4FQQ: Germline Antibody PGT121-GL Fab

Crystal Structure of Germline Antibody PGT121-GL Fab. Determined by X-ray diffraction at 2.42 Å resolution. Released 14 Nov 2012.

Method: X-ray diffraction
Resolution: 2.42 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,753
Mol. weight: 197.6 kDa
Released: 14 Nov 2012

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

Secondary structure: helices and β-sheets

4FQQ contains 59 α-helices and 181 β-strands across 8 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	13
β-strand	10-13	4	14
β-strand	19-24	6	13
α-helix	28-30	3
β-strand	34-38	5	14
β-strand	45-48	4	14
β-strand	49	1	9
β-strand	53	1	9
α-helix	54-55	2
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-91	7	14
β-strand	96-98	3	14
β-strand	102-106	5	14
α-helix	109-111	3
β-strand	112	1	15
α-helix	113-114	2
β-strand	115-119	5	16
α-helix	120-122	3
α-helix	126-128	3
β-strand	131-140	10	16
β-strand	141	1	15
β-strand	146-151	6	17
β-strand	155-156	2	17
β-strand	160-162	3	16
α-helix	163-165	3
β-strand	166-167	2	16
β-strand	173-181	9	16
α-helix	183-186	4
β-strand	192-197	6	17
β-strand	202-207	6	17

Chain B: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	11-12	2	19
β-strand	18-25	8	18
β-strand	33-39	7	20
β-strand	46-52	7	20
β-strand	57-59	3	20
β-strand	67-72	6	18
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	88-100A	14	20
β-strand	100J-103	10	20
β-strand	107-109	3	20
β-strand	110-111	2	19
β-strand	120-124	5	21
β-strand	135-145	11	21
β-strand	151-154	4	22
α-helix	155-157	3
β-strand	159	1	22
β-strand	163-165	3	21
α-helix	166-168	3
β-strand	169-170	2	21
β-strand	176-185	10	21
β-strand	195-200	6	22
α-helix	201-203	3
β-strand	205-210	6	22

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	23
β-strand	10-13	4	24
α-helix	18	1
β-strand	19-24	6	23
α-helix	28-30	3
β-strand	34-38	5	24
β-strand	45-48	4	24
β-strand	49	1	25
β-strand	53	1	25
α-helix	54-55	2
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	85-91	7	24
β-strand	96-98	3	24
β-strand	102-106	5	24
α-helix	109-111	3
β-strand	112	1	26
β-strand	115-119	5	27
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	27
β-strand	141	1	26
β-strand	146-150	5	28
β-strand	155	1	28
β-strand	160-162	3	27
α-helix	163-165	3
β-strand	166-167	2	27
β-strand	173-181	9	27
α-helix	183-187	5
β-strand	192-198	7	28
β-strand	201-207	7	28

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	11-12	2	30
β-strand	18-25	8	29
β-strand	33-39	7	31
β-strand	46-52	7	31
β-strand	57-59	3	31
β-strand	67-72	6	29
β-strand	77-82	6	29
α-helix	84-86	3
β-strand	88-100	13	31
β-strand	100K-103	9	31
β-strand	107-109	3	31
β-strand	110-111	2	30
α-helix	115-116	2
β-strand	117	1	32
β-strand	120-124	5	33
β-strand	135-145	11	33
β-strand	146	1	32
β-strand	151-154	4	34
α-helix	155-157	3
β-strand	163-165	3	33
α-helix	166-168	3
β-strand	169-170	2	33
β-strand	176-185	10	33
β-strand	194-200	7	34
α-helix	201-203	3
β-strand	205-211	7	34

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	35
β-strand	10-13	4	36
β-strand	19-24	6	35
α-helix	28-30	3
β-strand	33-38	6	36
β-strand	45-48	4	36
β-strand	49	1	37
β-strand	53	1	37
α-helix	54-55	2
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	85-91	7	36
β-strand	96-98	3	36
β-strand	102-106	5	36
α-helix	109-111	3
β-strand	112	1	38
α-helix	113-114	2
β-strand	115-119	5	39
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-140	10	39
β-strand	141	1	38
β-strand	146-151	6	40
β-strand	161-162	2	39
β-strand	166-167	2	39
α-helix	168	1
β-strand	173-181	9	39
β-strand	192-197	6	40
β-strand	202-207	6	40

Chain F: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	41
β-strand	11-12	2	42
β-strand	18-25	8	41
β-strand	33-39	7	43
β-strand	46-52	7	43
β-strand	57-59	3	43
α-helix	61-63	3
β-strand	67-72	6	41
β-strand	77-82	6	41
α-helix	84-86	3
β-strand	88-100A	14	43
β-strand	100J-103	10	43
β-strand	107-109	3	43
β-strand	110-111	2	42
α-helix	115-116	2
β-strand	117	1	44
β-strand	120-124	5	45
β-strand	135-145	11	45
β-strand	146	1	44
β-strand	151-154	4	46
α-helix	155-157	3
β-strand	163-165	3	45
α-helix	166-168	3
β-strand	169-171	3	45
β-strand	175-185	11	45
α-helix	186-188	3
β-strand	194-200	7	46
α-helix	201-203	3
β-strand	205-211	7	46

Chain H: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	33-39	7	9
β-strand	46-52	7	9
β-strand	57-59	3	9
α-helix	64-66	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	88-100A	14	9
α-helix	100E-100G	3
β-strand	100J-103	10	9
β-strand	104	1	7
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	131-132	2	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
β-strand	10-13	4	2
β-strand	19-24	6	1
α-helix	28-30	3
β-strand	34-38	5	2
β-strand	45-48	4	2
β-strand	49	1	3
β-strand	53	1	3
α-helix	54-55	2
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-91	7	2
β-strand	96-98	3	2
β-strand	102-106	5	2
α-helix	109-111	3
β-strand	112	1	4
α-helix	113-114	2
β-strand	115-119	5	5
α-helix	123-127	5
β-strand	131-140	10	5
β-strand	141	1	4
β-strand	146-151	6	6
β-strand	155	1	6
β-strand	160-162	3	5
α-helix	163-165	3
β-strand	166-167	2	5
β-strand	173-181	9	5
α-helix	183-187	5
β-strand	192-198	7	6
β-strand	201-207	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab light chain	A, C, E, L	protein	215	Homo sapiens	Q8N355 (AlphaFold model)
Fab heavy chain	B, D, F, H	protein	244	Homo sapiens	Q6GMX6 (AlphaFold model)

Sequence of entity 1 (A, C, E, L), FASTA

>4FQQ_1 Fab light chain (chains A, C, E, L)
SYVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPER
FSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHPWVFGGGTKLTVLGQPKAAPSVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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

>4FQQ_2 Fab heavy chain (chains B, D, F, H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTQQGKRIYGVVSFGDYYYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHH
HHHH

Primary citation

Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies. Mouquet, H., Scharf, L., Euler, Z. et al. Proc Natl Acad Sci U S A (2012) 109:E3268-E3277. DOI 10.1073/pnas.1217207109 · PubMed

Other PDB entries of the same protein (UniProt Q8N355 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2DD8 2.3 Å, Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing…
6VPY 2.36 Å, I33M (I3.2 mutant from CH103 Lineage)
4HK0 2.5 Å, UCA Fab (unbound) from CH65-CH67 Lineage
6UDJ 2.5 Å, HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074
5UGY 2.8 Å, Influenza hemagglutinin in complex with a neutralizing antibody
4HK3 3.0 Å, I2 Fab (unbound) from CH65-CH67 Lineage
6DC3 3.5 Å, RSV prefusion F bound to RSD5 Fab
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
6C5V 4.8 Å, An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of…

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