1RER: Structural polyprotein

Crystal structure of the homotrimer of fusion glycoprotein E1 from Semliki Forest Virus. Determined by X-ray diffraction at 3.2 Å resolution. Released 27 Jan 2004.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Semliki forest virus
Chains: 3
Atoms: 9,317
Mol. weight: 131.85 kDa
Ligands: HO, PO4
Released: 27 Jan 2004

Explore 1RER in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RER contains 25 α-helices and 108 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: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	15-19	5	2
β-strand	27-40	14	2
β-strand	46-48	3	3
β-strand	51-54	4	4
β-strand	59-60	2	5
β-strand	77-82	6	5
β-strand	101-106	6	5
β-strand	107-110	4	4
α-helix	114-116	3
β-strand	119-122	4	3
β-strand	126-137	12	2
β-strand	140-146	7	2
β-strand	153-156	4	6
β-strand	159-162	4	6
β-strand	177-179	3	3
β-strand	184-185	2	3
α-helix	192-194	3
β-strand	203-204	2	7
β-strand	205	1	3
β-strand	214-215	2	7
β-strand	220-221	2	8
α-helix	222-225	4
β-strand	233-234	2	8
α-helix	239-246	8
α-helix	251-253	3
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-280	6	1
β-strand	289-290	2	2
α-helix	293-295	3
β-strand	296-306	11	9
β-strand	307	1	10
β-strand	314-322	9	9
β-strand	326-329	4	11
β-strand	330-332	3	12
β-strand	338-339	2	9
β-strand	343-346	4	11
β-strand	351-357	7	9
β-strand	364-369	6	12
β-strand	372-377	6	12
α-helix	380	1
β-strand	381	1	10
α-helix	382-385	4

Chain B: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	13
β-strand	15-19	5	14
α-helix	26	1
β-strand	27-40	14	14
β-strand	46-48	3	15
β-strand	51-54	4	16
β-strand	59-61	3	17
β-strand	77-81	5	17
β-strand	101-106	6	17
β-strand	107-110	4	16
α-helix	114-116	3
β-strand	119-122	4	15
β-strand	126-137	12	14
β-strand	140-147	8	14
β-strand	153-156	4	18
β-strand	159-162	4	18
β-strand	177-179	3	15
β-strand	184-185	2	15
α-helix	192-194	3
β-strand	203-204	2	19
β-strand	205	1	15
β-strand	214-215	2	19
β-strand	220-221	2	20
α-helix	222-225	4
β-strand	233-234	2	20
α-helix	239-246	8
α-helix	251-253	3
β-strand	260-262	3	14
β-strand	267-269	3	14
β-strand	275-280	6	13
β-strand	289-290	2	14
α-helix	293-295	3
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	338-339	2	21
β-strand	343-346	4	23
β-strand	351-357	7	21
β-strand	364-369	6	24
β-strand	372-377	6	24
α-helix	380	1
β-strand	381	1	22
α-helix	382-385	4

Chain C: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	25
β-strand	15-19	5	26
β-strand	27-40	14	26
β-strand	46-48	3	27
β-strand	51-54	4	28
β-strand	59-60	2	29
α-helix	66-68	3
β-strand	77-81	5	29
β-strand	102-106	5	29
β-strand	107-110	4	28
α-helix	114-116	3
β-strand	119-122	4	27
β-strand	126-137	12	26
β-strand	140-146	7	26
β-strand	153-156	4	30
β-strand	159-162	4	30
β-strand	177-179	3	27
β-strand	184-185	2	27
α-helix	192-194	3
β-strand	203-204	2	31
β-strand	205	1	27
β-strand	214-215	2	31
β-strand	220-221	2	32
α-helix	222-225	4
β-strand	233-234	2	32
α-helix	239-246	8
α-helix	251-253	3
β-strand	260-262	3	26
β-strand	267-269	3	26
β-strand	275-280	6	25
β-strand	289-290	2	26
β-strand	296-306	11	33
β-strand	307	1	34
β-strand	314-322	9	33
β-strand	326-329	4	35
β-strand	330-332	3	36
β-strand	338-339	2	33
β-strand	343-346	4	35
β-strand	351-357	7	33
β-strand	364-369	6	36
β-strand	372-377	6	36
α-helix	380	1
β-strand	381	1	34
α-helix	382-385	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural polyprotein	A, B, C	protein	391	Semliki forest virus	P03315 (AlphaFold model)

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

>1RER_1 Structural polyprotein (chains A, B, C)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTNKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYA

Ligands and cofactors

ID	Name	Formula	Copies
HO	Holmium atom	Ho	4
PO4	Phosphate ion	O4 P	1

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

Primary citation

Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus. Gibbons, D.L., Vaney, M.C., Roussel, A. et al. Nature (2004) 427:320-325. DOI 10.1038/nature02239 · PubMed

Other PDB entries of the same protein (UniProt P03315 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2V33 1.55 Å, High resolution crystal structure of domain III of E1 fusion glycoprotein of Semliki…
1I9W 3.0 Å, Crystal structure of the fusion glycoprotein E1 from semliki forest virus
1VCP 3.0 Å, Semliki forest virus capsid protein (crystal form I)
2ALA 3.0 Å, Crystal structure of the Semliki Forest Virus envelope protein E1 in its monomeric…
8IHP 3.0 Å, Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3
8YVY 3.02 Å, Semliki Forest virus virion
1VCQ 3.1 Å, Semliki forest virus capsid protein (crystal form II)
8YW1 3.44 Å, Semliki Forest virus viron in complex with VLDLR
8YVZ 3.45 Å, Semliki Forest virus viron
8X0K 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)
8X0L 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)
8X0M 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(5-fold)

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