3KAS: Machupo virus GP1

Machupo virus GP1 bound to human transferrin receptor 1. Determined by X-ray diffraction at 2.4 Å resolution. Released 9 Mar 2010.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Machupo virus
Chains: 2
Atoms: 6,717
Mol. weight: 93.73 kDa
Ligands: NAG, PO4
Released: 9 Mar 2010

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

Secondary structure: helices and β-sheets

3KAS contains 37 α-helices and 36 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.

Chain A: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	124-136	13
α-helix	140-146	7
α-helix	160-176	17
β-strand	180-192	13	1
α-helix	197-198	2
β-strand	199-204	6	2
β-strand	209-214	6	2
β-strand	220-221	2	3
β-strand	226-230	5	2
β-strand	232-234	3	4
α-helix	240-244	5
β-strand	254-258	5	4
β-strand	260	1	5
β-strand	262	1	5
α-helix	264-272	9
β-strand	278-282	5	4
β-strand	299-300	2	3
β-strand	334-336	3	4
α-helix	339-346	8
β-strand	349-352	4	4
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-367	4	4
β-strand	371-377	7	2
β-strand	380-393	14	1
β-strand	398-408	11	1
α-helix	416-420	5
α-helix	421-438	18
β-strand	446-453	8	1
α-helix	456-458	3
α-helix	461-469	9
α-helix	474-476	3
β-strand	478-483	6	1
β-strand	488	1	1
β-strand	493-498	6	1
α-helix	500-502	3
α-helix	503-510	8
β-strand	514	1	6
β-strand	521	1	6
α-helix	528-531	4
α-helix	532-535	4
α-helix	541-542	2
α-helix	543-548	6
β-strand	552-558	7	1
α-helix	573-579	7
α-helix	583-603	21
α-helix	613-625	13
α-helix	626-628	3
α-helix	640-662	23
α-helix	668-681	14
α-helix	682-685	4
β-strand	686	1	7
β-strand	699	1	7
α-helix	709-717	9
α-helix	728-749	22

Chain B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	90-95	6	8
β-strand	98-103	6	8
β-strand	106-113	8	8
β-strand	124-126	3	8
α-helix	129-135	7
α-helix	139-141	3
α-helix	142-152	11
α-helix	160-161	2
β-strand	162-164	3	8
β-strand	175-178	4	8
α-helix	183-185	3
α-helix	186-199	14
β-strand	214-219	6	8
β-strand	220	1	9
β-strand	222	1	9
α-helix	223-225	3
α-helix	234-236	3
β-strand	240	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transferrin receptor protein 1	A	protein	640	Homo sapiens	P02786 (AlphaFold model)
Glycoprotein	B	protein	162	Machupo virus	Q8AZ57 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3KAS_1 Transferrin receptor protein 1 (chains A)
RLYWDDLKRKLSEKLDSTDFTSTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSK
VWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTK
KDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGH
AHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTD
STCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSG
VGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFT
YINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNA
AFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIK
LTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDF
GNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRK
QNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

Sequence of entity 2 (B), FASTA

>3KAS_2 Glycoprotein (chains B)
NHSNELPSLCMLNNSFYYMRGGVNTFLIRVSDISVLMKEYDVSIYEPEDLGNCLNKSDSS
WAIHWFSNALGHDWLMDPPMLCRNKTKKEGSNIQFNISKADDARVYGKKIRNGMRHLFRG
FHDPCEEGKVCYLTINQCGDPSSFDYCGVNHLSKCQFDHVNT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
PO4	Phosphate ion	O4 P	6

Water and common crystallization additives (K) are not listed.

Primary citation

Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses. Abraham, J., Corbett, K.D., Farzan, M. et al. Nat Struct Mol Biol (2010) 17:438-444. DOI 10.1038/nsmb.1772 · 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
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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