7URX: SJ25C1 Fab

SJ25C1 Fab in complex with soluble CD19. Determined by electron microscopy at 3.4 Å resolution. Released 15 Feb 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 4,492
Mol. weight: 83.45 kDa
Released: 15 Feb 2023

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

Secondary structure: helices and β-sheets

7URX contains 12 α-helices and 57 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 C: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	22-23	2
β-strand	24-28	5	1
β-strand	34-37	4	2
β-strand	50-56	7	1
β-strand	59-66	8	1
β-strand	71-75	5	2
β-strand	80-84	5	2
β-strand	93-98	6	1
β-strand	108-115	8	1
β-strand	120-123	4	3
β-strand	155-159	5	3
β-strand	164-166	3	3
α-helix	170-172	3
β-strand	187-190	4	1
β-strand	196-198	3	2
β-strand	212-217	6	1
β-strand	223	1	1
β-strand	226-230	5	1
β-strand	239-242	4	2
β-strand	245-248	4	2
β-strand	257-262	6	1
β-strand	267-274	8	1

Chain H: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	9
β-strand	29-31	3	10
β-strand	36-44	9	9
α-helix	48-50	3
β-strand	54-58	5	10
β-strand	64-70	7	10
β-strand	77-79	3	10
β-strand	87-92	6	9
β-strand	97-103	7	9
α-helix	107-109	3
β-strand	111-121	11	10
β-strand	125-131	7	10
β-strand	135-139	5	10
β-strand	148-150	3	11
β-strand	169-173	5	11
α-helix	187-188	2
β-strand	193	1	12
α-helix	194-196	3
β-strand	197-198	2	11
β-strand	204-207	4	11
β-strand	208	1	12

Chain L: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	4
β-strand	29-32	4	5
β-strand	38-44	7	4
β-strand	52-57	6	5
β-strand	64-68	5	5
β-strand	72-73	2	5
α-helix	74	1
β-strand	81-84	4	4
β-strand	89-94	6	4
α-helix	99-101	3
β-strand	104-109	6	5
β-strand	117	1	5
β-strand	121-125	5	5
α-helix	126-127	2
β-strand	135-139	5	6
α-helix	140-142	3
α-helix	143-148	6
β-strand	150-160	11	6
β-strand	166-169	4	7
β-strand	170-171	2	8
β-strand	174-175	2	8
β-strand	180-184	5	6
β-strand	194-203	10	6
α-helix	204-208	5
β-strand	212-219	8	7
β-strand	222-231	10	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B-lymphocyte antigen CD19	C	protein	278	Homo sapiens	P15391 (AlphaFold model)
SJ25C1 Fab light chain	L	protein	235	Mus musculus
SJ25C1 Fab heavy chain	H	protein	252	Mus musculus

Sequence of entity 1 (C), FASTA

>7URX_1 B-lymphocyte antigen CD19 (chains C)
MPPPRLLFFLLFLTPMEVRPEEPLVVKVEEGDNAVLQCLKGTSDGPTQQLTWSRESPLKP
FLKLSLGLPGLGIHVSPLAIWLFISNVSQQMGGFYLCQPGPPSEKAWQPGWTVNVEGSGE
LFRWNVSDLGGLGCGLKNRSSEGPSSPSGKLMSPKLYVWAKDRPEIWEGEPPCLPPRDSL
NQSLSQDLTMAPGSTLWLSCGVPPDSVSRGPLSWTHVHPKGPKSLLSLELKDDRPARDMW
VMETGLLLPRATAQDAGKYYCHRGNLTMSFHLEITARP

Sequence of entity 2 (L), FASTA

>7URX_2 SJ25C1 Fab light chain (chains L)
MGWSCIILFLVATATGVHSDIELTQSPKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPG
QSPKPLIYSATYRNSGVPDRFTGSGSGTDFTLTITNVQSKDLADYFCQQYNRYPYTSGGG
TKLEIKRTRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>7URX_3 SJ25C1 Fab heavy chain (chains H)
MGWSCIILFLVATATGVHSEVKLQQSGAELVRPGSSVKISCKASGYAFSSYWMNWVKQRP
GQGLEWIGQIYPGDGDTNYNGKFKGQATLTADKSSSTAYMQLSGLTSEDSAVYFCARKTI
SSVVDFYFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV
SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVE
PKSCHHHHHHHH

Primary citation

CD19 CAR antigen engagement mechanisms and affinity tuning. He, C., Mansilla-Soto, J., Khanra, N. et al. Sci Immunol (2023) 8:eadf1426-eadf1426. DOI 10.1126/sciimmunol.adf1426 · PubMed

Other PDB entries of the same protein (UniProt P15391 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AL5 3.0 Å, Complex between CD19 (N138Q mutant) and B43 FAB
7URV 3.05 Å, FMC63 scFv in complex with soluble CD19
7JIC 3.8 Å, Structure of human CD19-CD81 co-receptor complex bound to coltuximab Fab fragment

Browse structure collections

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