2K4A: Synaptotagmin-1

FGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway. Determined by solution NMR. Released 9 Jun 2009.

Method: Solution NMR
Organism: Homo sapiens
Chains: 2
Atoms: 2,108
Mol. weight: 29.9 kDa
Released: 9 Jun 2009

Explore 2K4A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2K4A contains 8 α-helices and 29 β-strands across 2 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: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
β-strand	18-27	10	1
α-helix	29-31	3
β-strand	33	1	2
β-strand	37	1	2
β-strand	41-46	6	3
β-strand	54-55	2	3
α-helix	56-58	3
β-strand	66	1	1
β-strand	70-74	5	1
α-helix	77-80	4
β-strand	84-90	7	3
β-strand	100-107	8	3
α-helix	108-110	3
β-strand	116-123	8	1
β-strand	124	1	3

Chain B: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	4
β-strand	7-9	3	5
β-strand	15-17	3	6
β-strand	25-27	3	6
β-strand	37	1	4
β-strand	40-43	4	5
β-strand	46-48	3	5
β-strand	50	1	7
β-strand	57-58	2	7
β-strand	61	1	8
β-strand	65	1	8
β-strand	68-69	2	7
α-helix	74-76	3
β-strand	77-83	7	5
β-strand	87-91	5	5
α-helix	93-96	4
β-strand	104-105	2	9
β-strand	109-110	2	9
α-helix	113-115	3
α-helix	121-123	3
β-strand	125-127	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	A	protein	128	Homo sapiens	P21579 (AlphaFold model)
Heparin-binding growth factor 1	B	protein	133	Homo sapiens	P05230 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2K4A_1 Synaptotagmin-1 (chains A)
EKLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHR
KTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEW
RDLQSAEK

Sequence of entity 2 (B), FASTA

>2K4A_2 Heparin-binding growth factor 1 (chains B)
YKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAM
DTDGLLYGSQTPNEECLFLERLEENHYNTYISKKHAEKNWFVGLKKNGSCKRGPRTHYGQ
KAILFLPLPVSSD

Primary citation

FGF-1-C2A binary complex structure: key component in the acidic fibroblast growth factor release. Mohan, S.K., Yu, C. To be published.

Other PDB entries of the same protein (UniProt P21579 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TZ3 1.17 Å, Crystal Structure of Human Synaptotagmin 1 C2B without Ca2+
6U4U 1.3 Å, 1.3 A structure of a pathogenic human Syt 1 C2B (I368T)
3F04 1.35 Å, Crystal Structure of Synaptotagmin I C2A domain
7TUA 1.35 Å, Human Synaptotagmin-1 C2B Y312F without Ca2+
3F00 1.36 Å, Crystal Structure of Synaptotagmin I C2A domain with Cu(II)
3F05 1.4 Å, Crystal Structure of Synaptotagmin I C2A domain with Mn(II)
6U4W 1.4 Å, 1.4 A structure of a pathogenic human Syt 1 C2B (D366E)
7U4Q 1.56 Å, Human Synaptotagmin-1 C2A Y181F Ca2+ bound
3F01 1.7 Å, Crystal Structure of Synaptotagmin I C2A domain with Cu(II)
6U41 1.7 Å, 1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G)
4V11 1.95 Å, Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84
6G5K 2.0 Å, Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with…

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