7CTH: Dengue virus serotype 2

Name: PDB 7CTH: Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the broadly neutralizing antibody EDE1 C10
Published: 2021-12-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the broadly neutralizing antibody EDE1 C10. Determined by electron microscopy at 3.5 Å resolution. Released 1 Dec 2021.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Dengue virus 2, Homo sapiens
Chains: 10
Atoms: 16,667
Mol. weight: 251.6 kDa
Ligands: NAG
Released: 1 Dec 2021

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

Secondary structure: helices and β-sheets

7CTH contains 65 α-helices and 165 β-strands across 10 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: 14 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	1
β-strand	20-26	7	2
β-strand	27	1	1
β-strand	30-34	5	1
β-strand	41-50	10	1
β-strand	54-60	7	3
β-strand	63-64	2	4
β-strand	69-73	5	5
β-strand	87	1	6
β-strand	91-99	9	5
α-helix	101-103	3
β-strand	109-117	9	5
β-strand	120-121	2	4
β-strand	124-129	6	3
α-helix	132-134	3
β-strand	135-143	9	1
β-strand	147	1	7
β-strand	160-164	5	1
β-strand	165	1	8
β-strand	168	1	8
β-strand	170-174	5	2
β-strand	179	1	9
β-strand	180-186	7	2
α-helix	187-190	4
α-helix	193-195	3
β-strand	196-200	5	3
β-strand	205-209	5	3
α-helix	210-214	5
β-strand	220-222	3	3
β-strand	232	1	3
α-helix	234-237	4
β-strand	238-241	4	10
β-strand	249-252	4	10
α-helix	257-263	7
β-strand	268-270	3	3
β-strand	271	1	1
β-strand	273	1	11
β-strand	275	1	11
β-strand	276-278	3	1
β-strand	282-288	7	2
β-strand	292	1	9
β-strand	301	1	12
β-strand	306-314	9	7
β-strand	320-326	7	7
β-strand	334	1	12
α-helix	335-336	2
β-strand	338-340	3	13
β-strand	347	1	13
β-strand	350-351	2	7
β-strand	357	1	12
β-strand	365-370	6	7
α-helix	371-372	2
β-strand	374-380	7	13
β-strand	387-393	7	13
α-helix	397-415	19
α-helix	416-421	6
α-helix	428-447	20
α-helix	453-468	16
α-helix	474-492	19

Chain B: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	14
β-strand	20-26	7	15
β-strand	27	1	14
β-strand	30-35	6	14
β-strand	38-50	13	14
β-strand	54-72	19	16
α-helix	83-86	4
β-strand	90-99	10	16
α-helix	101-103	3
β-strand	109-129	21	16
α-helix	132-134	3
β-strand	135-143	9	14
β-strand	160-164	5	14
β-strand	170-175	6	15
β-strand	179-185	7	15
α-helix	187-189	3
α-helix	193-195	3
β-strand	196-200	5	16
β-strand	205-209	5	16
α-helix	210-214	5
β-strand	220-222	3	16
β-strand	232	1	16
α-helix	234-236	3
β-strand	238-241	4	17
β-strand	249-252	4	17
α-helix	257-263	7
β-strand	268-270	3	16
β-strand	271	1	14
β-strand	276-278	3	14
β-strand	282-288	7	15
β-strand	292	1	15
β-strand	301	1	18
β-strand	306-310	5	19
β-strand	314	1	19
β-strand	320-326	7	19
β-strand	333-334	2	18
β-strand	337-340	4	20
β-strand	350	1	21
β-strand	357-358	2	18
β-strand	365-369	5	19
β-strand	370	1	21
α-helix	371-372	2
β-strand	374-375	2	22
β-strand	377-380	4	20
β-strand	387-389	3	20
β-strand	392-393	2	22
α-helix	397-415	19
α-helix	416-421	6
α-helix	428-447	20
α-helix	453-469	17
α-helix	474-492	19

Chain C: 16 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	23
β-strand	20-26	7	24
β-strand	27	1	23
β-strand	30-35	6	23
β-strand	38-50	13	23
β-strand	54-59	6	25
β-strand	60-70	11	26
α-helix	73-74	2
α-helix	84-86	3
β-strand	87	1	6
β-strand	90-99	10	26
α-helix	101-103	3
β-strand	109-124	16	26
β-strand	126-129	4	25
α-helix	132-134	3
β-strand	135-143	9	23
β-strand	160-164	5	23
β-strand	165	1	27
β-strand	168	1	27
β-strand	170-175	6	24
β-strand	179-185	7	24
α-helix	193-195	3
β-strand	196-200	5	25
β-strand	205-209	5	25
α-helix	210-214	5
β-strand	220-222	3	25
β-strand	232	1	25
α-helix	234-237	4
β-strand	238-241	4	28
β-strand	249-252	4	28
α-helix	257-263	7
β-strand	268-269	2	25
β-strand	271	1	23
β-strand	276-278	3	23
β-strand	282-288	7	24
α-helix	300	1
β-strand	301	1	29
α-helix	302	1
β-strand	306-314	9	30
β-strand	320-326	7	30
β-strand	333-334	2	29
β-strand	337-340	4	31
β-strand	351	1	30
β-strand	357-358	2	29
β-strand	365-369	5	30
α-helix	371-372	2
β-strand	374	1	32
β-strand	377-380	4	31
β-strand	387-389	3	31
β-strand	393	1	32
α-helix	397-415	19
α-helix	417-421	5
α-helix	428-447	20
α-helix	453-468	16
α-helix	474-492	19

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	91-93	3
α-helix	110-114	5
α-helix	116-127	12
α-helix	129-142	14
α-helix	146-159	14

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	91-93	3
α-helix	116-127	12
α-helix	129-142	14
α-helix	146-162	17

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	91-93	3
α-helix	112-115	4
α-helix	116-127	12
α-helix	129-142	14
α-helix	146-163	18

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	38
β-strand	10-12	3	39
β-strand	17-25	9	38
α-helix	29-31	3
β-strand	32-39	8	39
β-strand	45-52	8	39
β-strand	57-59	3	39
β-strand	67-72	6	38
β-strand	77-82A	7	38
α-helix	84-86	3
β-strand	88-96	9	39
β-strand	102-103	2	39
β-strand	107-111	5	39

Chain I: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	33
α-helix	7-9	3
β-strand	10-12	3	34
β-strand	18-25	8	33
β-strand	32-39	8	34
β-strand	45-52	8	34
β-strand	57-59	3	34
α-helix	61-63	3
β-strand	67-70	4	33
β-strand	77-82	6	33
α-helix	84-86	3
β-strand	88-96	9	34
β-strand	103	1	34
β-strand	107-111	5	34

2 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
Core protein	A, B, C	protein	495	Dengue virus 2	P14340
Core protein	D, E, F	protein	75	Dengue virus 2	P14340
Single Chain Variable Fragment	H, I	protein	144	Homo sapiens
Single Chain Variable Fragment	L, M	protein	154	Homo sapiens

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

>7CTH_1 Core protein (chains A, B, C)
MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYC
IEAKLTNTTTDSRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFT
CKKNMKGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGT
VTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF
KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYS
MCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTE
KDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMIETTMRGAKRMAILGDTAW
DFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVSLV
LVGVVTLYLGVMVQA

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

>7CTH_2 Core protein (chains D, E, F)
SVALVPHVGMGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQR
ALIFILLTAVAPSMT

Sequence of entity 3 (H, I), FASTA

>7CTH_3 Single Chain Variable Fragment (chains H, I)
MAEVQLVESGAEVKKPGASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNT
KYSQKFQDRVTITRDTSASTAYMELSSLRSEDTAIYYCARDKVDDYGDYWFPTLWYFDYW
GQGTLVTVSSGTGGSGGGGSGGGG

Sequence of entity 4 (L, M), FASTA

>7CTH_4 Single Chain Variable Fragment (chains L, M)
SGGGASQSALTQPASVSGSPGQSITISCTGTSSDVGGFNYVSWFQQHPGKAPKLMLYDVT
SRPSGVSSRFSGSKSGNTASLTISGLQAEDEADYYCSSHTSRGTWVFGGGTKLTVLAAAD
DDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses. Sharma, A., Zhang, X., Dejnirattisai, W. et al. Cell (2021) 184:6052. DOI 10.1016/j.cell.2021.11.010 · 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)
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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