6OKD: Human transferrin receptor

Crystal Structure of human transferrin receptor in complex with a cystine-dense peptide. Determined by X-ray diffraction at 1.85 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, Monosiga brevicollis
Chains: 4
Atoms: 11,117
Mol. weight: 164.22 kDa
Ligands: NAG
Released: 15 Apr 2020

Explore 6OKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OKD contains 67 α-helices and 52 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 30 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	23-28	6
α-helix	32-34	3
β-strand	37	1	1
α-helix	42-57	16
β-strand	62-74	13	2
α-helix	79-80	2
β-strand	81-85	5	3
β-strand	92-96	5	3
β-strand	102-103	2	4
β-strand	108-112	5	3
β-strand	114-116	3	5
α-helix	122-127	6
β-strand	136-140	5	5
α-helix	146-155	10
β-strand	160-164	5	5
β-strand	181-182	2	4
β-strand	216-218	3	5
α-helix	221-228	8
β-strand	231-234	4	5
α-helix	235-236	2
α-helix	237-239	3
β-strand	246-249	4	5
β-strand	254-259	6	3
β-strand	262-275	14	2
β-strand	280-290	11	2
β-strand	293	1	1
α-helix	298-302	5
α-helix	303-322	20
β-strand	328-335	8	2
α-helix	338-340	3
α-helix	343-350	8
α-helix	356-358	3
β-strand	360-365	6	2
β-strand	370	1	2
β-strand	375-380	6	2
α-helix	382-384	3
α-helix	385-392	8
β-strand	396	1	6
β-strand	403	1	6
α-helix	410-413	4
α-helix	414-418	5
α-helix	423-428	6
β-strand	434-440	7	2
α-helix	444-445	2
α-helix	455-461	7
α-helix	465-484	20
α-helix	495-508	14
α-helix	511-516	6
α-helix	522-544	23
α-helix	550-560	11
α-helix	565-567	3
β-strand	568	1	7
β-strand	581	1	7
α-helix	591-600	10
α-helix	610-630	21

Chain B: 31 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	23-28	6
α-helix	32-34	3
β-strand	37	1	8
α-helix	42-57	16
β-strand	62-74	13	9
α-helix	79-80	2
β-strand	81-85	5	10
β-strand	92-96	5	10
β-strand	102-103	2	11
α-helix	105-107	3
β-strand	108-112	5	10
β-strand	114-116	3	12
α-helix	122-127	6
β-strand	136-140	5	12
α-helix	146-155	10
β-strand	160-164	5	12
β-strand	181-182	2	11
β-strand	216-218	3	12
α-helix	221-228	8
β-strand	231-234	4	12
α-helix	235-236	2
α-helix	237-239	3
β-strand	246-249	4	12
β-strand	254-259	6	10
β-strand	262-275	14	9
β-strand	280-290	11	9
β-strand	293	1	8
α-helix	298-302	5
α-helix	303-322	20
β-strand	328-335	8	9
α-helix	338-340	3
α-helix	343-350	8
α-helix	356-358	3
β-strand	360-365	6	9
β-strand	370	1	9
β-strand	375-380	6	9
α-helix	382-384	3
α-helix	385-392	8
β-strand	396	1	13
β-strand	403	1	13
α-helix	410-413	4
α-helix	414-417	4
α-helix	423-428	6
β-strand	434-440	7	9
α-helix	444-445	2
α-helix	455-461	7
α-helix	465-484	20
α-helix	495-508	14
α-helix	511-516	6
α-helix	522-544	23
α-helix	550-560	11
α-helix	564-567	4
β-strand	568	1	14
β-strand	581	1	14
α-helix	591-598	8
α-helix	610-630	21

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-9	4
α-helix	11-24	14
α-helix	36-46	11

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-9	4
α-helix	11-24	14
α-helix	35-46	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transferrin receptor protein 1	A, B	protein	670	Homo sapiens	P02786 (AlphaFold model)
transferrin receptor binding cystine-dense peptide	C, D	protein	51	Monosiga brevicollis

Sequence of entity 1 (A, B), FASTA

>6OKD_1 Transferrin receptor protein 1 (chains A, B)
GSRLYWDDLKRKLSEKLDSTDFTSTIKLLNENSYVPREAGSQKDENLALYVENQFREFKL
SKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFG
TKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFF
GHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWK
TDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAK
SGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKA
FTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLD
NAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFV
IKLTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTT
DFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKL
RKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEFGGGSHHHHHHGGGSLNDI
FEAQKIEWHE

Sequence of entity 2 (C, D), FASTA

>6OKD_2 transferrin receptor binding cystine-dense peptide (chains C, D)
GSREGCASRCMKYNDELEKCEARMMSMSNTEEDCEQELEDLLYCLDHCHSQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (MES, GOL) are not listed.

Primary citation

A TfR-Binding Cystine-Dense Peptide Promotes Blood-Brain Barrier Penetration of Bioactive Molecules. Crook, Z.R., Girard, E., Sevilla, G.P. et al. J Mol Biol (2020) 432:3989-4009. DOI 10.1016/j.jmb.2020.04.002 · PubMed

Other PDB entries of the same protein (UniProt P02786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P0Z 1.88 Å, AP01-S2.3 - a variant of a redesigned transferrin receptor apical domain
6Y76 1.98 Å, AP01 - a redesigned transferrin receptor apical domain
9GH7 2.08 Å, Complex of human TfR1 with a potent bicyclic peptide
11QC 2.4 Å, Human transferrin receptor ectodomain
11RN 2.4 Å, Complex of B19V VP1u RBD and human transferrin receptor ectodomain
3KAS 2.4 Å, Machupo virus GP1 bound to human transferrin receptor 1
6WRV 2.47 Å, Crystal structure of computationally designed protein 3DS18 in complex with the human…
7ZQS 2.54 Å, Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer
1DE4 2.8 Å, Hemochromatosis protein hfe complexed with transferrin receptor
6WRW 2.84 Å, Crystal structure of computationally designed protein 2DS25.5 in complex with the human…
6WRX 3.07 Å, Crystal structure of computationally designed protein 2DS25.1 in complex with the human…
1CX8 3.2 Å, Crystal structure of the ectodomain of human transferrin receptor

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