Fold fold	a.48 — N-cbl like
Superfamily Superfamily superfamily	a.48.2 — Transferrin receptor-like dimerisation domain
Family Family family	a.48.2.1 — Transferrin receptor-like dimerisation domain

Domain ID domain_id	d1cx8h2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.4 — PA domain
Family Family family	c.8.4.1 — PA domain

Domain ID domain_id	d1cx8h3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.5 — FolH catalytic domain-like

CATH v4.4 (24 domains)

Domain ID domain_id	1cx8A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8A02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

Domain ID domain_id	1cx8B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8B02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8B03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

Domain ID domain_id	1cx8C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8C02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8C03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

Domain ID domain_id	1cx8D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8D02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8D03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

Domain ID domain_id	1cx8E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8E02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8E03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

Domain ID domain_id	1cx8F01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8F02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8F03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

Domain ID domain_id	1cx8G01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8G02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8G03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

Domain ID domain_id	1cx8H01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1cx8H02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1cx8H03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	40 — Transferrin receptor-like, dimerisation domain

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8. Citations (1)

▶

Unit-cell length a length_a	105.400 Å
Unit-cell length b length_b	216.900 Å
Unit-cell length c length_c	361.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2434
R_free r_free	0.2836