2R29: Envelope protein E

Neutralization of dengue virus by a serotype cross-reactive antibody elucidated by cryoelectron microscopy and x-ray crystallography. Determined by X-ray diffraction at 3.0 Å resolution. Released 25 Dec 2007.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Dengue virus 2 Thailand/16681/84, Mus musculus
Chains: 3
Atoms: 4,234
Mol. weight: 57.97 kDa
Released: 25 Dec 2007

Explore 2R29 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2R29 contains 9 α-helices and 61 β-strands across 3 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: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	301	1	1
α-helix	302	1
β-strand	305-314	10	2
β-strand	320-327	8	2
β-strand	334	1	1
β-strand	337	1	3
β-strand	340	1	4
β-strand	350-351	2	2
α-helix	364	1
β-strand	365-366	2	2
β-strand	369-370	2	2
β-strand	377	1	4
β-strand	380	1	3
β-strand	387	1	3
β-strand	390	1	4

Chain H: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	5
β-strand	18-23	6	6
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	59-60	2	7
α-helix	62-64	3
β-strand	70	1	6
β-strand	73	1	6
β-strand	78-83	6	6
β-strand	92-95	4	7
β-strand	110-112	3	7
β-strand	113-114	2	5
α-helix	118-119	2
β-strand	124-127	4	8
β-strand	141	1	9
β-strand	142-148	7	8
β-strand	154-156	3	10
β-strand	166	1	9
β-strand	169	1	8
β-strand	178-181	4	8
β-strand	184	1	9
β-strand	197-202	6	10
α-helix	203-205	3
β-strand	207-212	6	10

Chain L: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	11
β-strand	12-13	2	12
β-strand	19-21	3	13
β-strand	23	1	11
β-strand	30	1	14
β-strand	35	1	14
β-strand	37-42	6	15
β-strand	50	1	15
β-strand	52	1	16
α-helix	57	1
β-strand	58	1	16
α-helix	59	1
β-strand	67-70	4	13
β-strand	75-79	5	13
β-strand	89-94	6	15
β-strand	102	1	15
β-strand	106-107	2	15
β-strand	109-110	2	12
α-helix	114-115	2
β-strand	122	1	17
α-helix	123-125	3
β-strand	133	1	18
β-strand	136-137	2	17
β-strand	143	1	19
β-strand	151	1	20
β-strand	163-167	5	17
β-strand	177	1	19
β-strand	179-183	5	17
β-strand	186	1	18
β-strand	195-200	6	20
β-strand	205-210	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein E	A	protein	97	Dengue virus 2 Thailand/16681/84	P29991
Heavy chain of Fab 1A1D-2	H	protein	216	Mus musculus	P01863 (AlphaFold model)
Light chain of Fab 1A1D-2	L	protein	217	Mus musculus	P01660 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2R29_1 Envelope protein E (chains A)
SYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPI
VTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKK

Sequence of entity 2 (H), FASTA

>2R29_2 Heavy chain of Fab 1A1D-2 (chains H)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGYSKY
DPKFQGKATITADTSSNAAYLQLSSLTSEDTAVYFCARDYEGFAYWGQGTLVTVSSAKTT
PPSVYPLAPGAAAATSSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVTSSTWPSQTITCNVAHPASSTKVDKKIEPR

Sequence of entity 3 (L), FASTA

>2R29_3 Light chain of Fab 1A1D-2 (chains L)
DIVLTQSPASLAVSLGQRATISCRASESVVRYGNSFMHWYQQKPGQPPKLLIYRASSLES
GIPTRFSGSGSRTDFTLTINPVEADDVATYYCQQTNVDPWAFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Primary citation

Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins. Lok, S.M., Kostyuchenko, V., Nybakken, G.E. et al. Nat Struct Mol Biol (2008) 15:312-317. DOI 10.1038/nsmb.1382 · PubMed

Other PDB entries of the same protein (UniProt P29991), best resolution first:

3EVG 2.2 Å, Crystal structure of Dengue-2 virus methyltransferase complexed with…
6FLA 2.9 Å, 3H5 Fab bound to EDIII of DenV 2 Xtal form 1

Browse structure collections

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