7O52: CD22 d6-d7

CD22 d6-d7 in complex with Fab m971. Determined by X-ray diffraction at 2.41 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,746
Mol. weight: 71.03 kDa
Ligands: NAG
Released: 28 Jul 2021

Explore 7O52 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O52 contains 20 α-helices and 69 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: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-40	9	3
β-strand	44-52A	10	3
β-strand	55-59	5	3
β-strand	67-68	2	1
β-strand	71-72	2	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-97	10	3
β-strand	100B-103	6	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	115-116	2
β-strand	117	1	4
β-strand	120-124	5	5
α-helix	128-130	3
β-strand	131-132	2	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
α-helix	171	1
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-107	6	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-198	8	11
β-strand	205-210	6	11

Chain U: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	510	1	12
β-strand	520	1	13
β-strand	528	1	14
β-strand	529	1	12
β-strand	543-545	3	15
β-strand	548	1	15
β-strand	555	1	14
α-helix	563-565	3
β-strand	567-571	5	15
β-strand	572	1	16
β-strand	581	1	16
β-strand	585-587	3	15
β-strand	590	1	13
β-strand	591-601	11	17
β-strand	605-607	3	18
β-strand	612-621	10	17
α-helix	623-624	2
β-strand	626-630	5	19
β-strand	636-637	2	19
β-strand	643-646	4	17
α-helix	651-653	3
β-strand	655-657	3	20
β-strand	658-662	5	19
β-strand	667-669	3	19
β-strand	673-675	3	20
β-strand	676-678	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
m971 Fab Heavy chain	H	protein	229	Homo sapiens
m971 Fab Light chain	L	protein	216	Homo sapiens
CD22 d6-d7 Ig domains	U	protein	194	Homo sapiens	P20273 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7O52_1 m971 Fab Heavy chain (chains H)
TGQVQLQQSGPGLVKPSQTLSLTCAISGDSVSSNSAAWNWIRQSPSRGLEWLGRTYYRSK
WYNDYAVSVKSRITINPDTSKNQFSLQLNSVTPEDTAVYYCAREVTGDLEDAFDIWGQGT
MVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVSHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>7O52_2 m971 Fab Light chain (chains L)
TGDIQMTQSPSSLSASVGDRVTITCRASQTIWSYLNWYQQRPGKAPNLLIYAASSLQSGV
PSRFSGRGSGTDFTLTISSLQAEDFATYYCQQSYSIPQTFGQGTKLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (U), FASTA

>7O52_3 CD22 d6-d7 Ig domains (chains U)
TGPRDVRVRKIKPLSEIHSGNSVSLQCDFSSSHPKEVQFFWEKNGRLLGKESQLNFDSIS
PEDAGSYSCWVNNSIGQTASKAWTLEVLYAPRRLRVSMSPGDQVMEGKSATLTCESDANP
PVSHYTWFDWNNQSLPYHSQKLRLEPVKVQHSGAYWCQGTNSVGKGRSPLSTLTVYYSPE
TIGRRGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Structural details of monoclonal antibody m971 recognition of the membrane-proximal domain of CD22. Ereno-Orbea, J., Liu, X., Sicard, T. et al. J Biol Chem (2021) 297:100966-100966. DOI 10.1016/j.jbc.2021.100966 · PubMed

Other PDB entries of the same protein (UniProt P20273 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VKJ 2.12 Å, Crystal structure of human CD22 Ig domains 1-3
5VKM 2.2 Å, Crystal structure of human CD22 Ig domains 1-3 in complex with alpha 2-6 sialyllactose
9ROB 2.7 Å, Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 1B
9RM3 2.86 Å, Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 17
5VL3 3.1 Å, CD22 d1-d3 in complex with therapeutic Fab Epratuzumab
9RO7 3.15 Å, Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 7-012

Browse structure collections

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