7ZQS: Human Transferrin Receptor 1

Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer. Determined by electron microscopy at 2.54 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 2.54 Å
Organisms: unidentified, Homo sapiens
Chains: 4
Atoms: 11,354
Mol. weight: 204.15 kDa
Ligands: MG, NAG
Released: 17 Aug 2022

Explore 7ZQS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZQS contains 64 α-helices and 66 β-strands across 2 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.

Chains B and D: 32 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	124-136	13
α-helix	140-147	8
β-strand	155	1	1
α-helix	160-175	16
β-strand	180-182	3	2
β-strand	185-192	8	3
α-helix	197-198	2
β-strand	199-203	5	4
β-strand	209-214	6	4
β-strand	220-221	2	5
β-strand	227-230	4	4
β-strand	232-234	3	6
α-helix	240-244	5
β-strand	254-258	5	6
α-helix	264-273	10
β-strand	278-282	5	6
β-strand	297	1	7
β-strand	299-300	2	5
α-helix	317-319	3
β-strand	334-336	3	6
α-helix	339-346	8
β-strand	349	1	8
β-strand	352	1	9
β-strand	364	1	9
β-strand	366	1	6
β-strand	367	1	8
β-strand	372-376	5	4
β-strand	380-387	8	3
β-strand	389-393	5	2
β-strand	402-408	7	2
β-strand	411	1	1
α-helix	416-420	5
α-helix	421-435	15
α-helix	436-440	5
β-strand	447-453	7	2
α-helix	456-458	3
α-helix	461-469	9
α-helix	471-474	4
β-strand	478-483	6	2
β-strand	488-489	2	2
β-strand	493-498	6	2
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	10
α-helix	515	1
β-strand	521	1	10
α-helix	528-531	4
α-helix	532-535	4
α-helix	541-542	2
α-helix	543-547	5
β-strand	552-558	7	2
β-strand	568	1	7
α-helix	573-579	7
α-helix	583-602	20
α-helix	611-613	3
α-helix	614-625	12
α-helix	626-628	3
α-helix	629-634	6
α-helix	640-662	23
α-helix	668-683	16
β-strand	686	1	11
β-strand	699	1	11
α-helix	709-721	13
α-helix	728-750	23
α-helix	753-755	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (30-mer)	A, C	DNA	51	unidentified
Transferrin receptor protein 1	B, D	protein	760	Homo sapiens	P02786 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7ZQS_1 DNA (30-MER) (chains A, C)
GCAGCAGCGTAAAGGGGGTGTTTGTGCGGTGTGGAGTGCGCGTGCTGCTGC

Sequence of entity 2 (B, D), FASTA

>7ZQS_2 Transferrin receptor protein 1 (chains B, D)
MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLAVDEEENADNNTKANVTKPK
RCSGSICYGTIAVIVFFLIGFMIGYLGYCKGVEPKTECERLAGTESPVREEPGEDFPAAR
RLYWDDLKRKLSEKLDSTDFTGTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSK
VWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTK
KDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGH
AHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTD
STCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSG
VGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFT
YINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNA
AFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIK
LTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDF
GNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRK
QNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

Ligands and cofactors

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

Primary citation

Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing. Cheng, E.L., Cardle, I.I., Kacherovsky, N. et al. J Am Chem Soc (2022) 144:13851-13864. DOI 10.1021/jacs.2c05349 · PubMed

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

6OKD 1.85 Å, Crystal Structure of human transferrin receptor in complex with a cystine-dense peptide
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…
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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