7Q5U: Tyrosine-protein kinase SYK

The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 24 Nov 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 12
Atoms: 14,063
Mol. weight: 196.17 kDa
Ligands: P4G
Released: 24 Nov 2021

Explore 7Q5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q5U contains 96 α-helices and 114 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 AAA: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
β-strand	18	1	2
α-helix	22-31	10
β-strand	38-43	6	1
β-strand	51-57	7	1
β-strand	60-68	9	1
β-strand	74-76	3	1
α-helix	80-81	2
β-strand	82	1	1
α-helix	85-91	7
β-strand	105-106	2	1
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	2
α-helix	119-136	18
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169-172	4	3
α-helix	175-183	9
β-strand	192-196	5	3
β-strand	203-209	7	3
β-strand	212-218	7	3
β-strand	219-220	2	4
β-strand	226-227	2	4
α-helix	232-233	2
β-strand	234	1	4
α-helix	237-244	8
β-strand	249	1	5
β-strand	251	1	5
β-strand	258	1	3
α-helix	259-260	2

Chain BBB: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	16	1	6
β-strand	18	1	7
α-helix	22-31	10
β-strand	38-43	6	6
β-strand	51-57	7	6
β-strand	60-68	9	6
β-strand	74-76	3	6
α-helix	80-81	2
β-strand	82	1	6
α-helix	85-91	7
β-strand	105-106	2	6
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	7
α-helix	119-135	17
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169-172	4	8
α-helix	175-183	9
β-strand	192-196	5	8
β-strand	203-209	7	8
β-strand	212-218	7	8
β-strand	219-220	2	9
β-strand	226-227	2	9
β-strand	234	1	9
α-helix	237-246	10
β-strand	249	1	10
β-strand	251	1	10
β-strand	258	1	8
α-helix	259-260	2

Chain CCC: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	16	1	11
β-strand	18	1	12
α-helix	22-31	10
β-strand	38-43	6	11
β-strand	51-57	7	11
β-strand	60-68	9	11
β-strand	74-76	3	11
β-strand	82	1	11
α-helix	85-91	7
β-strand	105-106	2	11
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	12
α-helix	119-135	17
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169-172	4	13
α-helix	175-183	9
β-strand	192-196	5	13
β-strand	203-209	7	13
β-strand	212-218	7	13
β-strand	219-220	2	14
β-strand	226-227	2	14
α-helix	232-233	2
β-strand	234	1	14
α-helix	237-244	8
β-strand	249	1	15
β-strand	251	1	15
β-strand	258	1	13
α-helix	259-260	2

Chain DDD: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	16	1	16
β-strand	18	1	17
α-helix	22-31	10
β-strand	38-43	6	16
β-strand	51-57	7	16
β-strand	60-68	9	16
β-strand	74-76	3	16
α-helix	80-81	2
β-strand	82	1	16
α-helix	85-91	7
β-strand	105-106	2	16
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	17
α-helix	119-135	17
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169-172	4	18
α-helix	175-183	9
β-strand	192-196	5	18
β-strand	203-209	7	18
β-strand	212-218	7	18
β-strand	219-220	2	19
β-strand	226-227	2	19
β-strand	234	1	19
α-helix	237-244	8
β-strand	249	1	20
β-strand	251	1	20
β-strand	258	1	18
α-helix	259-261	3

Chain EEE: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	21
β-strand	18	1	22
α-helix	22-31	10
β-strand	38-43	6	21
β-strand	51-57	7	21
β-strand	60-68	9	21
β-strand	74-76	3	21
β-strand	82	1	21
α-helix	85-91	7
β-strand	105-106	2	21
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	22
α-helix	119-136	18
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169-172	4	23
α-helix	175-183	9
β-strand	192-196	5	23
β-strand	203-209	7	23
β-strand	212-218	7	23
β-strand	219-220	2	24
β-strand	226-227	2	24
α-helix	232-233	2
β-strand	234	1	24
α-helix	237-244	8
β-strand	249	1	25
β-strand	251	1	25
β-strand	258	1	23
α-helix	259-260	2

Chain FFF: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
β-strand	16	1	26
β-strand	18	1	27
α-helix	22-31	10
β-strand	38-43	6	26
β-strand	51-57	7	26
β-strand	60-68	9	26
β-strand	74-76	3	26
α-helix	80-81	2
β-strand	82	1	26
α-helix	85-91	7
β-strand	105-106	2	26
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	27
α-helix	119-135	17
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169-172	4	28
α-helix	175-183	9
β-strand	192-196	5	28
β-strand	203-209	7	28
β-strand	212-218	7	28
β-strand	219-220	2	29
β-strand	226-227	2	29
α-helix	232-233	2
β-strand	234	1	29
α-helix	237-244	8
β-strand	249	1	30
β-strand	251	1	30
β-strand	258	1	28
α-helix	259-260	2

Chains GGG, HHH, III, JJJ, KKK and LLL: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	161-163	3
α-helix	166-168	3
α-helix	170-172	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase SYK	AAA, BBB, CCC, DDD, EEE, FFF	protein	265	Homo sapiens	P43405 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	GGG, HHH, III, JJJ, KKK, LLL	protein	20	Homo sapiens	P09693 (AlphaFold model)

Sequence of entity 1 (AAA, BBB, CCC, DDD, EEE, FFF), FASTA

>7Q5U_1 Tyrosine-protein kinase SYK (chains AAA, BBB, CCC, DDD, EEE, FFF)
SMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHY
TIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLK
ENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPWFHGKISREESEQIVLI
GSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHY
SYKADGLLRVLTVPCQKIGTQGNVN

Sequence of entity 2 (GGG, HHH, III, JJJ, KKK, LLL), FASTA

>7Q5U_2 T-cell surface glycoprotein CD3 gamma chain (chains GGG, HHH, III, JJJ, KKK, LLL)
DQLYQPLKDREDDQYSHLQG

Ligands and cofactors

ID	Name	Formula	Copies
P4G	1-ethoxy-2-(2-ethoxyethoxy)ethane	C8 H18 O3	2

Water and common crystallization additives (PEG, EDO) are not listed.

Primary citation

The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures. Bradshaw, W.J., Harris, G., Gileadi, O. et al. Structure (2024) 32:2337-2351.e4. DOI 10.1016/j.str.2024.09.024 · PubMed

Other PDB entries of the same protein (UniProt P43405 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YJR 1.32 Å, SYK kinase domain in complex with inhibitor GTC000225
4YJQ 1.34 Å, SYK kinase domain in complex with inhibitor GTC000224
4FYO 1.4 Å, Crystal structure of spleen tyrosine kinase complexed with…
5LMA 1.43 Å, Human spleen tyrosine kinase kinase domain in complex with azanaphthyridine inhibitor
3BUW 1.45 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk
6ZCS 1.47 Å, SYK Kinase domain in complex with azabenzimidazole inhibitor 3
5TIU 1.49 Å, Crystal structure of SYK kinase domain with inhibitor
8XQ1 1.5 Å, Crystal structure of spleen tyrosine kinase(SYK) in complex with SKI-G-1673
8BI2 1.51 Å, Syk kinase domain in complex with macrocyclic inhibitor 20a
4YJT 1.52 Å, The kinase domain of human spleen tyrosine (SYK) in complex with GTC000233
1XBB 1.57 Å, Crystal structure of the syk tyrosine kinase domain with Gleevec
4RX8 1.59 Å, SYK Catalytic Domain Complexed with a Potent Triazine Inhibitor2

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