3S9M: Transferrin receptor protein 1

Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe, cryocooled 1. Determined by X-ray diffraction at 3.32 Å resolution. Released 10 Aug 2011.

Method: X-ray diffraction
Resolution: 3.32 Å
Organism: Homo sapiens
Chains: 4
Atoms: 16,658
Mol. weight: 301.78 kDa
Ligands: FE, CO3, CA, NAG
Released: 10 Aug 2011

Explore 3S9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3S9M contains 109 α-helices and 99 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: 31 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	124-137	14
α-helix	141-146	6
α-helix	150-152	3
α-helix	160-175	16
β-strand	180	1	1
β-strand	183-186	4	1
β-strand	189-192	4	2
β-strand	199-204	6	3
β-strand	212-214	3	3
β-strand	220-221	2	4
β-strand	228-230	3	3
β-strand	232-236	5	5
α-helix	240-244	5
β-strand	254-258	5	5
α-helix	264-273	10
β-strand	278-282	5	5
β-strand	297	1	6
β-strand	299-300	2	4
α-helix	317-319	3
β-strand	334-337	4	5
α-helix	339-347	9
β-strand	349-352	4	5
α-helix	353-354	2
β-strand	364-367	4	5
β-strand	371-376	6	3
β-strand	380-383	4	2
β-strand	386-393	8	1
β-strand	398-408	11	1
α-helix	416-420	5
α-helix	421-435	15
α-helix	436-440	5
β-strand	446-453	8	1
α-helix	456-458	3
α-helix	461-467	7
α-helix	471-474	4
β-strand	478-483	6	1
β-strand	488	1	7
β-strand	495-498	4	1
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	8
α-helix	515	1
β-strand	521	1	8
α-helix	528-531	4
α-helix	534-536	3
α-helix	542	1
α-helix	543-548	6
β-strand	552-556	5	1
β-strand	557	1	7
β-strand	568	1	6
α-helix	573-579	7
α-helix	583-602	20
α-helix	611-613	3
α-helix	614-626	13
α-helix	629-634	6
α-helix	640-661	22
β-strand	663	1	9
α-helix	668-684	17
β-strand	686	1	10
β-strand	699	1	10
α-helix	709-716	8
α-helix	728-747	20

Chain B: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	124-137	14
α-helix	141-147	7
α-helix	160-176	17
β-strand	180-192	13	11
β-strand	199-201	3	12
β-strand	212-214	3	12
β-strand	220-221	2	13
β-strand	227-230	4	12
β-strand	231-236	6	14
α-helix	240-245	6
β-strand	253-258	6	14
α-helix	264-272	9
β-strand	276-282	7	14
β-strand	297	1	15
β-strand	299-300	2	13
α-helix	317-319	3
β-strand	334-336	3	14
α-helix	339-347	9
β-strand	349	1	16
β-strand	366	1	14
β-strand	367	1	16
β-strand	373-376	4	12
β-strand	380-393	14	11
β-strand	402-408	7	11
α-helix	416-420	5
α-helix	421-435	15
α-helix	436-440	5
β-strand	447-453	7	11
α-helix	456-458	3
α-helix	461-469	9
α-helix	471-473	3
β-strand	478-483	6	11
β-strand	495-498	4	11
α-helix	500-512	13
β-strand	514	1	17
α-helix	515	1
β-strand	521	1	17
α-helix	532-536	5
α-helix	541-542	2
α-helix	543-547	5
β-strand	552-556	5	11
β-strand	568	1	15
α-helix	573-579	7
α-helix	583-603	21
α-helix	613-626	14
α-helix	629-634	6
α-helix	640-661	22
β-strand	663	1	18
α-helix	668-678	11
α-helix	683-685	3
β-strand	686	1	19
β-strand	699	1	19
α-helix	709-720	12
α-helix	728-749	22

Chain C: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	20
α-helix	12-26	15
β-strand	36-42	7	20
α-helix	45-53	9
β-strand	59	1	20
β-strand	60-62	3	21
α-helix	64-71	8
β-strand	73	1	9
β-strand	77-82	6	21
β-strand	85-86	2	22
β-strand	91-92	2	22
β-strand	94-102	9	23
β-strand	117-119	3	23
α-helix	125-129	5
α-helix	130-135	6
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
β-strand	157-158	2	23
α-helix	168-170	3
β-strand	171	1	23
α-helix	188-196	9
β-strand	202-206	5	23
α-helix	209-213	5
α-helix	220-222	3
β-strand	223-227	5	23
β-strand	231-233	3	23
β-strand	244-247	4	23
α-helix	248-249	2
β-strand	250-254	5	21
α-helix	260-274	15
β-strand	299	1	22
β-strand	303-304	2	21
α-helix	311-315	5
α-helix	317-328	12
α-helix	332-333	2
α-helix	335	1
α-helix	340-341	2
β-strand	342-346	5	24
α-helix	351-361	11
β-strand	366-370	5	24
α-helix	374-383	10
β-strand	388-391	4	24
α-helix	393-400	8
β-strand	405-411	7	24
β-strand	586-589	4	24
α-helix	594-608	15
β-strand	637-640	4	24
α-helix	647-650	4
α-helix	654-665	12
α-helix	669-674	6

Chain D: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	25
α-helix	12-27	16
β-strand	36-42	7	25
α-helix	45-53	9
β-strand	59	1	25
β-strand	60-62	3	26
α-helix	67-71	5
β-strand	73	1	18
β-strand	77-85	9	26
β-strand	94-96	3	27
α-helix	125-129	5
α-helix	130-133	4
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
α-helix	188-196	9
α-helix	207-209	3
α-helix	219-221	3
β-strand	245-247	3	27
β-strand	250-254	5	26
α-helix	260-273	14
β-strand	299-304	6	26
α-helix	305-306	2
α-helix	311-315	5
α-helix	317-327	11
α-helix	332-333	2
α-helix	335	1
α-helix	340-341	2
β-strand	342-346	5	28
α-helix	349-361	13
β-strand	366-370	5	28
α-helix	374-383	10
β-strand	388-391	4	28
α-helix	393-402	10
β-strand	405-411	7	28
β-strand	586-589	4	28
α-helix	594-608	15
β-strand	637-640	4	28
α-helix	647-650	4
α-helix	654-662	9
α-helix	669-674	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transferrin receptor protein 1	A, B	protein	654	Homo sapiens	P02786 (AlphaFold model)
Serotransferrin	C, D	protein	693	Homo sapiens	P02787 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3S9M_1 Transferrin receptor protein 1 (chains A, B)
VPDKHHHHHHIEGRRLYWDDLKRKLSEKLDSTDFTSTIKLLNENSYVPREAGSQKDENLA
LYVENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAA
TVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQT
KFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLF
GNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVG
AQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEW
LEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDS
NWASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKV
ARAAAEVAGQFVIKLTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSAR
GDFFRATSRLTTDFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGS
HTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

Sequence of entity 2 (C, D), FASTA

>3S9M_2 Serotransferrin (chains C, D)
VPDKHHHHHHIEGRVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYL
DCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSG
FQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTD
FPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELL
CLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFS
SPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKPVKWCA
LSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVP
VLAENYDKSDNCEDTPEAGFFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGL
LYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGFTGAFRCLVE
KGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLARAPNHA
VVTRKDKEACVHKILRQQQHLFGSDVTDCSGNFCLFRSETKDLLFRDDTVCLAKLHDRNT
YEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP

Ligands and cofactors

ID	Name	Formula	Copies
FE	FE (III) ion	Fe	2
CO3	Carbonate ion	C O3	2
CA	Calcium ion	Ca	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

How the binding of human transferrin primes the transferrin receptor potentiating iron release at endosomal pH. Eckenroth, B.E., Steere, A.N., Chasteen, N.D. et al. Proc Natl Acad Sci U S A (2011) 108:13089-13094. DOI 10.1073/pnas.1105786108 · 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…
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…

Browse structure collections

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