4QHL: I3.2 (unbound) from CH103 Lineage

I3.2 (unbound) from CH103 Lineage. Determined by X-ray diffraction at 3.15 Å resolution. Released 11 Jun 2014.

Method: X-ray diffraction
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,458
Mol. weight: 95.36 kDa
Released: 11 Jun 2014

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

Secondary structure: helices and β-sheets

4QHL contains 26 α-helices and 92 β-strands across 4 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: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-13	4	2
α-helix	17	1
β-strand	18-25	8	1
β-strand	32-40	9	2
β-strand	44-51	8	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-96	9	2
β-strand	101-103	3	2
β-strand	107-112	6	2
β-strand	117	1	3
β-strand	120-124	5	4
β-strand	136-145	10	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-184	9	4
α-helix	186-188	3
β-strand	189	1	6
β-strand	192	1	6
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain B: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-12	3	8
α-helix	17-18	2
β-strand	19-24	6	7
β-strand	34-38	5	8
β-strand	45-48	4	8
β-strand	49	1	9
β-strand	53	1	9
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	97-98	2	8
β-strand	102-105	4	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	11
β-strand	140	1	10
β-strand	144-150	7	12
β-strand	153-154	2	12
β-strand	159-161	3	11
β-strand	165-166	2	11
β-strand	172-180	9	11
α-helix	182-187	6
β-strand	191-197	7	12
β-strand	200-206	7	12

Chain C: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11-12	2	14
α-helix	17	1
β-strand	18-25	8	13
β-strand	32-40	9	15
β-strand	44-51	8	15
β-strand	57-59	3	15
β-strand	67-72	6	13
α-helix	73-75	3
β-strand	77-82	6	13
β-strand	88-96	9	15
β-strand	101-103	3	15
β-strand	107-109	3	15
β-strand	110-111	2	14
β-strand	117	1	16
β-strand	120-124	5	17
α-helix	125-127	3
β-strand	135-145	11	17
β-strand	146	1	16
β-strand	151-154	4	18
α-helix	155-157	3
β-strand	163-165	3	17
α-helix	166-168	3
β-strand	169-170	2	17
β-strand	176-185	10	17
α-helix	186-188	3
β-strand	189	1	19
β-strand	192	1	19
β-strand	195-200	6	18
α-helix	201-203	3
β-strand	205-210	6	18

Chain D: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	3	20
β-strand	19-23	5	21
β-strand	34-38	5	20
β-strand	45-48	4	20
β-strand	49	1	22
β-strand	53	1	22
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-90	6	20
β-strand	97-98	2	20
β-strand	102-105	4	20
β-strand	111	1	23
α-helix	112-113	2
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	24
β-strand	140	1	23
β-strand	145-150	6	25
β-strand	153-155	3	25
β-strand	159-161	3	24
α-helix	162-164	3
β-strand	165-166	2	24
β-strand	172-180	9	24
α-helix	182-187	6
β-strand	191-197	7	25
β-strand	200-206	7	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
I3 heavy chain	A, C	protein	232	Homo sapiens	Q6GMX6 (AlphaFold model)
UCA light chain	B, D	protein	213	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>4QHL_1 I3 heavy chain (chains A, C)
QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYN
PSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVA
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

Sequence of entity 2 (B, D), FASTA

>4QHL_2 UCA light chain (chains B, D)
SYELTQPPSVSVSPGQTASITCSGDKLGDKYACWYQQKPGQSPVLVIYQDSKRPSGIPER
FSGSNSGNTATLTISGTQAMDEADYYCQAWDSFSTFVFGTGTKVTVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains. Fera, D., Schmidt, A.G., Haynes, B.F. et al. Proc Natl Acad Sci U S A (2014) 111:10275-10280. DOI 10.1073/pnas.1409954111 · PubMed

Other PDB entries of the same protein (UniProt Q6GMX6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6DC4 1.7 Å, RSV-neutralizing human antibody AM22
4NPY 1.8 Å, Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive…
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
4LKX 1.92 Å, Humanized antibody 4B12 Fab complexed with a CemX segment
3ZL4 1.95 Å, Antibody structural organization: Role of kappa - lambda chain constant domain switch in…
6B9Y 2.14 Å, Trastuzumab Fab v3 in complex with 5-phenyl meditope variant
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
6VPY 2.36 Å, I33M (I3.2 mutant from CH103 Lineage)
4FQQ 2.42 Å, Crystal Structure of Germline Antibody PGT121-GL Fab
6AL4 2.45 Å, Crystal structure of anti-CD19 antibody B43 FAB
4D9L 2.48 Å, Fab structure of anti-HIV-1 gp120 V2 mAb 697

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