4R2G: PGT124 Fab

Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4. Determined by X-ray diffraction at 3.28 Å resolution. Released 8 Oct 2014.

Method: X-ray diffraction
Resolution: 3.28 Å
Organisms: Human immunodeficiency virus type 1 group M subtype B, Homo sapiens
Chains: 16
Atoms: 29,158
Mol. weight: 428.76 kDa
Ligands: NAG
Released: 8 Oct 2014

Explore 4R2G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R2G contains 92 α-helices and 365 β-strands across 16 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 A: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	93-94	2	88
α-helix	95-97	3
α-helix	100-115	16
β-strand	120-122	3	89
β-strand	200-202	3	89
α-helix	212-214	3
β-strand	218	1	90
α-helix	219-220	2
β-strand	223-228	6	91
β-strand	236-237	2	88
β-strand	242-245	4	91
β-strand	247	1	90
α-helix	251-253	3
β-strand	257	1	92
β-strand	259-261	3	93
α-helix	263-266	4
β-strand	271-273	3	93
β-strand	284-298	15	93
β-strand	330-334	5	93
α-helix	335-352	18
β-strand	358-361	4	93
β-strand	367	1	65
α-helix	369-372	4
β-strand	374-378	5	94
β-strand	381-385	5	94
β-strand	393-395	3	93
β-strand	401	1	93
β-strand	413-417	5	93
β-strand	418-421	4	94
β-strand	423-425	3	89
β-strand	432-434	3	89
α-helix	438	1
β-strand	443-456	14	93
β-strand	465-470	6	93
β-strand	472	1	92
α-helix	475-483	9
β-strand	488-490	3	91

Chain B: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	27
β-strand	12-14	3	28
β-strand	17	1	29
β-strand	26-29	4	27
β-strand	35-40	6	27
β-strand	43-46	4	27
α-helix	50-52	3
β-strand	55-56	2	28
α-helix	59-64	6
β-strand	66	1	29
β-strand	69-71	3	28
β-strand	80-86	7	27
β-strand	90-98	9	27
β-strand	99-101	3	30
α-helix	102	1
β-strand	114-119	6	30
β-strand	127-131	5	31
β-strand	137-140	4	31
β-strand	143-146	4	30
α-helix	151-153	3
β-strand	155-163	9	31
β-strand	166-174	9	31

Chain C: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	6	32
β-strand	19-22	4	33
β-strand	32-38	7	32
β-strand	45-48	4	32
β-strand	62-63	2	33
β-strand	72-75	4	33
α-helix	80-82	3
β-strand	84-91	8	32
β-strand	97	1	34
β-strand	101-106A	7	32
α-helix	108-111	3
β-strand	112	1	35
β-strand	117-119	3	36
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	36
β-strand	141	1	35
β-strand	146-151	6	37
β-strand	154-155	2	37
β-strand	160-162	3	36
β-strand	173-181	9	36
α-helix	183-188	6
β-strand	192-198	7	37
β-strand	201-207	7	37

Chain D: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	38
β-strand	11-12	2	39
α-helix	17	1
β-strand	18-24	7	38
β-strand	33-39	7	34
β-strand	45-51	7	34
β-strand	57-59	3	34
α-helix	61-63	3
β-strand	67-72	6	38
β-strand	77-82	6	38
α-helix	84-86	3
β-strand	88-100	13	34
β-strand	100K-103	9	34
β-strand	107-109	3	34
β-strand	110-111	2	39
β-strand	135	1	40
β-strand	139-142	4	41
β-strand	153-163	11	41
β-strand	164	1	40
β-strand	169-172	4	42
β-strand	181-183	3	41
α-helix	184-185	2
β-strand	188	1	41
β-strand	194-203	10	41
β-strand	213-217	5	42
β-strand	224	1	42
β-strand	227-228	2	42

Chain E: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	95-97	3
α-helix	100-115	16
β-strand	120-122	3	1
β-strand	202	1	1
α-helix	212-214	3
β-strand	215	1	2
β-strand	218	1	3
α-helix	219-220	2
β-strand	223-228	6	4
β-strand	242-245	4	4
β-strand	247	1	3
α-helix	248-250	3
β-strand	251	1	2
β-strand	259-261	3	5
α-helix	263-266	4
β-strand	271-273	3	5
α-helix	283	1
β-strand	284-298	15	5
β-strand	330-334	5	5
α-helix	335-352	18
β-strand	358-361	4	5
β-strand	367	1	6
α-helix	369-372	4
β-strand	374-378	5	7
β-strand	381-385	5	7
α-helix	388-390	3
β-strand	393-395	3	5
β-strand	401-402	2	5
β-strand	413-417	5	5
β-strand	418-421	4	7
β-strand	423-425	3	1
β-strand	432-434	3	1
β-strand	443-456	14	5
β-strand	465-470	6	5
α-helix	475-483	9
β-strand	487-490	4	4

Chain F: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	12-14	3	8
β-strand	17	1	9
β-strand	26-30	5	6
β-strand	35-40	6	6
β-strand	43-46	4	6
β-strand	55-56	2	8
α-helix	59-64	6
β-strand	66	1	9
β-strand	69-71	3	8
α-helix	76-78	3
β-strand	80-86	7	6
β-strand	90-98	9	6
β-strand	99-101	3	10
β-strand	115-119	5	10
β-strand	127-131	5	11
β-strand	137-140	4	11
β-strand	143-145	3	10
β-strand	155-163	9	11
β-strand	166-174	9	11

Chain H: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	43
β-strand	12-14	3	44
β-strand	17	1	45
β-strand	27-29	3	43
β-strand	35-40	6	43
β-strand	43-46	4	43
β-strand	55-56	2	44
α-helix	59-62	4
β-strand	66	1	45
β-strand	69-71	3	44
α-helix	76-78	3
β-strand	80-85	6	43
β-strand	90-98	9	43
β-strand	99-102	4	46
β-strand	107	1	47
β-strand	116-119	4	46
β-strand	127-131	5	48
β-strand	137-140	4	48
β-strand	143	1	46
β-strand	156-163	8	48
β-strand	166-173	8	48
β-strand	175	1	47

Chain I: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	6	49
β-strand	19-22	4	50
β-strand	31-38	8	49
β-strand	40	1	51
β-strand	42	1	51
β-strand	45-48	4	49
β-strand	49	1	52
β-strand	53	1	52
β-strand	62-63	2	50
β-strand	72-75	4	50
α-helix	80-82	3
β-strand	84-92	9	49
β-strand	97	1	53
β-strand	101-106A	7	49
α-helix	108-111	3
β-strand	112	1	54
β-strand	115-119	5	55
α-helix	123-127	5
β-strand	131-140	10	55
β-strand	141	1	54
β-strand	146-151	6	56
β-strand	154-155	2	56
β-strand	160-162	3	55
β-strand	173-181	9	55
α-helix	183-187	5
β-strand	192-197	6	56
β-strand	202-207	6	56

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Surface protein gp160	A, E, K, O	protein	309	Human immunodeficiency virus type 1 group M subtype B	P20871
T-cell surface glycoprotein CD4	B, F, H, L	protein	184	Homo sapiens	P01730 (AlphaFold model)
PGT124 Light Chain	C, I, M, P	protein	214	Homo sapiens	P0DOY3 (AlphaFold model)
PGT124 Heavy Chain	D, J, N, Q	protein	236	Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (A, E, K, O), FASTA

>4R2G_1 Surface protein gp160 (chains A, E, K, O)
DFNMWKNNMVEQMQEDVINLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNNKTFNGKGQCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEKVVIRSDNFTDNAKTI
IVQLNESVKINCTRPSNNTRPGEIIGDIRQAHCNISRAQWNNTLKQIVEKLREQFNNKTI
VFTHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEKSSGTEGNDTIILPCRIKQI
INMWQEVGKAMYAPPIKGQIRCSSNITGLLLTRDGGKNESEIEIFRPGGGDMRDNWRSEL
YKYKVVKIE

Sequence of entity 2 (B, F, H, L), FASTA

>4R2G_2 T-cell surface glycoprotein CD4 (chains B, F, H, L)
MKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRR
SLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLE
SPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAF
QKAS

Sequence of entity 3 (C, I, M, P), FASTA

>4R2G_3 PGT124 Light Chain (chains C, I, M, P)
SYVSPLSVALGETARISCGRQALGSRAVQWYQHKPGQAPILLIYNNQDRPSGIPERFSGT
PDINFGTTATLTISGVEVGDEADYYCHMWDSRSGFSWSFGGATRLTVLSQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (D, J, N, Q), FASTA

>4R2G_4 PGT124 Heavy Chain (chains D, J, N, Q)
QVQLQESGPGLVRPSETLSVTCIVSGGSISNYYWTWIRQSPGKGLEWIGYISDRETTTYN
PSLNSRAVISRDTSKNQLSLQLRSVTTADTAIYFCATARRGQRIYGVVSFGEFFYYYYMD
VWGKGTAVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	26

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

Primary citation

Structural Evolution of Glycan Recognition by a Family of Potent HIV Antibodies. Garces, F., Sok, D., Kong, L. et al. Cell (2014) 159:69-79. DOI 10.1016/j.cell.2014.09.009 · PubMed

Other PDB entries of the same protein (UniProt P20871), best resolution first:

9MMJ 1.78 Å, Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the…
5V6M 1.9 Å, Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A3 in complex with V3 peptide ConB
5V6L 2.55 Å, Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A37 in complex with V3 peptide JR-FL
1CE4 Conformational model for the consensus V3 loop of the envelope protein GP120 of HIV-1
2ESX The structure of the V3 region within gp120 of JR-FL HIV-1 strain (minimized average…
2ESZ The structure of the V3 region within gp120 of JR-FL HIV-1 strain (ensemble)

Browse structure collections

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