9DTT: DENV2 NS5

Cryo-EM structure of DENV2 NS5 in complex with Stem Loop A (SLA). Determined by electron microscopy at 3.6 Å resolution. Released 23 Oct 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: dengue virus type 2
Chains: 2
Atoms: 8,274
Mol. weight: 128.3 kDa
Ligands: ZN
Released: 23 Oct 2024

Explore 9DTT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DTT contains 45 α-helices and 24 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: 45 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
α-helix	22-29	8
β-strand	34-36	3	1
α-helix	37	1
α-helix	39-47	9
α-helix	58-67	10
β-strand	75-80	6	2
α-helix	86-92	7
β-strand	97-103	7	2
α-helix	113-115	3
β-strand	124-126	3	2
α-helix	132-134	3
α-helix	136-137	2
β-strand	142-145	4	2
α-helix	154-168	15
β-strand	177-182	6	2
α-helix	188-198	11
β-strand	204-206	3	2
β-strand	218-221	4	2
α-helix	229-241	13
β-strand	251-253	3	1
α-helix	254-257	4
α-helix	274-288	15
β-strand	304-311	8	3
α-helix	317-319	3
β-strand	320-321	2	4
α-helix	323-327	5
α-helix	330-332	3
α-helix	336-342	7
α-helix	350-354	5
α-helix	355-359	5
α-helix	368-385	18
α-helix	396-401	6
α-helix	422-428	7
α-helix	430-441	12
α-helix	442-444	3
α-helix	479-489	11
α-helix	492-495	4
α-helix	512-524	13
β-strand	530-533	4	5
β-strand	535-536	2	6
α-helix	544-547	4
α-helix	550-555	6
α-helix	559-571	13
β-strand	576-584	9	3
β-strand	587-595	9	3
α-helix	606-626	21
α-helix	637-656	20
β-strand	659-661	3	5
β-strand	664-667	4	5
α-helix	679-683	5
β-strand	687-688	2	6
α-helix	696-697	2
β-strand	699-700	2	5
α-helix	703-705	3
β-strand	708	1	7
β-strand	711	1	7
β-strand	712-717	6	8
β-strand	723-728	6	8
α-helix	731-738	8
β-strand	740-741	2	4
α-helix	749-765	17
α-helix	771-782	12
α-helix	802-804	3
α-helix	809-814	6
α-helix	815-819	5
α-helix	841-846	6
α-helix	854-861	8
α-helix	863-874	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase NS5	A	protein	920	dengue virus type 2	P14340
stem loop A	B	RNA	70	dengue virus type 2

Sequence of entity 1 (A), FASTA

>9DTT_1 RNA-directed RNA polymerase NS5 (chains A)
MGSSHHHHHHSSGENLYFQGGTGNIGETLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTL
AKEGIKRGETDHHAVSRGSAKLRWFVERNMVTPEGKVVDLGCGRGGWSYYCGGLKNVREV
KGLTKGGPGHEEPIPMSTYGWNLVRLQSGVDVFFTPPEKCDTLLCDIGESSPNPTVEAGR
TLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYW
VSNASGNIVSSVNMISRMLINRFTMRHKKATYEPDVDLGSGTRNIGIESEIPNLDIIGKR
IEKIKQEHETSWHYDQDHPYKTWAYHGSYETKQTGSASSMVNGVVRLLTKPWDVVPMVTQ
MAMTDTTPFGQQRVFKEKVDTRTQEPKEGTKKLMKITAEWLWKELGKKKTPRMCTREEFT
RKVRSNAALGAIFTDENKWKSAREAVEDSRFWELVDKERNLHLEGKCETCVYNMMGKREK
KLGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWFSRENSLSGVEGEGLHKLGYILR
DVSKKEGGAMYADDTAGWDTRITLEDLKNEEMVTNHMEGEHKKLAEAIFKLTYQNKVVRV
QRPTPRGTVMDIISRRDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGVFKSIQHLTVTEE
IAVQNWLARVGRERLSRMAISGDDCVVKPLDDRFASALTALNDMGKVRKDIQQWEPSRGW
NDWTQVPFCSHHFHELIMKDGRVLVVPCRNQDELIGRARISQGAGWSLRETACLGKSYAQ
MWSLMYFHRRDLRLAANAICSAVPSHWVPTSRTTWSIHAKHEWMTTEDMLTVWNRVWIQE
NPWMEDKTPVESWEEIPYLGKREDQWCGSLIGLTSRATWAKNIQTAINQVRSLIGNEEYT
DYMPSMKRFRREEEEAGVLW

Sequence of entity 2 (B), FASTA

>9DTT_2 stem loop A (chains B)
AGUUGUUAGUCUACGUGGACCGACAAAGACAGAUUCUUUGAGGGAGCUAAGCUCAACGUA
GUUCUAACAG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural Dynamics of the Dengue Virus Non-structural 5 (NS5) Interactions with Promoter Stem Loop A (SLA). Obi, J.O., Kihn, K.C., McQueen, L. et al. bioRxiv (2024). DOI 10.1101/2024.12.03.626708 · PubMed

Other PDB entries of the same protein (UniProt P14340), best resolution first:

6FLC 2.0 Å, 2C8 Fab bound to EDIII of DenV 2
6IZY 2.11 Å, The RNA-dependent RNA polymerase domain of dengue 2 NS5
6FLB 2.2 Å, 3H5 Fab bound to EDIII of DenV 2 Xtal form 2
6IZX 2.43 Å, The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678
6FLA 2.9 Å, 3H5 Fab bound to EDIII of DenV 2 Xtal form 1
7V3F 3.1 Å, DENV2_NGC_Fab_C10 28degree (1Fab:3E)
7V3G 3.3 Å, DENV2_NGC_Fab_C10 28degrees (2Fab:3E)
7CTH 3.5 Å, Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the…
3J27 3.6 Å, CryoEM structure of Dengue virus
3J2P 3.6 Å, CryoEM structure of Dengue virus envelope protein heterotetramer
7V3H 3.6 Å, DENV2_NGC_Fab_C10 28degrees (3Fab:3E)
4CBF 4.1 Å, Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus

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