6wrw

Crystal structure of computationally designed protein 2DS25.5 in complex with the human Transferrin receptor ectodomain

Method: X-RAY DIFFRACTION D_max: 128.8 Å Quality: GOOD

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

Transferrin receptor protein 1

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	Other combination Heteromer Protein × 4 其他Polymer 6 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 121–760 Chain B； UniProt 121–760	Not recorded	Computationally designed protein 2DS25.5 × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 6WRW	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 oligomeric state 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
1CX8 CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR Deposited 1999-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 122–760（639 aa） Fragment：RESIDUES 122-760 Chain B 122–760（639 aa） Fragment：RESIDUES 122-760	Not recorded	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
1CX8 CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR Deposited 1999-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 122–760（639 aa） Fragment：RESIDUES 122-760 Chain D 122–760（639 aa） Fragment：RESIDUES 122-760	Not recorded	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
1CX8 CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR Deposited 1999-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 122–760（639 aa） Fragment：RESIDUES 122-760 Chain F 122–760（639 aa） Fragment：RESIDUES 122-760	Not recorded	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
1CX8 CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR Deposited 1999-08-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 122–760（639 aa） Fragment：RESIDUES 122-760 Chain H 122–760（639 aa） Fragment：RESIDUES 122-760	Not recorded	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
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 oligomeric state 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 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 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 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 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 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
6WRX Crystal structure of computationally designed protein 2DS25.1 in complex with the human Transferrin receptor ectodomain Deposited 2020-04-30	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 33 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 1–640； UniProt 121–760 Author chain B； PDBConstruct 1–640； UniProt 121–760

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	6wrw
Deposition date deposition_date	2020-04-30
Structure title title	Crystal structure of computationally designed protein 2DS25.5 in complex with the human Transferrin receptor ectodomain
Keywords keywords	Complex, Beta sheet, Receptor, DE NOVO PROTEIN; DE NOVO PROTEIN
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	38.99 Å
Radius of gyration Rg (electron density) rg_electron	38.55 Å
Forward intensity I(0) i0	398232000.00
Molecular weight molecular_weight	166480.0 kDa
Excluded volume excluded_volume	209890 Å³
Envelope volume envelope_volume	271010 Å³
Hydration-shell volume shell_volume	58867 Å³
Envelope diameter envelope_diameter	130.5 Å
Shell Rg shell_rg	44.16 Å
Envelope Rg envelope_rg	38.57 Å
Shape Rg shape_rg	38.50 Å
Total Rg total_rg	39.06 Å
Total atoms total_atoms	11757
Residues n_residues	1455
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	128.8 Å
Rg (real space) rg_real	39.05 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	3.9820e+08
I(0) uncertainty (real space) i0_real_error	7.0760e+06
Rg (reciprocal space) rg_reciprocal	39.02 Å
I(0) (reciprocal space) i0_reciprocal	398200000.0000
Solution quality estimate total_estimate	0.8754
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.0 Å
Skewness Skewness skewness	0.383
Kurtosis Kurtosis kurtosis	-0.393
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	89500000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.759

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Transferrin receptor protein 1
Molecular weight formula_weight	71807.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11757

RLYWDDLKRKLSEKLDSTDFTSTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIKLTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Computationally designed protein 2DS25.5
Molecular weight formula_weight	10175.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

DEEEIQKAIEELLRKGVSEEEAAIIIVQRFNVAVVVVVQDERQGKHISEYIRRYIPEADVILFANLVVIKVETHELSTRVWEAAQKAY

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	138.399 Å
Unit-cell length b length_b	138.399 Å
Unit-cell length c length_c	279.847 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	2.840 Å
Low-resolution limit resolution_low	69.200 Å
R factor r_factor	0.2121
R_work r_work	0.2109
R_free r_free	0.2353

fit	/app/data/saxs_computation/wr/6wrw/6wrw.fit
pddf	/app/data/pr_computation/wr/6wrw/6wrw.pr.out
profile	/app/data/saxs_computation/wr/6wrw/6wrw.dat

Crystal structure of computationally designed protein 2DS25.5 in complex with the human Transferrin receptor ectodomain

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

Transferrin receptor protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)