8R7H: Human SHMT1

Cryo-EM structure of Human SHMT1. Determined by electron microscopy at 3.29 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 3.29 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,258
Mol. weight: 214.2 kDa
Released: 24 Jul 2024

Explore 8R7H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R7H contains 102 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: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	26-29	4
α-helix	31-45	15
β-strand	48	1	1
α-helix	59-65	7
α-helix	68-70	3
α-helix	87-103	17
β-strand	111-114	4	2
α-helix	120-127	8
α-helix	128-132	5
β-strand	137-139	3	2
β-strand	141	1	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
α-helix	171	1
β-strand	172	1	3
α-helix	173	1
β-strand	174	1	5
α-helix	175	1
β-strand	181	1	5
α-helix	183-193	11
β-strand	197-201	5	2
α-helix	211-221	11
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
α-helix	282	1
β-strand	283-285	3	6
α-helix	286	1
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-319	14
α-helix	322-344	23
β-strand	348-349	2	7
β-strand	358-362	5	7
α-helix	370-379	10
β-strand	382	1	1
β-strand	385-387	3	7
β-strand	400-404	5	7
α-helix	406-409	4
α-helix	415-439	25
α-helix	445-452	8
α-helix	458-472	15

Chain B: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	26-29	4
α-helix	31-46	16
β-strand	48	1	8
α-helix	59-65	7
α-helix	68-70	3
α-helix	87-103	17
β-strand	111-114	4	9
α-helix	120-131	12
β-strand	137-139	3	9
β-strand	141	1	10
α-helix	162-166	5
β-strand	168-169	2	9
β-strand	172	1	10
α-helix	173	1
β-strand	174	1	11
α-helix	175	1
β-strand	181	1	11
α-helix	183-193	11
β-strand	197-201	5	9
α-helix	208-209	2
α-helix	211-221	11
β-strand	224-228	5	9
α-helix	244-246	3
β-strand	250-254	5	9
β-strand	265-270	6	9
β-strand	273-276	4	12
β-strand	283-285	3	12
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-319	14
α-helix	322-344	23
β-strand	348	1	13
β-strand	359-362	4	13
α-helix	370-379	10
β-strand	382	1	8
β-strand	385-387	3	13
α-helix	388-389	2
β-strand	400-403	4	13
α-helix	407-411	5
α-helix	415-439	25
α-helix	445-450	6
α-helix	455-472	18

Chain C: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	26-29	4
α-helix	31-45	15
β-strand	48-49	2	14
α-helix	59-65	7
α-helix	68-70	3
β-strand	76-77	2	15
β-strand	80-81	2	15
α-helix	87-103	17
β-strand	111-114	4	16
α-helix	120-131	12
β-strand	137-139	3	16
β-strand	141	1	17
α-helix	162-166	5
β-strand	168-169	2	16
β-strand	172	1	17
α-helix	183-193	11
β-strand	197-201	5	16
α-helix	211-221	11
β-strand	224-228	5	16
α-helix	233-237	5
α-helix	244-246	3
β-strand	250-254	5	16
β-strand	265-270	6	16
β-strand	273-277	5	18
β-strand	282-285	4	18
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-319	14
α-helix	322-344	23
β-strand	349	1	19
α-helix	350-352	3
β-strand	358-362	5	19
α-helix	370-379	10
β-strand	382-383	2	14
β-strand	385-386	2	19
β-strand	400-404	5	19
α-helix	406-411	6
α-helix	415-439	25
α-helix	445-452	8
α-helix	455-472	18

Chain D: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	26-29	4
α-helix	31-46	16
β-strand	48-49	2	20
α-helix	59-65	7
α-helix	68-70	3
β-strand	76-77	2	21
β-strand	80-81	2	21
α-helix	87-103	17
β-strand	111-114	4	22
α-helix	120-127	8
α-helix	128-132	5
β-strand	137-139	3	22
β-strand	141	1	23
α-helix	143-145	3
α-helix	149-151	3
β-strand	154	1	24
β-strand	159	1	24
α-helix	162-166	5
β-strand	168-169	2	22
α-helix	171	1
β-strand	172	1	23
α-helix	173	1
β-strand	174	1	25
α-helix	175	1
β-strand	181	1	25
α-helix	183-193	11
β-strand	197-201	5	22
α-helix	211-221	11
β-strand	224-228	5	22
α-helix	244-246	3
β-strand	250-254	5	22
β-strand	265-270	6	22
β-strand	273-276	4	26
α-helix	282	1
β-strand	283-285	3	26
α-helix	286	1
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-319	14
α-helix	322-344	23
β-strand	348-349	2	27
β-strand	358-362	5	27
α-helix	370-379	10
β-strand	382-383	2	20
β-strand	385-387	3	27
β-strand	400-404	5	27
α-helix	406-409	4
α-helix	415-439	25
α-helix	445-452	8
α-helix	455-472	18

Molecules and chains

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

Sequence of entity 1 (A, D), FASTA

>8R7H_1 Serine hydroxymethyltransferase, cytosolic (chains A, D)
GSHMTMPVNGAHKDADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFA
SRAVLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQCWGVNVQP
YSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPD
TGYINYDQLEENARLFHPKLIIAGTSCYSRNLEYARLRKIADENGAYLMADMAHISGLVA
AGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVF
PGLQGGPHNHAIAGVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNH
LILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEKD
FQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAAVQALREEVESFASLFPL
PGLPDF

Sequence of entity 2 (B, C), FASTA

>8R7H_2 Serine hydroxymethyltransferase, cytosolic (chains B, C)
GSHMTMPVNGAHKDADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFA
SRAVLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQCWGVNVQP
YSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPD
TGYINYDQLEENARLFHPKLIIAGTSCYSRNLEYARLRKIADENGAYLMADMAHISGLVA
AGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVF
PGLQGGPHNHAIAGVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNH
LILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEKD
FQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAAVQALREEVESFASLFPL
PGLPDF

Primary citation

Structure-based mechanism of riboregulation of the metabolic enzyme SHMT1. Spizzichino, S., Di Fonzo, F., Marabelli, C. et al. Mol Cell (2024) 84:2682. 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…
8XND 3.45 Å, Crystal structure of serine hydroxymethyltransferase 1
8A11 3.52 Å, Cryo-EM structure of the Human SHMT1-RNA complex
6FL5 3.6 Å, Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution

Browse structure collections

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