4XNY: PDB entry 4XNY

Crystal structure of broadly and potently neutralizing antibody VRC08C in complex with HIV-1 clade A strain Q842.d12 gp120. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 Apr 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,386
Mol. weight: 90.33 kDa
Ligands: NAG
Released: 29 Apr 2015

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

Secondary structure: helices and β-sheets

4XNY contains 25 α-helices and 75 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	47	1	1
α-helix	52	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	83-85	3	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-123	4	4
β-strand	199-202	4	4
β-strand	215	1	5
β-strand	216-218	3	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: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
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	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
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
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	136-145	10	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	176-184	9	10
α-helix	186-188	3
β-strand	189	1	12
β-strand	192	1	12
β-strand	194-200	7	11
β-strand	205-211	7	11

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	28	1	15
α-helix	30-32	3
β-strand	34-38	5	14
β-strand	45-48	4	14
β-strand	54	1	14
β-strand	62-67	6	13
β-strand	68	1	15
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	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-154	2	18
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-182	10	17
α-helix	183-188	6
β-strand	191-197	7	18
β-strand	205-210	6	18

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 VRC08C	H	protein	235	Homo sapiens	P01857 (AlphaFold model)
Light chain of antibody VRC08C	L	protein	211	Homo sapiens	P01834 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>4XNY_1 Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 (chains G)
VWKEAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQ
MHTDIISLWDQSLKPCVKLTGGSAITQACPKVTFEPIPIHYCAPAGFAILKCKDEEFNGI
GPCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKEVKIRCENITNNAKTIIVQLVNPVKINC
TRPNNGGSGSGGDIRQAHCNVNRTEWNNTLHQVVEQLRKHFNKTINFANSTGGDLEITTH
SFNCGGEFFYCNTTNLFNSTWNHTASMNSTESNDTIILPCRIKQIINMWQRVGQAMYAPP
IRGVIRCESNITGLILTRDGGNTNSTRETFRPGGGDMRDNWRSELYKYKVVKIE

Sequence of entity 2 (H), FASTA

>4XNY_2 HEAVY CHAIN OF ANTIBODY VRC08C (chains H)
QHSQVQSGTQIKTPGASVTLSCGTSGYDFMESLINWVRQEIGKRPEWLGWMNPRGGGVNY
AQRFQGKVTMTRDVSSGTAYLTLRGLTSDDTAKYYCVRGKSCCNGRRYCNGADCFNWDFE
YWGQGTLVIVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L), FASTA

>4XNY_3 LIGHT CHAIN OF ANTIBODY VRC08C (chains L)
YIGLTQSPGTLSVSPGERATLSCRPSQAISKSHLAWYSQKSGQPPRLLLTGTYERASGVP
DRFVGSGSGTNYTLTIASVEAEDFAVYFCQCFEGFGQGTKLEIKRTVAAPSVFIFPPSDE
QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK
ADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

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:

4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 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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