3N42: E3 envelope glycoprotein

Crystal structures of the mature envelope glycoprotein complex (furin cleavage) of Chikungunya virus. Determined by X-ray diffraction at 3.0 Å resolution. Released 1 Dec 2010.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Chikungunya virus
Chains: 3
Atoms: 6,205
Mol. weight: 99.07 kDa
Ligands: NAG
Released: 1 Dec 2010

Explore 3N42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3N42 contains 21 α-helices and 74 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: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
β-strand	15	1	1
α-helix	26-29	4
α-helix	31-39	9
α-helix	47-54	8

Chain B: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	2
β-strand	17-19	3	3
β-strand	21	1	4
β-strand	28-30	3	3
β-strand	34-38	5	5
β-strand	46-56	11	5
β-strand	62-71	10	5
β-strand	74-79	6	5
β-strand	84-86	3	4
β-strand	90	1	4
β-strand	92-104	13	5
β-strand	108-116	9	4
β-strand	122-131	10	4
α-helix	133-135	3
β-strand	139	1	6
α-helix	144-145	2
β-strand	149-156	8	7
β-strand	166-170	5	8
β-strand	175-176	2	9
α-helix	178-180	3
β-strand	181-182	2	10
β-strand	188-190	3	10
β-strand	197-201	5	9
β-strand	210-211	2	9
β-strand	215-217	3	10
α-helix	222-224	3
β-strand	225-229	5	9
β-strand	235	1	2
β-strand	236-237	2	8
α-helix	243-245	3
β-strand	253-256	4	8
β-strand	261-268	8	7
α-helix	271-274	4
β-strand	275-279	5	11
β-strand	282-287	6	11
β-strand	293-299	7	6
β-strand	307-311	5	6
β-strand	315-320	6	11
β-strand	326-330	5	6
α-helix	334-335	2
β-strand	336-338	3	6
β-strand	339-340	2	12

Chain F: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	0-8	9	13
β-strand	15-19	5	14
β-strand	24	1	15
β-strand	27-48	22	14
β-strand	51-54	4	16
β-strand	59-61	3	17
β-strand	77-82	6	17
β-strand	87-88	2	18
β-strand	91-92	2	18
β-strand	101-106	6	17
β-strand	107-110	4	16
α-helix	112-115	4
β-strand	119-137	19	14
β-strand	140-147	8	14
β-strand	153-156	4	13
β-strand	159-163	5	13
β-strand	176-180	5	14
β-strand	183-186	4	14
α-helix	195-196	2
β-strand	203-205	3	14
β-strand	213-215	3	14
β-strand	220-221	2	19
α-helix	223-225	3
β-strand	233-234	2	19
α-helix	239-243	5
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	14
β-strand	267-269	3	14
β-strand	275-283	9	13
α-helix	284-286	3
β-strand	289	1	15
α-helix	294-295	2
β-strand	296-305	10	20
β-strand	307	1	21
β-strand	314-322	9	20
β-strand	326-329	4	22
β-strand	330-332	3	23
β-strand	337-339	3	20
β-strand	343-346	4	22
β-strand	351-358	8	20
β-strand	362-369	8	23
β-strand	372-379	8	23
α-helix	380	1
β-strand	381	1	21
α-helix	382-383	2
β-strand	387-388	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 envelope glycoprotein	A	protein	65	Chikungunya virus	Q1H8W5
E2 envelope glycoprotein	B	protein	360	Chikungunya virus	Q1H8W5
E1 envelope glycoprotein	F	protein	473	Chikungunya virus	Q1H8W5

Sequence of entity 1 (A), FASTA

>3N42_1 E3 envelope glycoprotein (chains A)
MSLAIPVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSP
HRQRR

Sequence of entity 2 (B), FASTA

>3N42_2 E2 envelope glycoprotein (chains B)
STKDNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDD
SHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRK
ISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTL
MSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSP
LVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNM
GEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYY

Sequence of entity 3 (F), FASTA

>3N42_3 E1 envelope glycoprotein (chains F)
ELYGGGGSGGGGSGGGGSGGGGYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTL
EPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDA
ENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKD
AKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQ
LVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPI
SIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVT
IREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLG
VQDISATAMSWVQKGPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography. Voss, J.E., Vaney, M.C., Duquerroy, S. et al. Nature (2010) 468:709-712. DOI 10.1038/nature09555 · PubMed

Other PDB entries of the same protein (UniProt Q1H8W5), best resolution first:

3N40 2.17 Å, Crystal structure of the immature envelope glycoprotein complex of Chikungunya virus.
3N44 2.35 Å, Crystal structure of the mature envelope glycoprotein complex (trypsin cleavage; Osmium…
3N43 2.58 Å, Crystal structures of the mature envelope glycoprotein complex (trypsin cleavage) of…
3N41 3.01 Å, Crystal structure of the mature envelope glycoprotein complex (spontaneous cleavage) of…
9IW2 3.2 Å, Chikungunya virus E protein complexed with C37 Fab
3J2W 5.0 Å, Electron cryo-microscopy of Chikungunya virus
2XFB 9.0 Å, Chikungunya E1 E2 envelope glycoproteins fitted in sindbis virus cryo- EM map
2XFC 9.0 Å, Chikungunya E1 E2 envelope glycoproteins fitted in semliki forest virus cryo-EM map
5ANY 16.9 Å, Electron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab…

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