9J8A: Antibody BA8

Structure of antibody BA8 in complex with sulfated peptide from CCR5. Determined by X-ray diffraction at 1.75 Å resolution. Released 2 Jul 2025.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 3
Atoms: 3,792
Mol. weight: 47.62 kDa
Released: 2 Jul 2025

Explore 9J8A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J8A contains 24 α-helices and 44 β-strands across 3 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 H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	9-11	3	2
β-strand	17-24	8	1
α-helix	28-30	3
β-strand	33-38	6	2
β-strand	44-50	7	2
β-strand	56-58	3	2
β-strand	66-71	6	1
β-strand	76-81	6	1
α-helix	86-88	3
β-strand	90-96	7	2
β-strand	104	1	2
β-strand	108-112	5	2
α-helix	116-117	2
β-strand	118	1	3
α-helix	119-120	2
β-strand	121-125	5	4
α-helix	127-128	2
β-strand	129	1	5
β-strand	131	1	5
β-strand	137-146	10	4
β-strand	147	1	3
β-strand	152-155	4	6
α-helix	156-158	3
β-strand	165-166	2	4
α-helix	167-169	3
β-strand	170-171	2	4
β-strand	177-185	9	4
β-strand	192-198	7	6
α-helix	199-201	3
β-strand	203-209	7	6
α-helix	210	1
α-helix	215-216	2

Chain L: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
α-helix	8	1
α-helix	10	1
β-strand	11-14	4	8
β-strand	19-25	7	7
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	8
β-strand	47-51	5	8
β-strand	55-56	2	8
α-helix	57	1
β-strand	64-69	6	7
β-strand	72-77	6	7
α-helix	82-84	3
β-strand	86-93	8	8
β-strand	98-100	3	8
β-strand	104-109	6	8
β-strand	113	1	9
α-helix	114-115	2
β-strand	116-120	5	10
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-141	11	10
β-strand	142	1	9
β-strand	146-151	6	11
β-strand	154-155	2	11
α-helix	156	1
β-strand	160-164	5	10
α-helix	165-168	4
β-strand	174-183	10	10
α-helix	184-187	4
β-strand	192-199	8	11
β-strand	202-209	8	11
α-helix	210-212	3

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of BA8 Fab	H	protein	226	Oryctolagus cuniculus
Light Chain of Fab BA8	L	protein	213	Oryctolagus cuniculus
Sulfated peptide from CCR5	P	protein	11	Homo sapiens	P51681 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9J8A_1 Heavy chain of BA8 Fab (chains H)
QSLEESGGGLFKPTDTLTLTCTVSGFSLSSYSIRWVRQAPGNGLEWIGAIGSGGNAYYTS
WAKSRSTITRNTNENTVTLKMTSLTVADTATYFCARGGINFGIWGPGTLVTVSSGQPKAP
SVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLS
SVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTCSKPGGSHHHHHH

Sequence of entity 2 (L), FASTA

>9J8A_2 Light Chain of Fab BA8 (chains L)
AAVLTQTPSPVSAAVGSTVTINCQSSQSVYSKNWLSWFQQKPGQPPKQLIYSASTLDSGV
PSRFSGSGSGTQFTLTISGVQCDDAATYYCQGTYGDASAFGGGTEVVVKGDPVAPTVLIF
PPSADLVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTL
TLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC

Sequence of entity 3 (P), FASTA

>9J8A_3 Sulfated peptide from CCR5 (chains P)
PIYDINYYTSE

Primary citation

Specific recognition mechanism of an antibody to sulfated tyrosine and its potential use in biological research. Ujiie, K., Nakakido, M., Kinoshita, S. et al. J Biol Chem (2025) 301:108176-108176. DOI 10.1016/j.jbc.2025.108176 · PubMed

Other PDB entries of the same protein (UniProt P51681 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YD3 1.35 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide
5YD4 1.35 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)
5YY4 1.59 Å, Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide
5YD5 1.96 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)
5UIW 2.2 Å, Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV…
7F1T 2.6 Å, Crystal structure of the human chemokine receptor CCR5 in complex with MIP-1a
4MBS 2.71 Å, Crystal Structure of the CCR5 Chemokine Receptor
6AKX 2.8 Å, The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21
6AKY 2.8 Å, The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34
7F1S 2.8 Å, Cryo-EM structure of the apo chemokine receptor CCR5 in complex with Gi
7F1Q 2.9 Å, Cryo-EM structure of the chemokine receptor CCR5 in complex with MIP-1a and Gi
7F1R 3.0 Å, Cryo-EM structure of the chemokine receptor CCR5 in complex with RANTES and Gi

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