6D04: 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 1. Determined by electron microscopy at 3.74 Å resolution. Released 20 Jun 2018.

Method: Electron microscopy
Resolution: 3.74 Å
Organisms: Homo sapiens, Plasmodium vivax
Chains: 6
Atoms: 28,748
Mol. weight: 499.76 kDa
Ligands: CO3, FE, NAG, CA
Released: 20 Jun 2018

Explore 6D04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D04 contains 150 α-helices and 120 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: 28 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	124-135	12
α-helix	140-146	7
β-strand	155	1	1
α-helix	160-175	16
β-strand	180-193	14	2
β-strand	199-203	5	3
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	349-352	4	5
α-helix	353-354	2
β-strand	364-367	4	5
β-strand	372-377	6	3
β-strand	379-393	15	2
β-strand	398-408	11	2
β-strand	411	1	1
α-helix	416-420	5
α-helix	421-435	15
α-helix	436-440	5
β-strand	446-453	8	2
α-helix	461-469	9
β-strand	478-483	6	2
β-strand	488	1	7
β-strand	495-498	4	2
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	8
β-strand	521	1	8
α-helix	528-530	3
α-helix	532-536	5
α-helix	542	1
α-helix	543-547	5
β-strand	552-556	5	2
β-strand	557	1	7
α-helix	562-563	2
β-strand	568	1	6
α-helix	574-579	6
α-helix	584-602	19
α-helix	611-613	3
α-helix	614-626	13
α-helix	629-634	6
α-helix	640-661	22
α-helix	669-680	12
α-helix	683-685	3
β-strand	686	1	9
β-strand	699	1	9
α-helix	709-720	12
α-helix	728-749	22

Chains C and D: 34 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	19
α-helix	13-28	16
β-strand	36-41	6	19
α-helix	45-53	9
β-strand	59	1	19
β-strand	60-62	3	20
α-helix	64-67	4
β-strand	78-84	7	20
β-strand	95-101	7	21
β-strand	117-118	2	21
α-helix	125-129	5
α-helix	130-135	6
α-helix	136-138	3
α-helix	140	1
α-helix	142	1
α-helix	146-153	8
β-strand	157-158	2	21
β-strand	171	1	21
α-helix	188-196	9
β-strand	202-206	5	21
α-helix	209-213	5
α-helix	217-222	6
β-strand	224-226	3	21
β-strand	232-234	3	21
β-strand	244-246	3	21
α-helix	247-249	3
β-strand	250-253	4	20
α-helix	260-270	11
α-helix	271-275	5
β-strand	301-304	4	20
α-helix	305-306	2
α-helix	311-314	4
α-helix	317-328	12
α-helix	340-341	2
β-strand	342-347	6	22
α-helix	352-361	10
β-strand	366-371	6	22
α-helix	374-383	10
β-strand	388-391	4	22
α-helix	393-402	10
β-strand	405-410	6	22
α-helix	422-423	2
β-strand	426-427	2	23
β-strand	428-433	6	24
β-strand	449-450	2	24
α-helix	457-461	5
α-helix	462-471	10
β-strand	483-484	2	24
α-helix	493-495	3
α-helix	516-526	11
β-strand	530-534	5	24
α-helix	537-541	5
α-helix	549-552	4
β-strand	559-562	4	24
β-strand	568-570	3	24
β-strand	581-582	2	23
α-helix	583-585	3
β-strand	586-589	4	22
α-helix	594-608	15
β-strand	638-640	3	22
α-helix	647-651	5
α-helix	653-660	8
α-helix	669-675	7

Chains E and F: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	180-181	2	31
β-strand	188-189	2	31
α-helix	197-211	15
α-helix	217-239	23
α-helix	241-254	14
α-helix	267-307	41
α-helix	320-334	15
α-helix	338-361	24
α-helix	369-405	37
α-helix	416-476	61
α-helix	479-509	31
α-helix	514-516	3
α-helix	520-565	46
α-helix	575-589	15
α-helix	591-632	42

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

>6D04_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

>6D04_2 Serotransferrin (chains C, D)
MRLAVGALLVCAVLGLCLAVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVK
KASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVV
KKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPC
ADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRD
QYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKE
FQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKP
VKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGK
CGLVPVLAENYNKSDNCEDTPEAGYFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWN
IPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAF
RCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLAR
APNHAVVTRKDKEACVHKILRQQQHLFGSNVTDCSGNFCLFRSETKDLLFRDDTVCLAKL
HDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP

Sequence of entity 3 (E, F), FASTA

>6D04_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
CO3	Carbonate ion	C O3	4
FE	FE (III) ion	Fe	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	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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