6S9J: TfR1 mimicry

Crystal structure of TfR1 mimicry in complex with GP1 from MACV. Determined by X-ray diffraction at 2.7 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Machupo virus, Neotoma albigula
Chains: 8
Atoms: 9,715
Mol. weight: 157.98 kDa
Ligands: NAG
Released: 15 Jan 2020

Explore 6S9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S9J contains 56 α-helices and 73 β-strands across 8 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: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	196-198	3
β-strand	199-203	5	2
β-strand	209-214	5	2
β-strand	220-221	2	3
β-strand	226-230	5	2
β-strand	232-234	3	3
α-helix	240-245	6
β-strand	254-258	5	3
α-helix	264-273	10
β-strand	278-282	5	3
α-helix	287-290	4
β-strand	334-337	4	3
α-helix	339-346	8
β-strand	350-352	3	3
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-366	3	3
β-strand	372-377	6	2

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	90-93	4	1
β-strand	98-103	6	1
β-strand	106-113	8	1
β-strand	124-126	3	1
α-helix	129-134	6
α-helix	142-152	11
α-helix	160-161	2
β-strand	162-164	3	1
β-strand	175-178	4	1
α-helix	183-185	3
α-helix	186-199	14
α-helix	207-208	2
β-strand	214-219	6	1
α-helix	223-225	3
α-helix	231-234	4
β-strand	240	1	1

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	199-203	5	6
β-strand	209-214	5	6
β-strand	220-221	2	7
β-strand	226-230	5	6
β-strand	232-234	3	7
α-helix	240-245	6
β-strand	254-258	5	7
α-helix	264-273	10
β-strand	278-282	5	7
α-helix	287-290	4
β-strand	334-337	4	7
α-helix	339-346	8
β-strand	350-352	3	7
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-366	3	7
β-strand	372-377	6	6

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	90-93	4	4
β-strand	98-103	6	4
β-strand	106-113	8	4
β-strand	124-126	3	4
α-helix	129-134	6
α-helix	142-152	11
α-helix	160-161	2
β-strand	162-164	3	4
β-strand	175-178	4	4
β-strand	181	1	5
α-helix	183-185	3
α-helix	186-199	14
α-helix	207-208	2
β-strand	209	1	5
β-strand	214-219	6	4
α-helix	223-225	3
α-helix	231-234	4

Chain E: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	199-203	5	9
β-strand	209-214	5	9
β-strand	226-230	5	9
β-strand	231-234	4	10
α-helix	240-245	6
β-strand	253-258	6	10
α-helix	264-273	10
β-strand	278-282	5	10
α-helix	287-290	4
β-strand	334-336	3	10
α-helix	339-347	9
β-strand	350-352	3	10
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-366	3	10
β-strand	372-377	6	9

Chain F: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	90-93	4	8
β-strand	99-103	5	8
β-strand	106-113	8	8
β-strand	124-126	3	8
α-helix	129-134	6
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
α-helix	207-208	2
β-strand	214-219	6	8
α-helix	223-225	3
α-helix	231-234	4

Chain G: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	199-203	5	12
β-strand	209-214	5	12
β-strand	226-230	5	12
β-strand	232-234	3	13
α-helix	240-245	6
β-strand	254-258	5	13
α-helix	264-273	10
β-strand	278-282	5	13
α-helix	287-290	4
β-strand	334-336	3	13
α-helix	339-346	8
β-strand	350-352	3	13
α-helix	353-354	2
α-helix	355-357	3
β-strand	364-366	3	13
β-strand	372-377	6	12

Chain H: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	90-93	4	11
β-strand	98-103	6	11
β-strand	106-113	8	11
β-strand	124-126	3	11
α-helix	129-134	6
α-helix	142-152	11
α-helix	160-161	2
β-strand	162-164	3	11
β-strand	175-178	4	11
α-helix	186-199	14
α-helix	207-208	2
β-strand	214-219	6	11
α-helix	223-225	3
α-helix	231-234	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pre-glycoprotein polyprotein GP complex	B, D, F, H	protein	168	Machupo virus	Q8AZ57 (AlphaFold model)
Transferrin receptor 1,Transferrin receptor 1	A, C, E, G	protein	178	Neotoma albigula	A0A060BIS8 (AlphaFold model)

Sequence of entity 1 (B, D, F, H), FASTA

>6S9J_1 Pre-glycoprotein polyprotein GP complex (chains B, D, F, H)
SNELPSLCMLNNSFYYMRGGVNTFLIRVSDISVLMKEYDVSIYEPEDLGNCLNKSDSSWA
IHWFSNALGHDWLMDPPMLCRNKTKKEGSNIQFNISKADDARVYGKKIRNGMRHLFRGFH
DPCEEGKVCYLTINQCGDPSSFDYCGVNHLSKCQFDHVNTGSHHHHHH

Sequence of entity 2 (A, C, E, G), FASTA

>6S9J_2 Transferrin receptor 1,Transferrin receptor 1 (chains A, C, E, G)
KIQVKCSAPNSVTITNASGGLYLVEYPEGYVAYSKATEVTGKLVHANFGTKKDFEDLDYA
VNGSIVIVRAGKITIAEKVANAQSFNAIGVLIYKDRTKYPISRADEPLQGHSGLPSIPVQ
TISREAAEKLFQNMERDCPRSWNTDSSCKLELLQNRNVKLTVNNCLKEGTSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Rational design of universal immunotherapy for TfR1-tropic arenaviruses. Cohen-Dvashi, H., Amon, R., Agans, K.N. et al. Nat Commun (2020) 11:67-67. DOI 10.1038/s41467-019-13924-6 · PubMed

Other PDB entries of the same protein (UniProt Q8AZ57 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KAS 2.4 Å, Machupo virus GP1 bound to human transferrin receptor 1
9MT2 2.9 Å, Structure of the Machupo virus glycoprotein complex
5W1M 3.91 Å, MACV GP1 CR1-07 Fab complex

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