5VL3: CD22 d1-d3

CD22 d1-d3 in complex with therapeutic Fab Epratuzumab. Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Oct 2017.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Mus musculus
Chains: 12
Atoms: 22,912
Mol. weight: 345.47 kDa
Released: 11 Oct 2017

Explore 5VL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VL3 contains 84 α-helices and 302 β-strands across 12 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	36
β-strand	10-12	3	37
β-strand	18-25	8	36
α-helix	29-31	3
β-strand	34-39	6	37
β-strand	45-52	8	37
β-strand	56-59	4	37
α-helix	61-63	3
β-strand	67-72	6	36
β-strand	77-82	6	36
α-helix	84-86	3
β-strand	88-95	8	37
β-strand	101-103	3	37
β-strand	107-111	5	37
β-strand	118	1	38
α-helix	119-120	2
β-strand	121-125	5	39
β-strand	136-146	11	39
β-strand	147	1	38
β-strand	152-155	4	40
α-helix	156-158	3
β-strand	160	1	40
β-strand	164-166	3	39
α-helix	167-169	3
β-strand	170-171	2	39
β-strand	177-186	10	39
α-helix	187-189	3
β-strand	195-201	7	40
α-helix	202-204	3
β-strand	206-212	7	40

Chain B: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	57
β-strand	10-13	4	58
β-strand	19-25	7	57
β-strand	27C	1	59
β-strand	31	1	59
β-strand	33-38	6	58
β-strand	45-49	5	58
β-strand	53-54	2	58
α-helix	55	1
β-strand	62-67	6	57
β-strand	70-75	6	57
α-helix	80-82	3
β-strand	85-90	6	58
β-strand	97-98	2	58
β-strand	99	1	57
β-strand	102-106	5	58
β-strand	112	1	60
α-helix	113-114	2
β-strand	115-119	5	61
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	61
β-strand	141	1	60
β-strand	145-151	7	62
β-strand	154-155	2	62
α-helix	156	1
β-strand	160-164	5	61
α-helix	165-168	4
β-strand	174-183	10	61
α-helix	184-188	5
β-strand	193-199	7	62
β-strand	206-208	3	62

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	41
β-strand	10-12	3	42
β-strand	18-25	8	41
β-strand	34-39	6	42
β-strand	46-52	7	42
β-strand	56-59	4	42
α-helix	61-63	3
β-strand	67-72	6	41
β-strand	77-82	6	41
α-helix	84-86	3
β-strand	88-95	8	42
β-strand	101-103	3	42
β-strand	107-111	5	42
β-strand	118	1	43
α-helix	119-120	2
β-strand	121-125	5	44
β-strand	136-146	11	44
β-strand	147	1	43
β-strand	152-155	4	45
α-helix	156-158	3
β-strand	164-166	3	44
α-helix	167-169	3
β-strand	170-171	2	44
β-strand	177-186	10	44
α-helix	187-189	3
β-strand	190	1	46
β-strand	192	1	46
β-strand	196-201	6	45
α-helix	202-204	3
β-strand	206-211	6	45

Chain D: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	63
β-strand	10-13	4	64
β-strand	19-25	7	63
β-strand	27C	1	65
β-strand	31	1	65
β-strand	33-38	6	64
β-strand	45-49	5	64
β-strand	53-54	2	64
α-helix	55	1
β-strand	62-67	6	63
β-strand	70-75	6	63
α-helix	80-82	3
β-strand	85-90	6	64
β-strand	97-98	2	64
β-strand	102-106	5	64
β-strand	112	1	66
α-helix	113-114	2
β-strand	115-119	5	67
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	67
β-strand	141	1	66
β-strand	145-151	7	68
β-strand	154-155	2	68
α-helix	156	1
β-strand	160-164	5	67
α-helix	165-168	4
β-strand	174-183	10	67
α-helix	184-188	5
β-strand	192-199	8	68
β-strand	206-211	6	68

Chain E: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	47
β-strand	10-11	2	48
β-strand	18-25	8	47
β-strand	34-39	6	48
β-strand	45-52	8	48
β-strand	56-59	4	48
α-helix	61-63	3
β-strand	67-72	6	47
β-strand	77-82	6	47
α-helix	84-86	3
β-strand	88-95	8	48
β-strand	101-103	3	48
β-strand	107-110	4	48
β-strand	118	1	49
α-helix	119-120	2
β-strand	121-125	5	50
β-strand	136-146	11	50
β-strand	147	1	49
β-strand	152-155	4	51
β-strand	165-166	2	50
α-helix	167-169	3
β-strand	170-171	2	50
β-strand	177-186	10	50
α-helix	187-189	3
β-strand	195-201	7	51
α-helix	202-204	3
β-strand	206-212	7	51

Chain F: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	69
β-strand	10-13	4	70
β-strand	19-25	7	69
β-strand	27C	1	71
β-strand	31	1	71
β-strand	33-38	6	70
β-strand	45-49	5	70
β-strand	53-54	2	70
α-helix	55	1
β-strand	62-67	6	69
β-strand	70-75	6	69
α-helix	80-82	3
β-strand	85-90	6	70
β-strand	97-98	2	70
β-strand	102-106	5	70
β-strand	112	1	72
α-helix	113-114	2
β-strand	115-119	5	73
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	73
β-strand	141	1	72
β-strand	145-151	7	74
β-strand	154-155	2	74
α-helix	156	1
β-strand	160-164	5	73
α-helix	165-168	4
β-strand	174-183	10	73
α-helix	184-188	5
β-strand	193-199	7	74
β-strand	206-208	3	74

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	52
β-strand	10-12	3	53
β-strand	18-25	8	52
α-helix	29-31	3
β-strand	34-39	6	53
β-strand	45-52	8	53
β-strand	56-59	4	53
α-helix	61-63	3
β-strand	67-72	6	52
α-helix	73-75	3
β-strand	77-82	6	52
α-helix	84-86	3
β-strand	88-95	8	53
β-strand	101-103	3	53
β-strand	107-111	5	53
β-strand	118	1	54
α-helix	119-120	2
β-strand	121-125	5	55
β-strand	136-146	11	55
β-strand	147	1	54
β-strand	152-155	4	56
α-helix	156-158	3
β-strand	160	1	56
β-strand	164-166	3	55
α-helix	167-169	3
β-strand	170-171	2	55
β-strand	177-186	10	55
α-helix	187-189	3
β-strand	196-201	6	56
α-helix	202-204	3
β-strand	206-211	6	56

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	75
β-strand	10-13	4	76
β-strand	19-25	7	75
β-strand	27C	1	77
β-strand	31	1	77
β-strand	33-38	6	76
β-strand	45-49	5	76
β-strand	53-54	2	76
α-helix	55	1
β-strand	62-67	6	75
β-strand	70-75	6	75
α-helix	80-82	3
β-strand	85-90	6	76
β-strand	97-98	2	76
β-strand	102-106	5	76
β-strand	112	1	78
α-helix	113-114	2
β-strand	115-119	5	79
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	79
β-strand	141	1	78
β-strand	145-151	7	80
β-strand	154-155	2	80
β-strand	160-164	5	79
α-helix	165-168	4
β-strand	174-183	10	79
α-helix	184-188	5
β-strand	193-199	7	80
β-strand	206-208	3	80

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B-cell receptor CD22	Q, R, S, T	protein	323	Homo sapiens	P20273 (AlphaFold model)
Epratuzumab Fab Heavy Chain	A, C, E, H	protein	222	Mus musculus, Homo sapiens	S6B291 (AlphaFold model)
Epratuzumab Fab Light Chain	B, D, F, L	protein	222	Mus musculus, Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (Q, R, S, T), FASTA

>5VL3_1 B-cell receptor CD22 (chains Q, R, S, T)
TGDSSKWVFEHPETLYAWEGACVWIPCTYRALDGDLESFILFHNPEYNKQTSKFDGTRLY
ESTKDGKVPSEQKRVQFLGDKNKNCTLSIHPVHLQDSGQLGLRMESKTEKWMERIHLQVS
ERPFPPHIQLPPEIQESQEVTLTCLLQFSCYGYPIQLQWLLEGVPMRQAAVTSTSLTIKS
VFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSNDTVQLNVKHTPKLEIKVTPSDAIVRE
GDSVTMTCEVSSSNPEYTTVSWLKDGTSLKKQNTFTLNLREVTKDQSGKYCCQVSNDVGP
GRSEEVFLQVQYAGGTKHHHHHH

Sequence of entity 2 (A, C, E, H), FASTA

>5VL3_2 Epratuzumab Fab Heavy Chain (chains A, C, E, H)
ETGQVQLVQSGAEVKKPGSSVKVSCKASGYTFTSYWLHWVRQAPGQGLEWIGYINPRNDY
TEYNQNFKDKATITADESTNTAYMELSSLRSEDTAFYFCARRDITTFYWGQGTTVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 3 (B, D, F, L), FASTA

>5VL3_3 Epratuzumab Fab Light Chain (chains B, D, F, L)
ETGDIQLTQSPSSLSASVGDRVTMSCKSSQSVLYSANHKNYLAWYQQKPGKAPKLLIYWA
STRESGVPSRFSGSGSGTDFTLTISSLQPEDIATYYCHQYLSSWTFGGGTKLEIKRTVAA
PSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDST
YSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Molecular basis of human CD22 function and therapeutic targeting. Ereno-Orbea, J., Sicard, T., Cui, H. et al. Nat Commun (2017) 8:764-764. DOI 10.1038/s41467-017-00836-6 · 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
9RM3 2.86 Å, Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 17
9RO7 3.15 Å, Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 7-012

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