3N40: P62 envelope glycoprotein

Crystal structure of the immature envelope glycoprotein complex of Chikungunya virus. Determined by X-ray diffraction at 2.17 Å resolution. Released 1 Dec 2010.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Chikungunya virus
Chains: 2
Atoms: 6,669
Mol. weight: 89.37 kDa
Ligands: NAG
Released: 1 Dec 2010

Explore 3N40 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3N40 contains 22 α-helices and 75 β-strands across 2 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 F: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	1-8	8	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	189-191	3
α-helix	195-196	2
β-strand	203-204	2	19
β-strand	205	1	14
β-strand	214-215	2	19
β-strand	220-221	2	20
α-helix	223-225	3
β-strand	233-234	2	20
α-helix	239-246	8
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	14
β-strand	267-269	3	14
β-strand	275-282	8	13
α-helix	284-286	3
β-strand	289	1	15
α-helix	294-295	2
β-strand	296-306	11	21
β-strand	307	1	22
β-strand	314-322	9	21
β-strand	326-329	4	23
β-strand	330-332	3	24
β-strand	337-339	3	21
β-strand	343-346	4	23
β-strand	349-358	10	21
β-strand	362-369	8	24
β-strand	372-379	8	24
α-helix	380	1
β-strand	381	1	22
α-helix	382-383	2
β-strand	387-388	2	12

Chain P: 11 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
β-strand	13-16	4	1
α-helix	26-29	4
α-helix	31-40	10
α-helix	47-54	8
α-helix	72-74	3
β-strand	76	1	2
β-strand	81-83	3	3
β-strand	85	1	4
β-strand	92-94	3	3
β-strand	98-102	5	5
β-strand	110-120	11	5
β-strand	126-135	10	5
β-strand	138-143	6	5
β-strand	148-150	3	4
β-strand	154	1	4
β-strand	156-168	13	5
β-strand	172-180	9	4
β-strand	186-195	10	4
α-helix	197-199	3
β-strand	203	1	6
α-helix	208-209	2
β-strand	213-220	8	7
β-strand	230-234	5	8
β-strand	239-240	2	9
α-helix	242-244	3
β-strand	245-248	4	10
β-strand	251-254	4	10
β-strand	261-265	5	9
β-strand	272-275	4	9
β-strand	279-281	3	10
α-helix	286-288	3
β-strand	289-293	5	9
β-strand	299	1	2
β-strand	300-301	2	8
α-helix	307-309	3
β-strand	317-320	4	8
β-strand	325-332	8	7
α-helix	335-338	4
β-strand	339-343	5	11
β-strand	346-351	6	11
β-strand	357-363	7	6
β-strand	371-375	5	6
β-strand	379-384	6	11
β-strand	390-394	5	6
α-helix	398-399	2
β-strand	400-402	3	6
β-strand	403-404	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
P62 envelope glycoprotein	P	protein	401	Chikungunya virus	Q1H8W5
E1 envelope glycoprotein	F	protein	393	Chikungunya virus	Q1H8W5

Sequence of entity 1 (P), FASTA

>3N40_1 P62 envelope glycoprotein (chains P)
PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRE
STKDNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDD
SHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRK
ISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTL
MSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSP
LVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNM
GEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQ

Sequence of entity 2 (F), FASTA

>3N40_2 E1 envelope glycoprotein (chains F)
GGYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSP
YVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEF
ASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIV
VYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPS
GFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTD
MSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFST
ALASAEFRVQVCSTQVHCAAECHPPKDHIVNYP

Ligands and cofactors

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

Water and common crystallization additives (ACT) are not listed.

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:

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…
3N42 3.0 Å, Crystal structures of the mature envelope glycoprotein complex (furin 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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