5C69: Prefusion-stabilized RSV F variant PR-DM

Crystal Structure of Prefusion-stabilized RSV F variant PR-DM. Determined by X-ray diffraction at 2.3 Å resolution. Released 23 Sept 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Human respiratory syncytial virus A, Enterobacteria phage Ox2
Chains: 1
Atoms: 3,698
Mol. weight: 55.71 kDa
Ligands: NHE
Released: 23 Sept 2015

Explore 5C69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C69 contains 20 α-helices and 24 β-strands across 1 chain. 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: 20 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	1
β-strand	38-60	23	1
α-helix	74-96	23
α-helix	111-114	4
α-helix	122-130	9
α-helix	136-143	8
β-strand	149-153	5	1
β-strand	159-167	9	1
α-helix	168-171	4
α-helix	172-176	5
α-helix	178-180	3
α-helix	187-189	3
α-helix	190-212	23
β-strand	216-217	2	1
α-helix	220-221	2
α-helix	227-235	9
α-helix	241-248	8
α-helix	251-256	6
β-strand	259-266	8	1
β-strand	269-291	23	1
β-strand	294-295	2	2
β-strand	306-309	4	2
β-strand	313-318	6	1
β-strand	321-325	5	1
α-helix	328-330	3
β-strand	332-334	3	1
β-strand	337-341	5	1
α-helix	342-344	3
β-strand	346-348	3	1
α-helix	350-353	4
α-helix	354-357	4
β-strand	367-371	5	2
β-strand	377-380	4	3
β-strand	384-389	6	3
β-strand	395-399	5	4
β-strand	403-407	5	4
β-strand	411-416	6	3
β-strand	422-425	4	4
β-strand	428-431	4	4
α-helix	432-433	2
β-strand	438-442	5	1
α-helix	447-450	4
β-strand	463-464	2	2
α-helix	465-478	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fusion glycoprotein F0,Fibritin	A	protein	492	Human respiratory syncytial virus A, Enterobacteria phage Ox2	P03420, Q38650

Sequence of entity 1 (A), FASTA

>5C69_1 Fusion glycoprotein F0,Fibritin (chains A)
QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKEIKCNGTDAKVKLIKQELDK
YKNAVTELQLLMQSTPATNNRARRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALL
STNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSIPNIETVIEFQQKNNRLLE
ITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSII
KEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFF
PQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGA
IVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGE
PIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVR
KDGEWVLLSTFL

Ligands and cofactors

ID	Name	Formula	Copies
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	2

Water and common crystallization additives (CL, SO4) are not listed.

Primary citation

A highly stable prefusion RSV F vaccine derived from structural analysis of the fusion mechanism. Krarup, A., Truan, D., Furmanova-Hollenstein, P. et al. Nat Commun (2015) 6:8143-8143. DOI 10.1038/ncomms9143 · PubMed

Other PDB entries of the same protein (UniProt P03420), best resolution first:

29QJ 1.32 Å, Respiratory syncytial virus fusion protein N-terminal heptad repeat domain in complex…
6OJ7 1.45 Å, Respiratory syncytial virus fusion glycoprotein N-terminal heptad repeat domain+VIQKI…
3KPE 1.47 Å, Solution structure of the respiratory syncytial virus (RSV)six-helix bundle complexed…
9RA5 1.63 Å, Respiratory syncytial virus fusion protein N-terminal heptad repeat domain in complex…
3O41 1.95 Å, Crystal Structure of 101F Fab Bound to 15-mer Peptide Epitope
9VWE 2.06 Å, Cryo-EM structure of RSV pre-F (strain A2) in complex with Fabs 1A2 and 2D10
6VKE 2.1 Å, Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein
7LVW 2.1 Å, Structure of RSV F in Complex with VHH Cl184
6NTX 2.2 Å, Respiratory syncytial virus fusion protein N-terminal heptad repeat domain+VIQKI
8DG9 2.24 Å, Cryo-EM Structure of RSV prefusion F trimer in complex with three MxR Fabs
8PHI 2.29 Å, Crystal structure of prefusion-stabilized RSV F Variant DS-Cav1 in complex with Lonafarnib
5EA4 2.3 Å, Crystal Structure of Inhibitor JNJ-49153390 in Complex with Prefusion RSV F Glycoprotein

Browse structure collections

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