4BPB: Probable ATP-dependent RNA helicase DDX58

Structural insights into RNA recognition by rig-I. Determined by X-ray diffraction at 2.58 Å resolution. Released 19 Jun 2013.

Method: X-ray diffraction
Resolution: 2.58 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 5,518
Mol. weight: 86.55 kDa
Ligands: ZN
Released: 19 Jun 2013

Explore 4BPB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BPB contains 30 α-helices and 29 β-strands across 1 chain. 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: 30 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	245-255	11
β-strand	260-263	4	1
α-helix	270-283	14
α-helix	286	1
β-strand	287	1	2
β-strand	289	1	2
β-strand	293-296	4	1
α-helix	300-313	14
β-strand	321-324	4	1
α-helix	334-339	6
β-strand	343-346	4	1
α-helix	348-356	9
α-helix	363-365	3
β-strand	368-372	5	1
α-helix	374-376	3
α-helix	382-395	14
α-helix	401-403	3
β-strand	404-409	6	1
α-helix	420-433	14
β-strand	438-440	3	1
α-helix	446-450	5
β-strand	457-462	6	3
α-helix	464-466	3
α-helix	470-489	20
α-helix	493-495	3
α-helix	507-518	12
α-helix	531-557	27
α-helix	560-576	17
α-helix	581-591	11
α-helix	594-602	9
α-helix	609-622	14
β-strand	630-633	4	3
α-helix	637-648	12
α-helix	651-653	3
β-strand	658-659	2	3
β-strand	695-698	4	3
β-strand	711-715	5	3
β-strand	737-742	6	3
α-helix	745-770	26
α-helix	773-793	21
α-helix	795-801	7
β-strand	802	1	4
β-strand	806-810	5	5
β-strand	816-819	4	5
α-helix	820-822	3
β-strand	823-826	4	6
β-strand	830-833	4	6
β-strand	842-846	5	7
β-strand	852	1	7
β-strand	857-864	8	7
β-strand	872-879	8	7
β-strand	882-887	6	7
α-helix	889-891	3
β-strand	892-896	5	5
β-strand	902-904	3	5
α-helix	908-910	3
β-strand	913	1	4
β-strand	916-917	2	6
α-helix	918	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable ATP-dependent RNA helicase DDX58	A	protein	698	HOMO SAPIENS	O95786 (AlphaFold model)
5'-r(gpcpgpcpgpcpgpcpgpcp)-3'	C, D	RNA	10	HOMO SAPIENS

Sequence of entity 1 (A), FASTA

>4BPB_1 PROBABLE ATP-DEPENDENT RNA HELICASE DDX58 (chains A)
SEVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQ
KGKVVFFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQ
ILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLT
ASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISD
KFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKD
EESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQR
FEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEG
NPKLSFLKPGILTGRGKTNQNTFFGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIA
QCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILR
LQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIE
DCHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVI
KIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK

Sequence of entity 2 (C, D), FASTA

>4BPB_2 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3' (chains C, D)
GCGCGCGCGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Insights Into RNA Recognition by Rig-I. Luo, D., Ding, S.C., Vela, A. et al. Cell (2011) 147:409. DOI 10.1016/J.CELL.2011.09.023 · 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
7MK1 1.9 Å, Structure of a protein-modified aptamer complex
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…
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

About this viewer

MolViewer shows 4BPB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.