7TGF: Ricin chain A

Single-domain VHH intrabodies neutralize ricin toxin. Determined by X-ray diffraction at 1.35 Å resolution. Released 12 Oct 2022.

Method: X-ray diffraction
Resolution: 1.35 Å
Organisms: Ricinus communis, Vicugna pacos
Chains: 2
Atoms: 3,478
Mol. weight: 44.69 kDa
Released: 12 Oct 2022

Explore 7TGF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TGF contains 20 α-helices and 27 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: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
α-helix	18-32	15
β-strand	38-39	2	2
β-strand	42-43	2	2
β-strand	44	1	3
α-helix	45-47	3
α-helix	53-55	3
β-strand	57-63	7	1
β-strand	69-75	7	1
β-strand	81-86	6	1
β-strand	89-92	4	1
α-helix	93-95	3
α-helix	98-104	7
β-strand	113-116	4	1
α-helix	123-130	8
α-helix	134-136	3
β-strand	139	1	4
α-helix	141-154	14
α-helix	161-171	11
α-helix	172-177	6
α-helix	178-180	3
β-strand	181	1	5
α-helix	182-193	12
β-strand	198	1	4
α-helix	199-201	3
α-helix	202-219	18
β-strand	225-233	9	6
β-strand	239-244	6	6
α-helix	246-248	3
β-strand	252	1	5
β-strand	255	1	3
α-helix	260-262	3

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	46-51	6	8
β-strand	58-60	3	8
α-helix	62-64	3
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	8
β-strand	115	1	8
β-strand	119-123	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ricin chain A	A	protein	267	Ricinus communis	P02879 (AlphaFold model)
VHH camelid antibody	B	protein	133	Vicugna pacos

Sequence of entity 1 (A), FASTA

>7TGF_1 Ricin chain A (chains A)
IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILV
ELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFG
GNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAAR
FQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKF
SVYDVSILIPIIALMVYRCAPPPSSQF

Sequence of entity 2 (B), FASTA

>7TGF_2 VHH camelid antibody (chains B)
QVQLAETGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQAPGKEREGVSCISSSDGRTYY
ADSVKGRFTISRDNAKNTVYLQMNSLKSEDTAVYYCATEEVCTLGIFGHGPDDYWGQGTQ
VTVSSEPKTPKPQ

Primary citation

Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins. Czajka, T.F., Vance, D.J., Davis, S. et al. J Biol Chem (2022) 298:101742-101742. DOI 10.1016/j.jbc.2022.101742 · PubMed

Other PDB entries of the same protein (UniProt P02879 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Y07 1.25 Å, Crystal structure of Ricin A chain bound with (S)-2-amino-N-(1-hydroxy-3-phenylpropan-2-y…
7Y08 1.25 Å, Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbo…
3PX8 1.29 Å, RTA in complex with 7-carboxy-pterin
7XZT 1.3 Å, Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbo…
7Y03 1.35 Å, Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7…
7Y06 1.35 Å, Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7…
2VC4 1.39 Å, Ricin A-Chain (Recombinant) E177D Mutant
1UQ5 1.4 Å, Ricin a-chain (recombinant) N122A mutant
7XZW 1.45 Å, Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbo…
7Y4M 1.45 Å, Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-ca…
1J1M 1.5 Å, Ricin A-Chain (Recombinant) at 100K
4Z9K 1.5 Å, Ricin A chain bound to camelid nanobody (VHH2)(F5)

Browse structure collections

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