6VPY: I33M

I33M (I3.2 mutant from CH103 Lineage). Determined by X-ray diffraction at 2.36 Å resolution. Released 15 Jul 2020.

Method: X-ray diffraction
Resolution: 2.36 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,662
Mol. weight: 95.39 kDa
Released: 15 Jul 2020

Explore 6VPY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VPY contains 31 α-helices and 96 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	3-7	5	8
β-strand	11-13	3	9
β-strand	18-25	8	8
β-strand	32-40	9	10
β-strand	44-51	8	10
β-strand	57-59	3	10
α-helix	64-66	3
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-96	9	10
α-helix	100-100B	3
β-strand	101-103	3	10
β-strand	107-109	3	10
β-strand	110-112	3	9
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	159	1	13
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-185	10	12
β-strand	194-200	7	13
α-helix	201-203	3
β-strand	205-211	7	13

Chain B: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-13	4	3
α-helix	18-19	2
β-strand	20-24	5	2
α-helix	28-30	3
β-strand	34-38	5	3
β-strand	45-48	4	3
β-strand	49	1	4
β-strand	53	1	4
β-strand	63-67	5	2
β-strand	70-74	5	2
α-helix	80-82	3
β-strand	84-92	9	3
β-strand	95A-98	4	3
β-strand	99	1	1
β-strand	102-106	5	3
β-strand	112	1	5
α-helix	113-114	2
β-strand	115-119	5	6
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	6
β-strand	141	1	5
β-strand	146-151	6	7
β-strand	154-155	2	7
α-helix	156	1
β-strand	160-162	3	6
α-helix	163-165	3
β-strand	166-167	2	6
β-strand	173-181	9	6
α-helix	183-188	6
β-strand	192-198	7	7
β-strand	201-207	7	7

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	14
β-strand	11-13	3	15
β-strand	18-26	9	14
β-strand	32-40	9	16
β-strand	44-51	8	16
β-strand	57-59	3	16
β-strand	67-72	6	14
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-96	9	16
α-helix	100-100B	3
β-strand	102-103	2	16
β-strand	107-109	3	16
β-strand	110-112	3	15
β-strand	117	1	17
α-helix	118-119	2
β-strand	120-124	5	18
β-strand	135-145	11	18
β-strand	146	1	17
β-strand	151-154	4	19
α-helix	155-157	3
β-strand	159	1	19
β-strand	163-165	3	18
α-helix	166-168	3
β-strand	169-170	2	18
β-strand	176-185	10	18
α-helix	186-188	3
β-strand	189	1	20
β-strand	192	1	20
β-strand	195-200	6	19
α-helix	201-203	3
β-strand	205-210	6	19

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	21
β-strand	9-13	4	22
α-helix	17-18	2
β-strand	19-24	6	21
α-helix	28-30	3
β-strand	34-38	5	22
β-strand	45-48	4	22
β-strand	49	1	23
β-strand	53	1	23
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-92	9	22
β-strand	95A-98	4	22
β-strand	102-106	5	22
β-strand	112	1	24
α-helix	113-114	2
β-strand	115-119	5	25
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	25
β-strand	141	1	24
β-strand	146-151	6	26
β-strand	154-156	3	26
β-strand	160-162	3	25
α-helix	163-165	3
β-strand	166-167	2	25
β-strand	173-181	9	25
α-helix	183-188	6
β-strand	192-198	7	26
β-strand	201-207	7	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
I33M light chain	B, L	protein	213	Homo sapiens	Q8N355 (AlphaFold model)
I33M heavy chain	A, H	protein	232	Homo sapiens	Q6GMX6 (AlphaFold model)

Sequence of entity 1 (B, L), FASTA

>6VPY_1 I33M light chain (chains B, L)
SYELTQPPSVSVSPGQTASITCSGDKLGDKNACWYQVKPGQSPVVVIYQDSKRPSGIPER
FSGSNSGNTATLTISGTQAMDEADYYCQAWDSFSTFVFGTGTKVTVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (A, H), FASTA

>6VPY_2 I33M heavy chain (chains A, H)
QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYN
PSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVA
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

Primary citation

The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage. Zhou, J.O., Zaidi, H.A., Ton, T. et al. Front Immunol (2020) 11:1529-1529. DOI 10.3389/fimmu.2020.01529 · 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…
4FQQ 2.42 Å, Crystal Structure of Germline Antibody PGT121-GL Fab
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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