Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope

IGG,Immunoglobulin gamma-1 heavy chain NIE

EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVE
PEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAY
MELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYF
PEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

ammonium sulfate, lithium sulfate, CAPS buffer, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

The uncomplexed intact IgG of this Fab entry.

Sequence
The Genbank database sequence (AAA52919) is the
correct match for the variable portion of the heavy
chain except that the N-terminus has been changed from
LEQSGAE to QVQLVQSGAE in the process of cloning
from the recombinant Fab fragment to the IgG.

The constant domains of the heavy chains H and K have
the same sequence as all human IgG1 antibodies.

The variable region of the light chain matches the
Genbank database sequence (AAA52920) except that the
N-terminus was changed in cloning to the IgG from ELTQAPG
to EIVLTQSPG; the constant domains of the light chains L
and M have the same sequence as all human kappa light
chains.

The authors maintain that the sequence of L and M,
residue ALA 34 should be an ALA and not ARG (residue
33 in the sequence database).

selected from phage display peptide library, then chemically synthesized.

Fab domains from uncomplexed IgG1 b12 structure (1HZH)

10% test set (9419) reflections selected for initial rounds of refinement. For final round of refinement, a 2% test set was randomly selected from reflections contained in the original 10% test set.

Fab #1 is comprised of chains L and H.
Fab #2 is comprised of chains M and K.

The peptide chains P and R form a dimer.
Peptide chain P binds Fab #1 (LH)
Peptide chain R binds Fab #2 (MK)

antibody-peptide complex, peptide dimer, IMMUNE SYSTEM

KRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY
EKHKVYACEVTHQGLSSPVTKSFNRGEC

VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLG
TQTYICNVNHKPSNTKVDKKVEPKSC