3RU8: HIV epitope scaffold

Structure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab. Determined by X-ray diffraction at 2.07 Å resolution. Released 2 Nov 2011.

Method: X-ray diffraction
Resolution: 2.07 Å
Organisms: Human immunodeficiency virus, synthetic construct, Thermomonospora fusca
Chains: 3
Atoms: 5,881
Mol. weight: 79.06 kDa
Released: 2 Nov 2011

Explore 3RU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RU8 contains 30 α-helices and 59 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 H: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-51	7	7
β-strand	57-59	3	7
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-94	7	7
α-helix	97-99	3
α-helix	100B-100C	2
β-strand	102-103	2	7
β-strand	107-111	5	7
α-helix	114-116	3
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	134	1	9
β-strand	137-147	11	9
β-strand	148	1	8
β-strand	153-157	4	10
α-helix	162-164	3
β-strand	166	1	10
β-strand	171-173	3	9
α-helix	174-176	3
β-strand	177-178	2	9
β-strand	185-194	10	9
α-helix	195-197	3
β-strand	207-212	6	10
α-helix	213-215	3
β-strand	217-222	6	10

Chain L: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-29	11	11
β-strand	34-39	6	12
β-strand	46-50	5	12
β-strand	54-55	2	12
α-helix	56	1
β-strand	63-76	14	11
α-helix	81-83	3
β-strand	85-91	7	12
β-strand	98-99	2	12
β-strand	103-107	5	12
β-strand	112	1	13
α-helix	113-114	2
β-strand	115-119	5	14
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	14
β-strand	141	1	13
β-strand	146-151	6	15
β-strand	154-155	2	15
β-strand	160-164	5	14
α-helix	165-168	4
β-strand	174-183	10	14
α-helix	184-187	4
β-strand	192-198	7	15
β-strand	206-211	6	15

Chain X: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	11-18	8
α-helix	25-28	4
α-helix	29-33	5
β-strand	37	1	2
β-strand	39-41	3	3
α-helix	49-63	15
β-strand	66	1	1
α-helix	67	1
β-strand	68-71	4	3
α-helix	83-95	13
β-strand	103-106	4	3
α-helix	115-135	21
β-strand	140-144	5	3
α-helix	153-162	10
α-helix	165-168	4
β-strand	171-174	4	3
α-helix	182-196	15
β-strand	202-206	5	3
β-strand	215	1	4
β-strand	218	1	4
β-strand	232	1	3
β-strand	240-244	5	3
β-strand	245	1	2
β-strand	251	1	5
β-strand	262	1	5
α-helix	264-275	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epitope Scaffold 2bodx43	X	protein	282	Human immunodeficiency virus, synthetic construct, Thermomonospora fusca
Antibody b12, Heavy Chain	H	protein	230	Homo sapiens
Antibody b12, Light Chain	L	protein	215	Homo sapiens	P01834 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>3RU8_1 Epitope Scaffold 2bodx43 (chains X)
DSPFYVNPNMSSAEWVRNNPNDPRTPVIRNRIASVPQGTWHNQHNPGQITGQVDALMSAA
QAAGKIPILVVDVGPTGDMSQGEEAGKQWIDEFAAGLKNRPAYIIVYPLYSGGDPEIVQE
WLRTVAYAGKALKAGSSQARIYFDAGHSAWHSPAQMAAALQRADISNSAHGIATNTSNYR
WTADEVAYAKAVLSAIGNPSLRAVIDTSRNGNGPAGNESCDPSGRAIGTPSTTNTGDPMI
DAFLWIKLPGEADGCIAGAGQFVPQAAYEMAIAALEHHHHHH

Sequence of entity 2 (H), FASTA

>3RU8_2 Antibody b12, Heavy Chain (chains H)
QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEF
SAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKG
TTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L), FASTA

>3RU8_3 Antibody b12, Light Chain (chains L)
EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGIS
DRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Primary citation

Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Azoitei, M.L., Correia, B.E., Ban, Y.E. et al. Science (2011) 334:373-376. DOI 10.1126/science.1209368 · PubMed

Other PDB entries of the same protein (UniProt P01834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
1NGZ 1.6 Å, Chimeric Germline Fab 7g12-apo
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement
4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with…
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
3VH8 1.8 Å, KIR3DL1 in complex with HLA-B*5701
3X12 1.8 Å, Crystal structure of HLA-B*57:01.I80N
6B9Z 1.82 Å, Trastuzumab Fab v3
2VXQ 1.9 Å, Crystal structure of the major grass pollen allergen Phl p 2 in complex with its…
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
6DCV 1.9 Å, Crystal structure of human anti-tau antibody CBTAU-27.1

Browse structure collections

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