7V3H: DENV2_NGC_Fab_C10 28degrees

DENV2_NGC_Fab_C10 28degrees (3Fab:3E). Determined by electron microscopy at 3.6 Å resolution. Released 29 Dec 2021.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Dengue virus type 2 (strain Thailand/NGS-C/1944), Homo sapiens
Chains: 12
Atoms: 18,610
Mol. weight: 265.61 kDa
Ligands: NAG
Released: 29 Dec 2021

Explore 7V3H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V3H contains 55 α-helices and 188 β-strands across 12 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: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	15
β-strand	20-26	7	16
β-strand	31-34	4	15
β-strand	41-50	10	15
β-strand	54-73	20	17
α-helix	83-85	3
β-strand	87	1	6
β-strand	90-98	9	17
β-strand	110-129	20	17
β-strand	135-143	9	15
β-strand	160-164	5	15
β-strand	172-175	4	16
β-strand	179-186	8	16
β-strand	196-200	5	17
β-strand	205-209	5	17
α-helix	210-214	5
β-strand	220-222	3	17
α-helix	234-236	3
β-strand	238-241	4	18
β-strand	249-252	4	18
β-strand	255	1	17
α-helix	257-261	5
α-helix	267	1
β-strand	268-269	2	17
β-strand	271-272	2	15
β-strand	276-278	3	15
β-strand	282-288	7	16
β-strand	292	1	16
β-strand	306	1	19
β-strand	310-314	5	20
β-strand	320-324	5	20
β-strand	326	1	19
β-strand	332-334	3	21
β-strand	337-340	4	22
β-strand	347	1	22
β-strand	351	1	20
β-strand	357-359	3	21
β-strand	365-369	5	20
β-strand	375-380	6	22
β-strand	388-392	5	22
α-helix	399-414	16
α-helix	417-420	4
α-helix	430-445	16
α-helix	453-469	17
α-helix	475-479	5
α-helix	480-484	5
α-helix	485-491	7

Chain B: 14 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	20-26	7	2
β-strand	30-34	5	1
β-strand	41-50	10	1
β-strand	54-57	4	3
β-strand	60-62	3	4
β-strand	65-73	9	5
α-helix	83-85	3
β-strand	87	1	6
β-strand	90-95	6	5
β-strand	98-99	2	7
β-strand	109-110	2	7
β-strand	112-119	8	5
β-strand	123-124	2	4
β-strand	126-129	4	3
β-strand	135-143	9	1
β-strand	146	1	8
β-strand	160-164	5	1
β-strand	172-173	2	2
β-strand	181-183	3	2
β-strand	186	1	2
α-helix	188-191	4
β-strand	196-197	2	9
β-strand	198-200	3	3
β-strand	208-209	2	9
α-helix	210-214	5
β-strand	222	1	3
α-helix	234-236	3
β-strand	238-241	4	10
β-strand	249-252	4	10
α-helix	258-261	4
α-helix	267-269	3
β-strand	271-272	2	1
β-strand	276-278	3	1
β-strand	282-288	7	2
α-helix	300	1
β-strand	301	1	11
α-helix	302	1
β-strand	306-313	8	8
β-strand	321-326	6	8
β-strand	333-334	2	11
β-strand	338-340	3	12
β-strand	347	1	12
β-strand	351	1	13
β-strand	357-358	2	11
β-strand	365-368	4	8
β-strand	369	1	13
β-strand	374-380	7	12
α-helix	383-385	3
β-strand	387-393	7	12
α-helix	399-414	16
α-helix	418-420	3
α-helix	430-444	15
β-strand	450	1	14
α-helix	455-467	13
α-helix	484-492	9

Chain C: 15 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	23
β-strand	20-26	7	24
β-strand	31-34	4	23
β-strand	41-50	10	23
β-strand	54-60	7	25
β-strand	63-72	10	26
α-helix	75-77	3
β-strand	90-98	9	26
α-helix	101-103	3
β-strand	110-121	12	26
β-strand	124-129	6	25
β-strand	135-143	9	23
β-strand	160-162	3	23
β-strand	165	1	27
β-strand	168	1	27
β-strand	173-174	2	28
β-strand	180-181	2	28
β-strand	182-186	5	24
β-strand	197	1	29
β-strand	198-200	3	25
β-strand	205	1	25
β-strand	208	1	29
α-helix	210-214	5
β-strand	220-222	3	25
α-helix	234-236	3
β-strand	238-241	4	30
α-helix	243-245	3
β-strand	249-252	4	30
α-helix	257-261	5
β-strand	277-278	2	23
β-strand	282-288	7	24
α-helix	300	1
β-strand	301	1	31
α-helix	302	1
β-strand	308-314	7	32
β-strand	320-324	5	32
β-strand	333-334	2	31
β-strand	338-340	3	33
β-strand	347	1	33
β-strand	350-351	2	32
β-strand	357-358	2	31
β-strand	365-370	6	32
β-strand	375-379	5	33
β-strand	389-392	4	33
α-helix	399-414	16
α-helix	417-422	6
α-helix	431-443	13
β-strand	450	1	34
α-helix	455-466	12
α-helix	475	1
α-helix	476-481	6
α-helix	483-492	10

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	27-36	10
α-helix	41-51	11
α-helix	57-70	14

Chains E and F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9	1	14
α-helix	27-38	12
α-helix	41-52	12
α-helix	57-70	14

Chain G: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	44
β-strand	18	1	44
β-strand	21-25	5	44
α-helix	29-31	3
β-strand	32-39	8	45
β-strand	46-47	2	45
β-strand	68-73	6	44
β-strand	78-83	6	44
β-strand	93-100	8	45
α-helix	101-102	2
β-strand	118	1	45
β-strand	122-123	2	45

Chain H: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	46
β-strand	17-22	6	47
β-strand	35-40	6	48
β-strand	47-50	4	48
β-strand	64-65	2	47
β-strand	68	1	47
β-strand	73-78	6	47
β-strand	87-93	7	48
β-strand	99-101	3	48
β-strand	105	1	48
β-strand	106-108	3	46

Chain I: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	35
β-strand	11	1	36
β-strand	17-24	8	35
α-helix	29-31	3
β-strand	32	1	37
β-strand	34	1	38
β-strand	35-39	5	39
β-strand	45-47	3	39
β-strand	52	1	38
β-strand	68-73	6	35
β-strand	78-84	7	35
β-strand	93-97	5	39
β-strand	100	1	37
α-helix	110-111	2
β-strand	118	1	39
β-strand	119	1	35
β-strand	122-123	2	39
β-strand	125	1	36

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

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
C10 IgG light chain variable region	G, I, K	protein	127	Homo sapiens
C10 IgG heavy chain variable region	H, L, M	protein	109	Homo sapiens

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

>7V3H_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

>7V3H_2 Small envelope protein M (chains D, E, F)
SVALVPHVGMGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQR
ALIFILLTAVAP

Sequence of entity 3 (G, I, K), FASTA

>7V3H_3 C10 IgG light chain variable region (chains G, I, K)
EVQLVESGAEVKKPGASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNTKY
SQKFQDRVTITRDTSASTAYMELSSLRSEDTAIYYCARDKVDDYGDYWFPTLWYFDYWGQ
GTLVTVS

Sequence of entity 4 (H, L, M), FASTA

>7V3H_4 C10 IgG heavy chain variable region (chains H, L, M)
SALTQPASVSGSPGQSITISCTGTSSDVGGFNYVSWFQQHPGKAPKLMLYDVTSRPSGVS
SRFSGSKSGNTASLTISGLQAEDEADYYCSSHTSRGTWVFGGGTKLTVL

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
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
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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