7MK1: Protein-modified aptamer complex

Structure of a protein-modified aptamer complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 3 Nov 2021.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 4,454
Mol. weight: 59.58 kDa
Ligands: MG, ZN
Released: 3 Nov 2021

Explore 7MK1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MK1 contains 14 α-helices and 24 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: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	806-810	5	1
β-strand	816-819	4	1
α-helix	820-822	3
β-strand	823-826	4	2
β-strand	830-833	4	2
α-helix	836-839	4
β-strand	842-846	5	3
β-strand	852-853	2	3
β-strand	856-864	9	3
β-strand	872-879	8	3
β-strand	882-887	6	3
α-helix	889-891	3
β-strand	892-896	5	1
β-strand	902-904	3	1
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	2
α-helix	918	1
α-helix	920-922	3

Chain B: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	806-810	5	4
β-strand	816-819	4	4
α-helix	820-822	3
β-strand	823-826	4	5
β-strand	830-833	4	5
α-helix	836-841	6
β-strand	842-846	5	6
β-strand	852-853	2	6
β-strand	856-864	9	6
β-strand	872-879	8	6
β-strand	882-887	6	6
α-helix	889-891	3
β-strand	892-896	5	4
β-strand	902-903	2	4
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	5
α-helix	918	1
α-helix	920-922	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antiviral innate immune response receptor RIG-I	A, B	protein	125	Homo sapiens	O95786 (AlphaFold model)
DNA (41-mer)	C, D	DNA	41	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7MK1_1 Antiviral innate immune response receptor RIG-I (chains A, B)
PDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRA
KIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDP
AEMSK

Sequence of entity 2 (C, D), FASTA

>7MK1_2 DNA (41-MER) (chains C, D)
ATCTCXGXGXCAXGXGXXXXAAXGXCAGXXXAAXGAXGAGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

Primary citation

Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA. Ren, X., Gelinas, A.D., Linehan, M. et al. J Mol Biol (2021) 433:167227-167227. DOI 10.1016/j.jmb.2021.167227 · PubMed

Other PDB entries of the same protein (UniProt O95786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BAH 1.89 Å, Structure of RIG-I CTD bound to OH-RNA
3LRR 2.15 Å, Crystal structure of human RIG-I CTD bound to a 12 bp AU rich 5' ppp dsRNA
3OG8 2.4 Å, Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA
9KU4 2.4 Å, Cryo-EM structure of E373A mutant RIG-I with 5'p-RNA
2YKG 2.5 Å, Structural insights into RNA recognition by RIG-I
3ZD7 2.5 Å, Snapshot 3 of RIG-I scanning on RNA duplex
3NCU 2.55 Å, Structural and functional insights into pattern recognition by the innate immune…
4BPB 2.58 Å, Structural insights into RNA recognition by rig-I
3LRN 2.6 Å, Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp dsRNA
9KTW 2.6 Å, Cryo-EM structure of wild type RIG-I with 5'p-RNA
5F9F 2.6 Å, Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA
2QFD 2.7 Å, Crystal structure of the regulatory domain of human RIG-I with bound Hg

Browse structure collections

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