8G16: Cytoplasmic GAPDH under 24h Oxidative Stress

CryoEM structure of cytoplasmic GAPDH under 24h Oxidative Stress. Determined by electron microscopy at 2.07 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 2.07 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,104
Mol. weight: 143.87 kDa
Released: 27 Dec 2023

Explore 8G16 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G16 contains 60 α-helices and 77 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.

Chains A, C and D: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-9	5	1
α-helix	13-25	13
β-strand	29-34	6	1
α-helix	40-48	9
β-strand	60-63	4	2
β-strand	66-69	4	2
β-strand	72-74	3	2
β-strand	75-77	3	1
α-helix	82-84	3
β-strand	94-97	4	1
α-helix	105-108	4
α-helix	109-112	4
β-strand	118-121	4	1
α-helix	129	1
β-strand	130	1	1
α-helix	137-139	3
β-strand	146-148	3	1
α-helix	152-168	17
β-strand	170-179	10	3
β-strand	186	1	4
α-helix	197-199	3
β-strand	201	1	4
β-strand	208-210	3	3
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	3
β-strand	240-249	10	3
α-helix	255-267	13
β-strand	274-277	4	3
α-helix	283-286	4
β-strand	293-304	12	3
β-strand	307-315	9	3
α-helix	318-333	16

Chain B: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-9	5	5
α-helix	13-25	13
β-strand	29-34	6	5
α-helix	40-48	9
β-strand	60-63	4	6
β-strand	66-69	4	6
β-strand	72-74	3	6
β-strand	75-77	3	5
α-helix	82-84	3
β-strand	94-97	4	5
α-helix	105-108	4
α-helix	109-112	4
β-strand	118-121	4	5
α-helix	129	1
β-strand	130	1	5
α-helix	137-139	3
β-strand	146-148	3	5
α-helix	152-168	17
β-strand	170-179	10	7
β-strand	186	1	8
α-helix	197-199	3
β-strand	201	1	8
β-strand	208-210	3	7
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	7
β-strand	240-249	10	7
α-helix	255-267	13
β-strand	274-277	4	7
α-helix	283-286	4
β-strand	293-296	4	7
β-strand	301-304	4	7
β-strand	307-315	9	7
α-helix	318-333	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	protein	334	Homo sapiens	P04406 (AlphaFold model)

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

>8G16_1 Glyceraldehyde-3-phosphate dehydrogenase (chains A, B, C, D)
GKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK
AENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVII
SAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAI
TATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVS
VVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGI
ALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE

Primary citation

Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Choi, W., Wu, H., Yserentant, K. et al. Proc Natl Acad Sci U S A (2023) 120:e2302471120-e2302471120. DOI 10.1073/pnas.2302471120 · PubMed

Other PDB entries of the same protein (UniProt P04406 (AlphaFold model), which also has an AlphaFold model), best resolution first:

27FM 1.46 Å, Crystal structure of human glyceraldehyde-3-phosphate dehydrogenase bound to gold(I)
6YND 1.52 Å, GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4.
1U8F 1.75 Å, Crystal Structure Of Human Placental Glyceraldehyde-3-Phosphate Dehydrogenase At 1.75…
9L3E 1.77 Å, Structure of GAPDH complexed with Leu-F
8P5F 1.82 Å, Human wild-type GAPDH,orthorhombic form
6M61 1.82 Å, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid
6YNE 1.85 Å, GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.
9UNY 1.87 Å, Natural product inhibitor of glyceraldehyde-3-phosphate dehydrogenase(GAPDH)
8G17 1.98 Å, CryoEM structure of wild-type GAPDH
4WNC 1.99 Å, Crystal structure of human wild-type GAPDH at 1.99 angstroms resolution
8G15 2.07 Å, CryoEM structure of nuclear GAPDH under 24h Oxidative Stress
8G12 2.17 Å, CryoEM structure of nuclear GAPDH under 8h Oxidative Stress

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