7Q5T: Tyrosine-protein kinase SYK

The tandem SH2 domains of SYK with a bound FCER1G diphospho-ITAM peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 24 Nov 2021.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 12
Atoms: 13,506
Mol. weight: 195.55 kDa
Ligands: PO4
Released: 24 Nov 2021

Explore 7Q5T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q5T contains 88 α-helices and 124 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
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
α-helix	69	1
β-strand	74-76	3	1
β-strand	80	1	3
β-strand	82	1	1
α-helix	85-94	10
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	140-161	22
α-helix	162-165	4
β-strand	169	1	4
α-helix	175-182	8
β-strand	192-196	5	4
β-strand	203-209	7	4
β-strand	212-218	7	4
β-strand	219-220	2	5
β-strand	226-227	2	5
α-helix	232-233	2
β-strand	234	1	5
α-helix	237-246	10
β-strand	249	1	6
β-strand	251	1	6
β-strand	258	1	4
α-helix	259-261	3

Chain BBB: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	7
β-strand	18	1	8
α-helix	22-31	10
β-strand	38-43	6	7
β-strand	51-57	7	7
β-strand	60-68	9	7
α-helix	69	1
β-strand	74-76	3	7
β-strand	82	1	7
α-helix	85-94	10
β-strand	105-106	2	7
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	8
α-helix	119-136	18
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169	1	9
α-helix	175-182	8
β-strand	192-196	5	9
β-strand	203-209	7	9
β-strand	212-218	7	9
β-strand	219-220	2	10
β-strand	226-227	2	10
β-strand	234	1	10
α-helix	237-246	10
β-strand	249	1	11
β-strand	251	1	11
β-strand	258	1	9
α-helix	259-261	3

Chain CCC: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	12
β-strand	18	1	13
α-helix	22-31	10
β-strand	38-43	6	12
β-strand	51-57	7	12
β-strand	60-66	7	12
β-strand	67-68	2	14
α-helix	69	1
β-strand	74-75	2	14
β-strand	82	1	14
α-helix	85-94	10
β-strand	105-106	2	12
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	13
α-helix	119-136	18
α-helix	140-161	22
α-helix	162-165	4
β-strand	169	1	15
β-strand	171	1	3
α-helix	175-183	9
β-strand	192-196	5	15
β-strand	203-209	7	15
β-strand	212-218	7	15
β-strand	219-220	2	16
β-strand	226-227	2	16
α-helix	232-233	2
β-strand	234	1	16
α-helix	237-246	10
β-strand	249	1	17
β-strand	251	1	17
β-strand	258	1	15
α-helix	259-261	3
β-strand	265	1	3

Chain DDD: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	18
β-strand	18	1	19
α-helix	22-31	10
β-strand	38-43	6	18
β-strand	51-57	7	18
β-strand	60-66	7	18
β-strand	67-68	2	20
α-helix	69	1
β-strand	74-75	2	20
β-strand	82	1	20
α-helix	85-94	10
β-strand	105-106	2	18
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	19
α-helix	119-136	18
α-helix	143-149	7
α-helix	152-161	10
α-helix	162-165	4
β-strand	169	1	21
α-helix	175-183	9
β-strand	192-196	5	21
β-strand	203-209	7	21
β-strand	212-218	7	21
β-strand	219-220	2	22
β-strand	226-227	2	22
α-helix	232-233	2
β-strand	234	1	22
α-helix	237-246	10
β-strand	249	1	23
β-strand	251	1	23
β-strand	258	1	21
α-helix	259-261	3

Chain EEE: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	24
β-strand	18	1	25
α-helix	22-31	10
β-strand	38-43	6	24
β-strand	51-57	7	24
β-strand	60-66	7	24
β-strand	67-68	2	26
α-helix	69	1
β-strand	74-75	2	26
β-strand	82	1	26
α-helix	85-94	10
β-strand	105-106	2	24
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	25
α-helix	119-135	17
α-helix	140-149	10
α-helix	151-161	11
α-helix	162-165	4
β-strand	169	1	27
α-helix	175-183	9
β-strand	192-196	5	27
β-strand	203-209	7	27
β-strand	212-218	7	27
β-strand	219-220	2	28
β-strand	226-227	2	28
α-helix	232-233	2
β-strand	234	1	28
α-helix	237-246	10
β-strand	249	1	29
β-strand	251	1	29
β-strand	258	1	27
α-helix	259-261	3

Chain FFF: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	30
β-strand	18	1	31
α-helix	22-31	10
β-strand	38-43	6	30
β-strand	51-57	7	30
β-strand	60-66	7	30
β-strand	67-68	2	32
α-helix	69	1
β-strand	74-75	2	32
β-strand	82	1	32
α-helix	85-94	10
β-strand	105-106	2	30
α-helix	108-110	3
α-helix	113-115	3
β-strand	116	1	31
α-helix	119-130	12
α-helix	141-149	9
α-helix	151-161	11
α-helix	162-165	4
β-strand	169	1	33
α-helix	175-183	9
β-strand	192-196	5	33
β-strand	203-209	7	33
β-strand	212-218	7	33
β-strand	219-220	2	34
β-strand	226-227	2	34
α-helix	232-233	2
β-strand	234	1	34
α-helix	237-246	10
β-strand	249	1	35
β-strand	251	1	35
β-strand	258	1	33
α-helix	259-261	3

Chain GGG: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	65-72	8
α-helix	75-77	3

Chains HHH and JJJ: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	65-68	4
α-helix	74-76	3
β-strand	77	1	12

3 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
Tyrosine-protein kinase SYK	AAA, BBB, CCC, DDD, EEE, FFF	protein	265	Homo sapiens	P43405 (AlphaFold model)
High affinity immunoglobulin epsilon receptor subunit gamma	GGG, HHH, III, JJJ, KKK, LLL	protein	20	Homo sapiens	P30273 (AlphaFold model)

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

>7Q5T_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

>7Q5T_2 High affinity immunoglobulin epsilon receptor subunit gamma (chains GGG, HHH, III, JJJ, KKK, LLL)
DGVYTGLSTRNQETYETLKH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	9

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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