6DC3: RSV prefusion F

RSV prefusion F bound to RSD5 Fab. Determined by X-ray diffraction at 3.5 Å resolution. Released 10 Jul 2019.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Homo sapiens, Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1
Chains: 3
Atoms: 6,890
Mol. weight: 112.18 kDa
Ligands: NAG
Released: 10 Jul 2019

Explore 6DC3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DC3 contains 34 α-helices and 76 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 F: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	16
β-strand	38-60	23	16
α-helix	74-96	23
α-helix	138-141	4
α-helix	149-158	10
α-helix	163-170	8
β-strand	176-180	5	16
β-strand	186-194	9	16
α-helix	195-198	4
α-helix	199-203	5
α-helix	204-207	4
α-helix	217-238	22
β-strand	243-244	2	16
α-helix	247-248	2
α-helix	254-262	9
α-helix	268-275	8
α-helix	278-283	6
β-strand	286-293	8	16
β-strand	296-318	23	16
β-strand	321-322	2	17
β-strand	333-336	4	17
β-strand	340-345	6	16
β-strand	348-352	5	16
α-helix	355-357	3
β-strand	359-361	3	16
β-strand	364-368	5	16
α-helix	369-371	3
β-strand	373-375	3	16
α-helix	377-380	4
α-helix	381-384	4
β-strand	394-398	5	17
β-strand	404-407	4	18
β-strand	411-416	6	18
β-strand	422-426	5	19
β-strand	430-434	5	19
β-strand	438-443	6	18
β-strand	449-452	4	19
β-strand	455-458	4	19
α-helix	459-460	2
β-strand	465-469	5	16
α-helix	474-477	4
β-strand	490-491	2	17
α-helix	492-510	19

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	3
α-helix	100D-100G	4
β-strand	100J-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
β-strand	121-124	4	5
α-helix	125-127	3
α-helix	128-131	4
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	194-200	7	6
β-strand	205-211	7	6

Chain L: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4	1	7
β-strand	5	1	8
β-strand	9-13	4	9
β-strand	15	1	10
β-strand	18-21	4	8
β-strand	24	1	8
β-strand	33-38	6	9
α-helix	43	1
β-strand	44-48	5	9
β-strand	49	1	11
β-strand	53	1	11
β-strand	56	1	12
β-strand	58	1	12
β-strand	62-67	6	8
β-strand	70-76	7	8
β-strand	78	1	10
α-helix	80-82	3
β-strand	85-91	7	9
β-strand	96-98	3	9
β-strand	99	1	7
β-strand	102-106	5	9
β-strand	112	1	13
β-strand	115-119	5	14
α-helix	120-122	3
α-helix	126-128	3
β-strand	131-140	10	14
β-strand	141	1	13
β-strand	146-151	6	15
β-strand	154-156	3	15
β-strand	160-162	3	14
α-helix	163-165	3
β-strand	166-167	2	14
β-strand	173-181	9	14
α-helix	183-187	5
β-strand	192-198	7	15
β-strand	201-207	7	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab RSD5-Germline Heavy Chain	H	protein	230	Homo sapiens	Q6N089 (AlphaFold model)
Fab RSD5-Germline Light Chain	L	protein	216	Homo sapiens	Q8N355 (AlphaFold model)
RSV fusion glycoprotein	F	protein	568	Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1, unidentified	M1E1E4 (AlphaFold model), P03420

Sequence of entity 1 (H), FASTA

>6DC3_1 Fab RSD5-Germline Heavy Chain (chains H)
QVQLVESGGGVVQPGRSLRLSCAASGFAFNNFAMHWVRQAPGKGLEWVAVVSYDGTSPYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGLGSGSYSWIGYFYAMDVWGQG
TTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (L), FASTA

>6DC3_2 Fab RSD5-Germline Light Chain (chains L)
QSALTQPASVSGSPGQSITISCTGTSSDVGGYVYVSWYQQHPGKAPKLMIYDVSNRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCISYTDRNTVVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (F), FASTA

>6DC3_3 RSV fusion glycoprotein (chains F)
MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIE
LSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRELPRFMNYTLN
NAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVS
LSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVN
AGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYV
VQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKV
QSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKT
KCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDP
LVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLL
STFLGGLVPRGSHHHHHHSAWSHPQFEK

Ligands and cofactors

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

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

Primary citation

Alternative conformations of a major antigenic site on RSV F. Jones, H.G., Battles, M.B., Lin, C.C. et al. PLoS Pathog (2019) 15:e1007944-e1007944. DOI 10.1371/journal.ppat.1007944 · PubMed

Other PDB entries of the same protein (UniProt Q6N089 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HPY 1.5 Å, Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide
5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
3QCU 1.98 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3QCT 2.15 Å, Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab…
3MNV 2.4 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
3QCV 2.51 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5XRQ 2.6 Å, Crystal structure of human monoclonal antibody H3v-47
2OQJ 2.8 Å, Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006

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