7V3F: DENV2_NGC_Fab_C10 28degree

Name: PDB 7V3F: DENV2_NGC_Fab_C10 28degree (1Fab:3E)
Published: 2021-12-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

DENV2_NGC_Fab_C10 28degree (1Fab:3E). Determined by electron microscopy at 3.1 Å resolution. Released 29 Dec 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Dengue virus type 2 (strain Thailand/NGS-C/1944)
Chains: 6
Atoms: 13,224
Mol. weight: 189.11 kDa
Ligands: NAG
Released: 29 Dec 2021

Explore 7V3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V3F contains 49 α-helices and 107 β-strands across 6 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: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	12
β-strand	20-26	7	13
β-strand	30-34	5	12
β-strand	41-50	10	12
β-strand	54-73	20	14
α-helix	83-85	3
β-strand	87	1	5
β-strand	90-99	10	14
α-helix	101-103	3
β-strand	109-129	21	14
β-strand	135-143	9	12
β-strand	160-164	5	12
β-strand	172-175	4	13
β-strand	179-183	5	13
β-strand	186	1	13
β-strand	196-200	5	14
β-strand	205-209	5	14
α-helix	210-213	4
β-strand	220-222	3	14
α-helix	234-236	3
β-strand	238-241	4	15
β-strand	249-252	4	15
α-helix	257-263	7
α-helix	267	1
β-strand	268-270	3	14
β-strand	271-272	2	12
β-strand	276-278	3	12
β-strand	282-288	7	13
β-strand	292	1	13
β-strand	296	1	16
β-strand	298	1	16
β-strand	306-313	8	17
α-helix	314-315	2
β-strand	320-326	7	17
β-strand	333-334	2	18
β-strand	337-340	4	19
β-strand	347	1	19
β-strand	350-351	2	17
β-strand	357-358	2	18
β-strand	365-370	6	17
β-strand	375-380	6	19
β-strand	388-392	5	19
α-helix	399-414	16
α-helix	417-420	4
α-helix	433-446	14
α-helix	453-468	16
α-helix	475-479	5
α-helix	483-491	9

Chain B: 13 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	20-26	7	2
β-strand	31-34	4	1
β-strand	41-50	10	1
β-strand	54-60	7	3
β-strand	63-73	11	4
α-helix	83-86	4
β-strand	87	1	5
β-strand	90-99	10	4
β-strand	109-121	13	4
β-strand	124-129	6	3
β-strand	135-143	9	1
β-strand	146	1	6
β-strand	160	1	1
β-strand	163-164	2	1
β-strand	172-174	3	2
β-strand	180-186	7	2
β-strand	196-200	5	3
β-strand	205-209	5	3
α-helix	210-214	5
β-strand	222	1	3
α-helix	234-236	3
β-strand	238-241	4	7
β-strand	249-252	4	7
α-helix	257-260	4
β-strand	268-270	3	3
β-strand	271-272	2	1
β-strand	276-278	3	1
β-strand	282-291	10	2
α-helix	300	1
β-strand	301	1	8
α-helix	302	1
β-strand	306-310	5	6
α-helix	314-315	2
β-strand	321-326	6	6
β-strand	333-334	2	8
β-strand	337-340	4	9
β-strand	347	1	9
β-strand	350-351	2	10
β-strand	357-358	2	8
β-strand	365-368	4	6
β-strand	369-370	2	10
β-strand	374-380	7	9
β-strand	387-393	7	9
α-helix	399-414	16
α-helix	418-420	3
α-helix	431-444	14
β-strand	450	1	11
α-helix	453-468	16
α-helix	475-479	5
α-helix	483-492	10

Chain C: 14 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	20
β-strand	20-26	7	21
β-strand	31-34	4	20
β-strand	41-50	10	20
β-strand	54-72	19	22
β-strand	90-98	9	22
β-strand	110-129	20	22
β-strand	135-143	9	20
β-strand	160-164	5	20
β-strand	165	1	23
β-strand	168	1	23
β-strand	173-174	2	24
β-strand	180-181	2	24
β-strand	182-185	4	21
β-strand	196-200	5	22
β-strand	205-209	5	22
α-helix	210-213	4
β-strand	220-222	3	22
α-helix	234-236	3
β-strand	238-241	4	25
β-strand	249-252	4	25
α-helix	257-263	7
α-helix	267	1
β-strand	268-270	3	22
β-strand	277-278	2	20
β-strand	282-288	7	21
α-helix	299	1
β-strand	300-301	2	26
α-helix	302	1
β-strand	306-310	5	27
α-helix	314-315	2
β-strand	320-326	7	27
β-strand	333-334	2	26
β-strand	338-340	3	28
β-strand	347	1	28
β-strand	350-351	2	27
β-strand	357-358	2	26
β-strand	365-370	6	27
β-strand	375-379	5	28
β-strand	389-392	4	28
α-helix	399-414	16
α-helix	417-422	6
α-helix	429-444	16
α-helix	453-468	16
α-helix	475-478	4
α-helix	480-484	5
α-helix	485-492	8

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	27-38	12
α-helix	41-52	12
α-helix	57-70	14

Chain E: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9	1	11
α-helix	27-38	12
α-helix	41-52	12
α-helix	57-69	13

Chain F: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	27-38	12
α-helix	40-52	13
α-helix	57-70	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein E	A, B, C	protein	495	Dengue virus type 2 (strain Thailand/NGS-C/1944)	P14340
Small envelope protein M	D, E, F	protein	72	Dengue virus type 2 (strain Thailand/NGS-C/1944)	P14340

Sequence of entity 1 (A, B, C), FASTA

>7V3F_1 Envelope protein E (chains A, B, C)
MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIETEAKQPATLRKYC
IEAKLTNTTTDSRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFT
CKKNMKGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGT
VTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF
KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYS
MCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTE
KDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMIETTMRGAKRMAILGDTAW
DFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWIMKILIGVIITWIGMNSRSTSLSVSLV
LVGVVTLYLGVMVQA

Sequence of entity 2 (D, E, F), FASTA

>7V3F_2 Small envelope protein M (chains D, E, F)
SVALVPHVGMGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQR
ALIFILLTAVAP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Human antibody C10 neutralizes by diminishing Zika but enhancing dengue virus dynamics. Lim, X.X., Shu, B., Zhang, S. et al. Cell (2021) 184:6067-6080.e13. DOI 10.1016/j.cell.2021.11.009 · 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
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)
9DTT 3.6 Å, Cryo-EM structure of DENV2 NS5 in complex with Stem Loop A (SLA)
4CBF 4.1 Å, Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus

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