9RM3: Human CD22 Ig domains 1-3

Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 17. Determined by X-ray diffraction at 2.86 Å resolution. Released 28 Jan 2026.

Method: X-ray diffraction
Resolution: 2.86 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,650
Mol. weight: 152.93 kDa
Ligands: A1JJP
Released: 28 Jan 2026

Explore 9RM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RM3 contains 15 α-helices and 119 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: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	31-35	5	2
β-strand	40-42	3	3
β-strand	45-48	4	1
β-strand	55-65	11	2
β-strand	70-78	9	2
β-strand	92-94	3	3
β-strand	104-106	3	3
α-helix	111-113	3
β-strand	115-122	8	2
β-strand	127-137	11	2
α-helix	140-142	3
β-strand	144-146	3	4
β-strand	151-152	2	5
β-strand	157-163	7	4
β-strand	167	1	6
β-strand	170	1	6
β-strand	172-178	7	7
β-strand	181-182	2	7
β-strand	187-193	7	4
β-strand	198-206	9	4
α-helix	210-212	3
β-strand	216-223	8	7
β-strand	228-235	8	7
β-strand	238-239	2	5
β-strand	240-249	10	8
β-strand	261-271	11	8
β-strand	276-281	6	9
β-strand	284-286	3	9
β-strand	293-296	4	8
β-strand	305-312	8	9
β-strand	317-319	3	9
β-strand	323-325	3	9

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	10
β-strand	31-35	5	11
β-strand	40-42	3	12
β-strand	45-47	3	10
β-strand	55-65	11	11
β-strand	70-78	9	11
β-strand	92-94	3	12
β-strand	101	1	10
β-strand	104-106	3	12
α-helix	111-113	3
β-strand	115-122	8	11
β-strand	127-137	11	11
α-helix	140-142	3
β-strand	144-146	3	13
β-strand	151-152	2	14
β-strand	157-163	7	13
β-strand	173-178	6	15
β-strand	181-182	2	15
β-strand	187-193	7	13
β-strand	198-206	9	13
α-helix	210-212	3
β-strand	216-222	7	15
β-strand	228-235	8	15
β-strand	238-239	2	14
β-strand	240-249	10	16
β-strand	261-271	11	16
β-strand	276-281	6	17
β-strand	284-285	2	17
β-strand	293-296	4	16
β-strand	307-312	6	17
β-strand	317-319	3	17
β-strand	323	1	17

Chain C: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	18
β-strand	31-35	5	19
β-strand	40-42	3	20
β-strand	45-48	4	18
β-strand	55-65	11	19
β-strand	70-78	9	19
β-strand	92-94	3	20
β-strand	101	1	18
β-strand	104-106	3	20
α-helix	111-113	3
β-strand	115-122	8	19
β-strand	127-137	11	19
α-helix	140-142	3
β-strand	144-146	3	21
α-helix	147-148	2
β-strand	151-152	2	22
β-strand	157-163	7	21
β-strand	172-178	7	23
β-strand	181-182	2	23
α-helix	186-187	2
β-strand	188-193	6	21
β-strand	198-206	9	21
α-helix	210-212	3
β-strand	216-223	8	23
β-strand	228-235	8	23
β-strand	238-239	2	22
β-strand	240-247	8	24
β-strand	262-271	10	24
β-strand	276-281	6	25
β-strand	284-285	2	25
α-helix	286	1
β-strand	293-295	3	24
β-strand	307-312	6	25
β-strand	317-319	3	25
β-strand	323	1	25

Chain D: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	26
β-strand	32-35	4	27
β-strand	40-42	3	28
β-strand	45-47	3	26
β-strand	56-60	5	29
β-strand	74-78	5	29
β-strand	92-94	3	28
β-strand	104-106	3	28
α-helix	111-113	3
β-strand	115	1	27
β-strand	117-121	5	29
β-strand	134-137	4	27
α-helix	140-142	3
β-strand	144-146	3	30
β-strand	151-152	2	31
β-strand	157-163	7	30
β-strand	167	1	32
β-strand	170	1	32
β-strand	172-178	7	33
β-strand	181-182	2	33
β-strand	187-193	7	30
β-strand	198-206	9	30
α-helix	210-212	3
β-strand	216-223	8	33
β-strand	228-235	8	33
β-strand	238-239	2	31
β-strand	240-248	9	34
β-strand	261-271	11	34
β-strand	277-281	5	35
β-strand	284-285	2	35
β-strand	293-296	4	34
β-strand	306-312	7	35
β-strand	317-319	3	35
β-strand	323-324	2	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B-cell receptor CD22	A, B, C, D	protein	324	Homo sapiens	P20273 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9RM3_1 B-cell receptor CD22 (chains A, B, C, D)
ETGDSSKWVFEHPETLYAWEGACVWIPCTYRALDGDLESFILFHNPEYNKATSKFDGTRL
YESTKDGKVPSEQKRVQFLGDKNKNCTLSIHPVHLADSGQLGLRMESKTEKWMERIHLAV
SERPFPPHIQLPPEIQESQEVTLTCLLAFSCYGYPIQLQWLLEGVPMRQAAVTSTSLTIK
SVFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSADTVQLNVKHTPKLEIKVTPSDAIVR
EGDSVTMTCEVSSSNPEYTTVSWLKDGTSLKKQNTFTLNLREVTKDQSGKYCCQVSNDVG
PGRSEEVFLQVQYAGGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1JJP	(2R,4S,5R,6R)-5-acetamido-2-[[(2R,3R,4S,5R,6S)-6-[(2R,3S,4R,5R,6R)-5-acetamido-…	C40 H56 N4 O20	4

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

Primary citation

Molecular Insights into the Engagement of High-Affinity Sialylated Ligands to Human CD22. Ereno-Orbea, J., Pang, L., Sicard, T. et al. JACS Au (2025) 5:5524-5537. DOI 10.1021/jacsau.5c01013 · 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
7O52 2.41 Å, CD22 d6-d7 in complex with Fab m971
9ROB 2.7 Å, Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 1B
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

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