4PVF: Serine hydroxymethyltransferase, mitochondrial

Name: PDB 4PVF: Crystal structure of Homo sapiens holo serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), isoform 3, transcript variant 5, 483 aa, at 2.6 ang. resolution
Published: 2015-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of Homo sapiens holo serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), isoform 3, transcript variant 5, 483 aa, at 2.6 ang. resolution. Determined by X-ray diffraction at 2.6 Å resolution. Released 28 Jan 2015.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,229
Mol. weight: 107.8 kDa
Released: 28 Jan 2015

Explore 4PVF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PVF contains 53 α-helices and 44 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: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	28-31	4
α-helix	33-48	16
β-strand	50-51	2	1
α-helix	61-67	7
α-helix	70-73	4
β-strand	78-79	2	2
β-strand	82-83	2	2
α-helix	89-105	17
β-strand	113-116	4	3
α-helix	122-133	12
β-strand	139-143	5	3
α-helix	145-147	3
α-helix	151-153	3
β-strand	156	1	4
β-strand	161	1	4
α-helix	165-168	4
β-strand	170-174	5	3
β-strand	176-177	2	5
β-strand	182-183	2	5
α-helix	185-195	11
β-strand	199-202	4	3
α-helix	213-223	11
β-strand	226-230	5	3
α-helix	232-234	3
α-helix	235-239	5
α-helix	246-248	3
β-strand	252-256	5	3
α-helix	259-261	3
β-strand	267-272	6	3
β-strand	275	1	6
β-strand	287	1	6
α-helix	290-296	7
α-helix	297-302	6
α-helix	308-322	15
α-helix	324-345	22
β-strand	350-351	2	7
α-helix	352-354	3
β-strand	360-364	5	7
α-helix	366-368	3
α-helix	372-381	10
β-strand	384-385	2	1
β-strand	387-389	3	7
α-helix	390-391	2
β-strand	396	1	8
β-strand	398	1	8
α-helix	399-400	2
β-strand	402-406	5	7
α-helix	408-412	5
α-helix	417-439	23
α-helix	444-453	10
α-helix	455-473	19

Chain B: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	28-31	4
α-helix	33-48	16
β-strand	50-51	2	9
α-helix	61-67	7
α-helix	70-73	4
β-strand	78-79	2	10
β-strand	82-83	2	10
α-helix	89-105	17
β-strand	113-116	4	11
α-helix	122-133	12
β-strand	139-143	5	11
α-helix	145-147	3
α-helix	151-153	3
β-strand	156	1	12
β-strand	161	1	12
α-helix	165-168	4
β-strand	170-174	5	11
β-strand	176	1	13
β-strand	183	1	13
α-helix	185-195	11
β-strand	199-202	4	11
α-helix	213-223	11
β-strand	226-230	5	11
α-helix	232-234	3
α-helix	235-239	5
α-helix	246-248	3
β-strand	252-256	5	11
α-helix	259-261	3
β-strand	267-272	6	11
β-strand	275	1	14
β-strand	287	1	14
α-helix	290-296	7
α-helix	297-302	6
α-helix	308-322	15
α-helix	324-345	22
β-strand	350-351	2	15
α-helix	352-354	3
β-strand	360-364	5	15
α-helix	372-381	10
β-strand	384-385	2	9
β-strand	387-389	3	15
β-strand	402-406	5	15
α-helix	408-412	5
α-helix	417-439	23
α-helix	444-453	10
α-helix	455-473	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, mitochondrial	A, B	protein	483	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4PVF_1 Serine hydroxymethyltransferase, mitochondrial (chains A, B)
MAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCS
RAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPY
SGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKT
GLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAA
KVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFP
SLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHL
VLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDF
RRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF
DEH

Primary citation

How pyridoxal 5'-phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state. Giardina, G., Brunotti, P., Fiascarelli, A. et al. FEBS J (2015) 282:1225-1241. DOI 10.1111/febs.13211 · PubMed

Other PDB entries of the same protein (UniProt P34897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8AQL 1.23 Å, High-resolution crystal structure of human SHMT2
29LK 1.26 Å, High-resolution structure of human SHMT2 in complex with PLP-Ser (external aldimine)
9RWD 1.3 Å, High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)
32JY 1.8 Å, Structure of the pathogenic variant G423S of Human SHMT2
6DK3 2.04 Å, Human mitochondrial serine hydroxymethyltransferase 2
9BOX 2.1 Å, Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase…
32JA 2.2 Å, Structure of the pathogenic variant T186R of Human SHMT2 in the apo open dimeric…
6QVL 2.28 Å, Human SHMT2 in complex with pemetrexed
6M5O 2.3 Å, Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with…
6QVG 2.32 Å, Human SHMT2 in complex with lometrexol
8GKW 2.38 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…
5V7I 2.47 Å, Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial)…

Browse structure collections

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