7OPM: Phosphorylated ERK2

Name: PDB 7OPM: Phosphorylated ERK2 in complex with ORF45
Published: 2022-02-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: viral protein

Phosphorylated ERK2 in complex with ORF45. Determined by X-ray diffraction at 2.45 Å resolution. Released 2 Feb 2022.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Homo sapiens, synthetic construct, Human herpesvirus 8
Chains: 3
Atoms: 3,208
Mol. weight: 46.37 kDa
Ligands: 08G
Released: 2 Feb 2022

Explore 7OPM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OPM contains 25 α-helices and 13 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: 24 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1-7	7
β-strand	12-14	3	1
β-strand	17-19	3	1
β-strand	25-33	9	2
β-strand	37-44	8	2
β-strand	49-56	8	2
α-helix	62-77	16
β-strand	83	1	3
β-strand	88-90	3	2
α-helix	95-97	3
β-strand	101-106	6	2
β-strand	110-111	2	3
α-helix	112-118	7
α-helix	120-122	3
α-helix	123-142	20
β-strand	145-146	2	4
α-helix	152-154	3
β-strand	155-157	3	3
β-strand	163-165	3	3
β-strand	172-173	2	4
α-helix	191-193	3
α-helix	196-200	5
α-helix	208-223	16
α-helix	233-244	12
α-helix	247-248	2
α-helix	249-253	5
α-helix	258-266	9
α-helix	268-269	2
α-helix	271-274	4
α-helix	275-278	4
α-helix	284-293	10
α-helix	302-303	2
α-helix	304-308	5
α-helix	311-313	3
α-helix	319-321	3
α-helix	331-334	4
α-helix	340-350	11

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 1	A	protein	364	Homo sapiens	P28482 (AlphaFold model)
synthetic ERK2 inhibitor peptide	B	protein	18	synthetic construct
Protein ORF45	C	protein	14	Human herpesvirus 8	F5HDE4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7OPM_1 Mitogen-activated protein kinase 1 (chains A)
GSASMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKI
SPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLL
KTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADP
DHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQ
LNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTF
NPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQP
GYRS

Sequence of entity 2 (B), FASTA

>7OPM_2 synthetic ERK2 inhibitor peptide (chains B)
MQLXLDSSNLARRRRRRR

Sequence of entity 3 (C), FASTA

>7OPM_3 Protein ORF45 (chains C)
RPPVKFIFPPPPLS

Ligands and cofactors

ID	Name	Formula	Copies
08G	1-[4-(hydroxymethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-3-[(1S)-1-phenylethyl]urea	C16 H17 N5 O2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host. Alexa, A., Sok, P., Gross, F. et al. Nat Commun (2022) 13:472-472. DOI 10.1038/s41467-022-28109-x · PubMed

Other PDB entries of the same protein (UniProt P28482 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8AOJ 1.12 Å, Specific covalent inhibitor of ERK2
4ZZN 1.33 Å, Human ERK2 in complex with an inhibitor
6SLG 1.33 Å, Human ERK2 with ERK1/2 inhibitor, AZD0364.
5WP1 1.4 Å, Complex of ERK2 with 5,7-dihydroxychromone
4QTA 1.45 Å, Structure of human ERK2 in complex with SCH772984 revealing a novel inhibitor-induced…
4QTE 1.5 Å, Structure of ERK2 in complex with VTX-11e, 4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYL…
2Y9Q 1.55 Å, Crystal structure of human ERK2 complexed with a MAPK docking peptide
6QA3 1.57 Å, ERK2 mini-fragment binding
6QAL 1.57 Å, ERK2 mini-fragment binding
6GJD 1.58 Å, Erk2 signalling protein
6QA1 1.58 Å, ERK2 mini-fragment binding
6QAH 1.58 Å, ERK2 mini-fragment binding

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