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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "RNA/IMMUNE SYSTEM"

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Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Homo sapiens (18)
	synthetic construct (9)
	Aeropyrum pernix (4)
	Saguaro cactus virus (4)
	Hepacivirus hominis (2)
	Mus musculus (2)
	Vicugna pacos (2)
	Escherichia coli (1)
	Hepatovirus A (1)
	Pea enation mosaic virus 2 (1)

More...

Taxonomy

	Eukaryota (22)
	Riboviria (11)
	other sequences (9)
	Archaea (4)
	Bacteria (1)

Experimental Method

X-RAY DIFFRACTION (24)

Polymer Entity Type

	Protein (24)
	RNA (24)

Refinement Resolution (Å)

	1.5 - 2.0 (6)
	2.0 - 2.5 (6)
	2.5 - 3.0 (5)
	3.0 - 3.5 (6)
	> 4.5 (1)

Release Date

	2010 - 2014 (1)
	2015 - 2019 (7)
	2020 - 2024 (16)

Symmetry Type

	Asymmetric (20)
	Cyclic (4)

AllSelected

1 to 24 of 24 Structures

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4Q9R \| pdb_00004q9r	Download File View File

Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab

Huang, H., Suslov, N.B., Li, N.-S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

(2014) Nat Chem Biol 10: 686-691

Released	2014-06-18
Method	X-RAY DIFFRACTION 3.12 Å
Organisms	Mus musculus synthetic construct
Macromolecule	Fab BL3-6, HEAVY CHAIN (protein) Fab BL3-6, LIGHT CHAIN (protein) Spinach RNA aptamer (nucleic acid)
Unique Ligands	2ZY, K

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6DB8 \| pdb_00006db8	Download File View File

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer

Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.

(2018) Nat Commun 9: 4542-4542

Released	2018-11-14
Method	X-RAY DIFFRACTION 1.86541345549 Å
Organisms	synthetic construct
Macromolecule	Fab-Heavy chain (protein) Fab-Light chain (protein) RNA (60-MER) (nucleic acid)
Unique Ligands	G4A

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6DB9 \| pdb_00006db9	Download File View File

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer

Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.

(2018) Nat Commun 9: 4542-4542

Released	2018-11-14
Method	X-RAY DIFFRACTION 2.025 Å
Organisms	synthetic construct
Macromolecule	Fab-Heavy-Chain (protein) Fab-Light-Chain (protein) RNA (60-MER) (nucleic acid)
Unique Ligands	MG

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6MWN \| pdb_00006mwn	Download File View File

Crystal structure of hepatitis A virus IRES domain V in complex with Fab HAVx

Koirala, D., Shao, Y., Piccirilli, J.A.

(2019) Nat Commun 10: 3629-3629

Released	2019-08-14
Method	X-RAY DIFFRACTION 2.838 Å
Organisms	Hepatovirus A Homo sapiens
Macromolecule	Fab HAVx Heavy Chain (protein) Fab HAVx Light Chain (protein) HAV dV RNA (92-MER) (nucleic acid)

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6U8D \| pdb_00006u8d	Download File View File

Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV2

Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli, J.A.

(2020) ACS Chem Biol 15: 205-216

Released	2019-12-04
Method	X-RAY DIFFRACTION 1.807 Å
Organisms	Hepacivirus hominis Homo sapiens
Macromolecule	Heavy chain of Fab HCV2 (protein) Light chain of Fab HCV2 (protein) JIIIabc RNA (68-MER) (nucleic acid)

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6U8K \| pdb_00006u8k	Download File View File

Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV3

Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli, J.A.

(2020) ACS Chem Biol 15: 205-216

Released	2019-12-04
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Hepacivirus hominis Homo sapiens
Macromolecule	Heavy chain of Fab HCV3 (protein) Light chain of Fab HCV3 (protein) JIIIabc RNA (68-MER) (nucleic acid)

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6XJQ \| pdb_00006xjq	Download File View File

Crystal structure of a self-alkylating ribozyme - alkylated form with biotinylated epoxide substrate

Koirala, D., Piccirilli, J.A.

(2022) Nat Chem Biol 18: 376-384

Released	2022-01-19
Method	X-RAY DIFFRACTION 1.708 Å
Organisms	Aeropyrum pernix Homo sapiens
Macromolecule	Fab HAVx Heavy Chain (protein) Fab HAVx Light Chain (protein) Self-alkylating ribozyme (58-MER) (nucleic acid)
Unique Ligands	V4J

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6XJW \| pdb_00006xjw	Download File View File

Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety

Koirala, D., Piccirilli, J.A.

(2022) Nat Chem Biol 18: 376-384

Released	2022-01-19
Method	X-RAY DIFFRACTION 1.918 Å
Organisms	Aeropyrum pernix Homo sapiens
Macromolecule	Fab HAVx Heavy Chain (protein) Fab HAVx Light Chain (protein) Self-alkylating Ribozyme (58-MER) (nucleic acid)
Unique Ligands	97C

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6XJY \| pdb_00006xjy	Download File View File

Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate

Koirala, D., Piccirilli, J.A.

(2022) Nat Chem Biol 18: 376-384

Released	2022-01-19
Method	X-RAY DIFFRACTION 2.156 Å
Organisms	Aeropyrum pernix Homo sapiens
Macromolecule	Fab HAVx Heavy Chain (protein) Fab HAVx Light Chain (protein) Self-alkylating ribozyme (58-MER) (nucleic acid)

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6XJZ \| pdb_00006xjz	Download File View File

Crystal structure of a self-alkylating ribozyme - apo form

Koirala, D., Piccirilli, J.A.

(2022) Nat Chem Biol 18: 376-384

Released	2022-01-19
Method	X-RAY DIFFRACTION 2.488 Å
Organisms	Aeropyrum pernix Homo sapiens
Macromolecule	Fab HAVx Heavy Chain (protein) Fab HAVx Light Chain (protein) Self-alkylating ribozyme (58-MER) (nucleic acid)

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7MLX \| pdb_00007mlx	Download File View File

SARS-CoV-2 programmed -1 frameshifting element three stem H-type pseudoknot

Roman, C., Lewicka, A.

(2021) ACS Chem Biol 16: 1469-1481

Released	2021-08-11
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	BL3-6 Fab Heavy Chain (protein) BL3-6 Fab Light Chain (protein) RNA (65-MER) (nucleic acid)

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8D29 \| pdb_00008d29	Download File View File

Crystal structure of theophylline aptamer - apo form

Menichelli, E., Spraggon, G.

(2022) Proc Natl Acad Sci U S A 119: e2213117119-e2213117119

Released	2022-11-30
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) RNA (34-MER) (nucleic acid)
Unique Ligands	K, NA

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8DK7 \| pdb_00008dk7	Download File View File

Crystal structure of theophylline aptamer soaked with TAL2

Menichelli, E., Spraggon, G.

(2022) Proc Natl Acad Sci U S A 119: e2213117119-e2213117119

Released	2022-11-30
Method	X-RAY DIFFRACTION 2.46 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	FAB heavy chain (protein) FAB light chain (protein) RNA (34-MER) (nucleic acid)

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8SH5 \| pdb_00008sh5	Download File View File

Crystal structure of 3'cap-independent translation enhancers (CITE) from Pea enation mosaic virus RNA 2 (PEMV2) with Fab BL3-6K170A

Lewicka, A., Roman, C., Rice, P.A., Piccirilli, J.A.

(2023) Nucleic Acids Res 51: 8891-8907

Released	2023-08-16
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Mus musculus Pea enation mosaic virus 2
Macromolecule	Fab BL3-6K170A heavy chain (protein) Fab BL3-6K170A light chain (protein) RNA (88-MER) (nucleic acid)

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8T29 \| pdb_00008t29	Download File View File

Crystal structure of SCV PTE RNA in complex with Fab BL3-6

Ojha, M., Koirala, D.

(2024) Proc Natl Acad Sci U S A 121: e2313677121-e2313677121

Released	2024-01-10
Method	X-RAY DIFFRACTION 3.13 Å
Organisms	Homo sapiens Saguaro cactus virus
Macromolecule	BL3-6 Fab heavy chain (protein) BL3-6 Fab light chain (protein) RNA (90-MER) (nucleic acid)

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8T2A \| pdb_00008t2a	Download File View File

Crystal structure of SCV PTE G18A mutant RNA in complex with Fab BL3-6

Ojha, M., Koirala, D.

(2024) Proc Natl Acad Sci U S A 121: e2313677121-e2313677121

Released	2024-01-10
Method	X-RAY DIFFRACTION 3.17 Å
Organisms	Homo sapiens Saguaro cactus virus
Macromolecule	BL3-6 Fab heavy chain (protein) BL3-6 Fab light chain (protein) RNA (90-MER) (nucleic acid)

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8T2B \| pdb_00008t2b	Download File View File

Crystal structure of SCV PTE G18C mutant RNA in complex with Fab BL3-6

Ojha, M., Koirala, D.

(2024) Proc Natl Acad Sci U S A 121: e2313677121-e2313677121

Released	2024-01-10
Method	X-RAY DIFFRACTION 3.18 Å
Organisms	Homo sapiens Saguaro cactus virus
Macromolecule	BL3-6 Fab heavy chain (protein) BL3-6 Fab light chain (protein) RNA (90-MER) (nucleic acid)

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8T2O \| pdb_00008t2o	Download File View File

Crystal structure of SCV PTE G18U RNA in complex with Fab BL3-6

Ojha, M., Koirala, D.

(2024) Proc Natl Acad Sci U S A 121: e2313677121-e2313677121

Released	2024-01-10
Method	X-RAY DIFFRACTION 3.29 Å
Organisms	Homo sapiens Saguaro cactus virus
Macromolecule	BL3-6 Fab heavy chain (protein) BL3-6 Fab light chain (protein) RNA (90-MER) (nucleic acid)

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8VM8 \| pdb_00008vm8	Download File View File

The crystal structure of coxsackievirus B3 RNA replication element sD-loop mutant in complex with Fab BL3-6

Das, N.K., Koirala, D.

(2024) Nucleic Acids Res 52: 11218-11233

Released	2024-07-24
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Heavy Chain of Fab BL3-6 (protein) Light Chain of Fab BL3-6 (protein) RNA (93-MER) (nucleic acid)

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8VM9 \| pdb_00008vm9	Download File View File

The crystal structure of rhinovirus B14 RNA replication element sD-loop mutant in complex with Fab BL3-6

Das, N.K., Koirala, D.

(2024) Nucleic Acids Res 52: 11218-11233

Released	2024-07-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Heavy Chain of Fab BL3-6 (protein) Light Chain of Fab BL3-6 (protein) RNA (85-MER) (nucleic acid)

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8VMA \| pdb_00008vma	Download File View File

The crystal structure of rhinovirus C15 RNA replication element sD-loop mutant in complex with Fab BL3-6

Das, N.K., Koirala, D.

(2024) Nucleic Acids Res 52: 11218-11233

Released	2024-07-24
Method	X-RAY DIFFRACTION 2.54 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Heavy Chain of Fab BL3-6 (protein) Light Chain of Fab BL3-6 (protein) RNA (88-MER) (nucleic acid)

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8VMB \| pdb_00008vmb	Download File View File

The crystal structure of rhinovirus C15 RNA replication element sB-loop mutant in complex with Fab BL3-6

Das, N.K., Koirala, D.

(2024) Nucleic Acids Res 52: 11218-11233

Released	2024-07-24
Method	X-RAY DIFFRACTION 2.97 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Heavy Chain of Fab BL3-6 (protein) Light Chain of Fab BL3-6 (protein) RNA (83-MER) (nucleic acid)

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5UK4 \| pdb_00005uk4	Download File View File

VESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1307

Hanke, L., Knockenhauer, K.E., Ploegh, H.L., Schwartz, T.U.

(2017) EMBO Rep 18: 1027-1037

Released	2017-04-19
Method	X-RAY DIFFRACTION 3.204 Å
Organisms	Vesicular stomatitis Indiana virus strain San Juan Vicugna pacos
Macromolecule	Anti-vesicular stomatitis virus N VHH (protein) Nucleoprotein (protein) RNA (45-MER) (nucleic acid)

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5UKB \| pdb_00005ukb	Download File View File

VSV N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1004

Hanke, L., Knockenhauer, K.E., Ploegh, H.L., Schwartz, T.U.

(2017) EMBO Rep 18: 1027-1037

Released	2017-04-19
Method	X-RAY DIFFRACTION 5.473 Å
Organisms	Escherichia coli Vesicular stomatitis Indiana virus Vicugna pacos
Macromolecule	Anti-vesicular stomatitis virus N VHH (protein) Nucleocapsid (protein) RNA (45-MER) (nucleic acid)

1 to 24 of 24 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Symmetry Type

4Q9R | pdb_00004q9r

6DB8 | pdb_00006db8

6DB9 | pdb_00006db9

6MWN | pdb_00006mwn

6U8D | pdb_00006u8d

6U8K | pdb_00006u8k

6XJQ | pdb_00006xjq

6XJW | pdb_00006xjw

6XJY | pdb_00006xjy

6XJZ | pdb_00006xjz

7MLX | pdb_00007mlx

8D29 | pdb_00008d29

8DK7 | pdb_00008dk7

8SH5 | pdb_00008sh5

8T29 | pdb_00008t29

8T2A | pdb_00008t2a

8T2B | pdb_00008t2b

8T2O | pdb_00008t2o

8VM8 | pdb_00008vm8

8VM9 | pdb_00008vm9

8VMA | pdb_00008vma

8VMB | pdb_00008vmb

5UK4 | pdb_00005uk4

5UKB | pdb_00005ukb