6D05: Transferrin receptor protein 1

Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2. Determined by electron microscopy at 3.8 Å resolution. Released 20 Jun 2018.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, Plasmodium vivax
Chains: 6
Atoms: 28,748
Mol. weight: 499.76 kDa
Ligands: NAG, FE, CO3, CA
Released: 20 Jun 2018

Explore 6D05 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D05 contains 136 α-helices and 128 β-strands across 6 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 A and B: 25 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	124-137	14
α-helix	141-146	6
β-strand	155	1	1
α-helix	160-175	16
β-strand	180-193	14	2
α-helix	197-198	2
β-strand	199-203	5	3
α-helix	204	1
β-strand	210-214	5	3
β-strand	220-221	2	4
β-strand	226-230	5	3
β-strand	232-234	3	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
β-strand	334-336	3	5
α-helix	339-346	8
β-strand	349-350	2	5
β-strand	366-367	2	5
β-strand	372-377	6	3
β-strand	379-393	15	2
β-strand	402-406	5	2
β-strand	408	1	7
β-strand	411	1	1
α-helix	416-420	5
α-helix	421-438	18
β-strand	447-452	6	2
β-strand	453	1	7
α-helix	461-469	9
β-strand	478-483	6	2
β-strand	488	1	8
β-strand	495-498	4	2
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	9
α-helix	515	1
β-strand	521	1	9
α-helix	541-543	3
α-helix	544-548	5
β-strand	552-556	5	2
β-strand	557	1	8
α-helix	562-563	2
β-strand	568	1	6
α-helix	573-579	7
α-helix	584-602	19
α-helix	612-626	15
α-helix	629-634	6
α-helix	640-661	22
β-strand	663	1	10
α-helix	669-683	15
β-strand	686	1	11
β-strand	699	1	11
α-helix	709-721	13
α-helix	729-749	21

Chains C and D: 31 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	23
α-helix	13-29	17
β-strand	39-41	3	23
α-helix	45-53	9
β-strand	59	1	23
β-strand	60-62	3	24
α-helix	64-71	8
β-strand	73	1	10
β-strand	77-84	8	24
β-strand	95-101	7	25
β-strand	117-118	2	25
α-helix	125-129	5
α-helix	130-134	5
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
β-strand	157-158	2	25
α-helix	169-171	3
α-helix	188-196	9
β-strand	202-206	5	25
α-helix	209-213	5
α-helix	217-222	6
β-strand	224-226	3	25
β-strand	232-233	2	25
β-strand	244-246	3	25
β-strand	250-254	5	24
α-helix	260-274	15
β-strand	301-304	4	24
α-helix	305-306	2
α-helix	311-315	5
α-helix	318-328	11
α-helix	340-341	2
β-strand	342-347	6	26
α-helix	351-361	11
β-strand	366-371	6	26
α-helix	374-383	10
β-strand	388-391	4	27
α-helix	393-402	10
β-strand	405-410	6	27
β-strand	427-432	6	28
β-strand	449-450	2	29
α-helix	457-461	5
α-helix	462-471	10
β-strand	483-484	2	29
α-helix	516-527	12
β-strand	530-534	5	28
α-helix	537-541	5
α-helix	549-552	4
β-strand	560-561	2	28
β-strand	569	1	28
β-strand	580-581	2	28
α-helix	583-585	3
β-strand	586-589	4	27
α-helix	591-593	3
α-helix	594-608	15
β-strand	638-640	3	27
α-helix	647-651	5
α-helix	653-662	10
α-helix	669-676	8

Chains E and F: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	181	1	37
β-strand	188	1	37
α-helix	197-209	13
α-helix	216-255	40
α-helix	257-262	6
α-helix	267-306	40
β-strand	317	1	38
α-helix	319-334	16
α-helix	338-364	27
α-helix	368-405	38
α-helix	409-411	3
β-strand	413	1	38
α-helix	416-476	61
α-helix	479-512	34
α-helix	520-566	47
α-helix	575-632	58

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transferrin receptor protein 1	A, B	protein	659	Homo sapiens	P02786 (AlphaFold model)
Serotransferrin	C, D	protein	698	Homo sapiens	P02787 (AlphaFold model)
Reticulocyte binding protein 2, putative	E, F	protein	820	Plasmodium vivax	A5K736

Sequence of entity 1 (A, B), FASTA

>6D05_1 Transferrin receptor protein 1 (chains A, B)
ADPHHHHHHSSGIEGRGEFRLYWDDLKRKLSEKLDSTDFTSTIKLLNENSYVPREAGSQK
DENLALYVENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVA
YSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLI
YMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAA
AEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDH
YVVVGAQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSV
GATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQF
LYQDSNWASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIP
ELNKVARAAAEVAGQFVIKLTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQW
LYSARGDFFRATSRLTTDFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVF
WGSGSHTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

Sequence of entity 2 (C, D), FASTA

>6D05_2 Serotransferrin (chains C, D)
MRLAVGALLVCAVLGLCLAVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVK
KASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVV
KKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPC
ADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRD
QYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKE
FQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKP
VKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGK
CGLVPVLAENYNKSDNCEDTPEAGYFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWN
IPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAF
RCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLAR
APNHAVVTRKDKEACVHKILRQQQHLFGSNVTDCSGNFCLFRSETKDLLFRDDTVCLAKL
HDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP

Sequence of entity 3 (E, F), FASTA

>6D05_3 Reticulocyte binding protein 2, putative (chains E, F)
GAMGSMHIPIQPSPESTQSTNTTDNIDYFDISDESNYYLISQLRPHFSNIYFFDEFKRYA
SYHTEIKRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDV
KLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYL
VDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFE
YHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIH
KEKIVHNLLGELFGHLEERISKLIDSEYFITESNNIISQSEETLKLAEDVYDKNTKLIED
LTLYPHLEINEFKKDYDNNVEDLRESIIYIQSYVSSIKSAYRYNVLEKDSVESKQKNIPA
NSNAQKKVDELLSIIDSISYSNFSVAENFQKMKDYYKEIEKLKIKILQLIEAIKKYQQHV
EELINKEKAVAILKEDINKIIEYIKGIIEKLKQLISANKDFDKIFQQVEQLINEALFNKD
QFEHNKNDLHTKMKEIMHTFHERDLQQFLDNMSKFLKDQEASYQNADSKEKLDQLLTTVK
AKQDELKEMKCDDIPDIIDNLKKESQNVLNLKDEVINKQFENMRTEMSSSLDQMTKEYNA
LKSSIEEYEAEKKGIENHKQNIIKRKNTFIVAEHENDEDVPEGKNTYNEFISNKDTILQK
ESAISNQMNTLEEKKRNRKTTLQTYGDAIQKLETYTEKKDEETKVLLDKFNTEVENFKLD
EDEKSFNDAKSIVSNTINEVENENKNIDSIKKVNIAMKRS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
FE	FE (III) ion	Fe	4
CO3	Carbonate ion	C O3	4
CA	Calcium ion	Ca	2

Primary citation

Cryo-EM structure of an essential Plasmodium vivax invasion complex. Gruszczyk, J., Huang, R.K., Chan, L.J. et al. Nature (2018) 559:135-139. DOI 10.1038/s41586-018-0249-1 · 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…

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