4XMP: Broadly and potently neutralizing antibody VRC08

Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with HIV-1 clade A strain Q842.d12 gp120. Determined by X-ray diffraction at 1.78 Å resolution. Released 29 Apr 2015.

Method: X-ray diffraction
Resolution: 1.78 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,842
Mol. weight: 90.55 kDa
Ligands: NAG, BU3
Released: 29 Apr 2015

Explore 4XMP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XMP contains 29 α-helices and 74 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 G: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	74-76	3	2
α-helix	77-78	2
β-strand	84-86	3	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-122	3	4
β-strand	201-202	2	4
β-strand	215	1	5
β-strand	216-218	3	2
α-helix	219-220	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	5
β-strand	259-261	3	6
β-strand	271-273	3	6
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-349	15
β-strand	358-361	4	6
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
β-strand	393-395	3	6
β-strand	413-421	9	6
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	6
β-strand	465-470	6	6
α-helix	476-483	8
β-strand	486-490	5	1

Chain H: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	8
α-helix	100G-100I	3
β-strand	102-103	2	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	132	1	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	189	1	12
β-strand	192	1	12
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	10-13	4	14
β-strand	19-25	7	13
α-helix	30-32	3
β-strand	33-38	6	14
α-helix	43-44	2
β-strand	45-49	5	14
β-strand	53-54	2	14
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-154	2	17
α-helix	155	1
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-188	6
β-strand	191-197	7	17
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160	G	protein	354	Human immunodeficiency virus 1	Q8JDI3
Heavy chain of antibody VRC08	H	protein	235	Homo sapiens	P01857 (AlphaFold model)
Light chain of antibody VRC08	L	protein	211	Homo sapiens	P01834 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>4XMP_1 Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 (chains G)
VWKEAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQ
MHTDIISLWDQSLKPCVKLTGGSAITQACPKVTFEPIPIHYCAPAGFAILKCKDEEFNGI
GPCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKEVKIRCENITNNAKTIIVQLVNPVKINC
TRPNNGGSGSGGDIRQAHCNVNRTEWNNTLHQVVEQLRKHFNKTINFANSTGGDLEITTH
SFNCGGEFFYCNTTNLFNSTWNHTASMNSTESNDTIILPCRIKQIINMWQRVGQAMYAPP
IRGVIRCESNITGLILTRDGGNTNSTRETFRPGGGDMRDNWRSELYKYKVVKIE

Sequence of entity 2 (H), FASTA

>4XMP_2 HEAVY CHAIN OF ANTIBODY VRC08 (chains H)
QVQLVQSGTQMKEPGASVTISCVTSGYEFVEILINWVRQVPGRGLEWMGWMNPRGGGVNY
ARQFQGKVTMTRDVYRDTAYLTLSGLTSGDTAKYFCVRGRSCCGGRRHCNGADCFNWDFQ
HWGQGTLVIVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L), FASTA

>4XMP_3 LIGHT CHAIN OF ANTIBODY VRC08 (chains L)
YIGVTQSPAILSVSLGERVTLSCKTSQAITPRHLVWHRQKGGQAPSLVMTGTSERASGIP
DRFIGSGSGTDFTLTITRLEAEDFAVYYCQCLEAFGQGTKLEIKRTVAAPSVFIFPPSDE
QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK
ADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11
BU3	(r,r)-2,3-butanediol	C4 H10 O2	2

Primary citation

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Wu, X., Zhang, Z., Schramm, C.A. et al. Cell (2015) 161:470-485. DOI 10.1016/j.cell.2015.03.004 · PubMed

Other PDB entries of the same protein (UniProt Q8JDI3), best resolution first:

4XNY 2.3 Å, Crystal structure of broadly and potently neutralizing antibody VRC08C in complex with…
4RX4 3.45 Å, Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134…

Browse structure collections

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