8A11: Human SHMT1-RNA complex

Cryo-EM structure of the Human SHMT1-RNA complex. Determined by electron microscopy at 3.52 Å resolution. Released 14 Jun 2023.

Method: Electron microscopy
Resolution: 3.52 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,450
Mol. weight: 214.48 kDa
Ligands: PLP
Released: 14 Jun 2023

Explore 8A11 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8A11 contains 103 α-helices and 82 β-strands across 4 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: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	17-22	6
α-helix	26-29	4
α-helix	32-45	14
β-strand	48	1	1
α-helix	59-65	7
α-helix	68-71	4
α-helix	87-103	17
β-strand	111-114	4	2
α-helix	120-131	12
α-helix	133	1
β-strand	137-139	3	2
β-strand	141	1	3
α-helix	143-145	3
α-helix	149-151	3
β-strand	154	1	4
β-strand	159	1	4
α-helix	162-166	5
β-strand	168-169	2	2
β-strand	172	1	3
β-strand	174	1	5
β-strand	181	1	5
α-helix	183-193	11
β-strand	197-200	4	2
α-helix	211-220	10
β-strand	224-228	5	2
α-helix	233-238	6
α-helix	244-246	3
β-strand	250-254	5	2
β-strand	265-270	6	2
β-strand	273-276	4	6
β-strand	283-285	3	6
α-helix	288-295	8
α-helix	296-300	5
α-helix	306-318	13
α-helix	322-345	24
β-strand	348-349	2	7
α-helix	350-352	3
β-strand	359-362	4	7
α-helix	370-379	10
β-strand	382	1	1
β-strand	385-387	3	7
α-helix	388-389	2
β-strand	400-403	4	7
α-helix	406-411	6
α-helix	415-439	25
α-helix	445-452	8
α-helix	455-472	18

Chain B: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	15-22	8
α-helix	26-29	4
α-helix	31-46	16
β-strand	48-49	2	8
α-helix	59-65	7
α-helix	68-70	3
α-helix	87-103	17
β-strand	111	1	9
β-strand	114	1	10
α-helix	120-131	12
α-helix	133	1
β-strand	137-139	3	10
β-strand	141	1	11
α-helix	162-166	5
β-strand	168-169	2	10
β-strand	172	1	11
β-strand	175	1	12
β-strand	180	1	12
α-helix	183-193	11
β-strand	197-201	5	10
α-helix	211-221	11
β-strand	224-228	5	10
α-helix	235-238	4
α-helix	242-243	2
α-helix	244-246	3
β-strand	250-254	5	10
β-strand	265-268	4	10
β-strand	270	1	9
β-strand	273-276	4	13
β-strand	283-285	3	13
α-helix	286	1
α-helix	288-296	9
α-helix	306-318	13
α-helix	322-344	23
β-strand	349	1	14
α-helix	350-352	3
β-strand	359-361	3	14
α-helix	364-366	3
α-helix	372-379	8
β-strand	382-383	2	8
β-strand	385	1	14
β-strand	401-403	3	14
α-helix	405-408	4
α-helix	409-411	3
α-helix	415-439	25
α-helix	445-450	6
α-helix	451-453	3
α-helix	455-472	18
α-helix	476-478	3

Chain C: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	15-22	8
α-helix	26-29	4
α-helix	31-45	15
β-strand	48	1	15
α-helix	56-58	3
α-helix	59-65	7
α-helix	68-70	3
α-helix	87-103	17
β-strand	111-114	4	16
α-helix	120-131	12
β-strand	137-138	2	17
β-strand	139	1	16
β-strand	141	1	18
α-helix	149-151	3
β-strand	154	1	19
β-strand	159	1	19
α-helix	162-166	5
β-strand	168-169	2	17
β-strand	172	1	18
β-strand	174	1	20
β-strand	181	1	20
α-helix	182	1
α-helix	184-193	10
β-strand	197-199	3	16
α-helix	211-220	10
β-strand	224-228	5	16
α-helix	234-238	5
β-strand	250-254	5	16
β-strand	265-270	6	16
β-strand	273-276	4	21
β-strand	283-285	3	21
α-helix	289-294	6
α-helix	295-300	6
α-helix	307-318	12
α-helix	322-345	24
β-strand	348-349	2	22
β-strand	359-362	4	22
α-helix	370-379	10
β-strand	382	1	15
β-strand	385-387	3	22
α-helix	388-389	2
β-strand	400-403	4	22
α-helix	408-411	4
α-helix	415-439	25
α-helix	445-451	7
α-helix	455-472	18

Chain D: 25 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	17-22	6
α-helix	26-29	4
α-helix	31-45	15
α-helix	59-65	7
α-helix	68-71	4
α-helix	87-103	17
α-helix	108-110	3
β-strand	111-114	4	23
α-helix	120-131	12
β-strand	138	1	24
β-strand	139	1	23
β-strand	141	1	25
α-helix	149-151	3
α-helix	162-166	5
β-strand	169	1	24
β-strand	172	1	25
β-strand	174	1	26
α-helix	180	1
β-strand	181	1	26
α-helix	182	1
α-helix	184-193	10
β-strand	197-201	5	23
α-helix	211-221	11
β-strand	224-228	5	23
α-helix	233-238	6
α-helix	244-246	3
β-strand	250-254	5	23
β-strand	265-270	6	23
β-strand	273-276	4	27
β-strand	283-285	3	27
α-helix	288-296	9
α-helix	306-317	12
α-helix	322-344	23
β-strand	349	1	28
β-strand	358-362	5	28
α-helix	370-379	10
β-strand	385-387	3	28
α-helix	388-389	2
β-strand	400-404	5	28
α-helix	406-411	6
α-helix	415-439	25
α-helix	445-451	7
α-helix	455-472	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, cytosolic	A, B, C, D	protein	486	Homo sapiens	P34896 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8A11_1 Serine hydroxymethyltransferase, cytosolic (chains A, B, C, D)
GSHMTMPVNGAHKDADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFA
SRAVLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQCWGVNVQP
YSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPD
TGYINYDQLEENARLFHPKLIIAGTSCYSRNLEYARLRKIADENGAYLMADMAHISGLVA
AGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVF
PGLQGGPHNHAIAGVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNH
LILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEKD
FQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAAVQALREEVESFASLFPL
PGLPDF

Ligands and cofactors

ID	Name	Formula	Copies
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	3

Primary citation

Structure-based mechanism of riboregulation of the metabolic enzyme SHMT1. Spizzichino, S., Di Fonzo, F., Marabelli, C. et al. Mol Cell (2024). DOI 10.1016/j.molcel.2024.06.016 · PubMed

Other PDB entries of the same protein (UniProt P34896 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RJP 1.25 Å, Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT
7RJL 1.5 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT
1BJ4 2.65 Å, Recombinant serine hydroxymethyltransferase (HUMAN)
6M5W 3.1 Å, Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with…
8R7H 3.29 Å, Cryo-EM structure of Human SHMT1
8XND 3.45 Å, Crystal structure of serine hydroxymethyltransferase 1
6FL5 3.6 Å, Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution

Browse structure collections

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