7UPI: SHOC2-PP1c-MRAS holophosphatase complex

Cryo-EM structure of SHOC2-PP1c-MRAS holophosphatase complex. Determined by electron microscopy at 2.89 Å resolution. Released 4 May 2022.

Method: Electron microscopy
Resolution: 2.89 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,775
Mol. weight: 124.23 kDa
Ligands: MG, MN, GTP
Released: 4 May 2022

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

Secondary structure: helices and β-sheets

7UPI contains 42 α-helices and 49 β-strands across 3 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-20	8	1
α-helix	26-34	9
β-strand	48-56	9	1
β-strand	59-67	9	1
α-helix	78-83	6
β-strand	87-93	7	1
α-helix	97-114	18
β-strand	121-126	6	1
α-helix	138-148	11
β-strand	152-154	3	1
β-strand	156	1	2
α-helix	161	1
β-strand	162	1	2
α-helix	164-177	14

Chain B: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	8-17	10
α-helix	32-47	16
β-strand	52-55	4	3
β-strand	59-62	4	4
β-strand	64	1	5
α-helix	69-79	11
β-strand	87-89	3	4
α-helix	100-113	14
β-strand	118-120	3	4
α-helix	128-134	7
α-helix	136-143	8
α-helix	146-156	11
β-strand	162-165	4	3
β-strand	169-172	4	3
α-helix	183-187	5
α-helix	194-196	3
α-helix	200-206	7
β-strand	208-209	2	6
β-strand	216-218	3	6
β-strand	225-227	3	6
α-helix	229-239	11
β-strand	243-246	4	3
β-strand	255-258	4	3
β-strand	263-266	4	3
β-strand	267	1	5
α-helix	272-274	3
β-strand	280-285	6	4
β-strand	290-291	2	7
β-strand	292-296	5	4

Chain C: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	65-68	4	7
β-strand	71-73	3	7
α-helix	88-100	13
β-strand	104-106	3	8
α-helix	117-121	5
β-strand	127-129	3	8
α-helix	140-144	5
β-strand	150-152	3	8
α-helix	163-167	5
β-strand	173-175	3	8
α-helix	186-190	5
β-strand	196-198	3	8
α-helix	209-213	5
β-strand	219-221	3	8
α-helix	232-236	5
β-strand	242-244	3	8
α-helix	255-259	5
β-strand	265-267	3	8
α-helix	278-282	5
β-strand	288-290	3	8
α-helix	301-305	5
β-strand	311-313	3	8
α-helix	326-329	4
β-strand	335-337	3	8
α-helix	346-347	2
α-helix	351-354	4
β-strand	359-361	3	8
α-helix	370-371	2
β-strand	383-385	3	8
α-helix	396-400	5
β-strand	406-408	3	8
α-helix	419-423	5
β-strand	429-431	3	8
β-strand	439	1	9
α-helix	440-441	2
α-helix	444-446	3
β-strand	452-454	3	8
β-strand	462	1	9
α-helix	465-469	5
β-strand	475-477	3	8
α-helix	488-492	5
β-strand	498-500	3	8
α-helix	511-515	5
β-strand	521-523	3	8
α-helix	535-539	5
β-strand	545-547	3	8
α-helix	558-563	6
α-helix	565-575	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein M-Ras	A	protein	183	Homo sapiens	O14807 (AlphaFold model)
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	B	protein	331	Homo sapiens	P62136 (AlphaFold model)
Leucine-rich repeat protein SHOC-2	C	protein	583	Homo sapiens	Q9UQ13 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7UPI_1 Ras-related protein M-Ras (chains A)
GMATSAVPSDNLPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPTIEDSYLKHTEIDNQ
WAILDVLDTAGLEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESF
PMILVANKVDLMHLRKITREQGKEMATKHNIPYIETSAKDPPLNVDKAFHDLVRVIRQQI
PEK

Sequence of entity 2 (B), FASTA

>7UPI_2 Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (chains B)
GMSDSEKLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPL
KICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFF
LLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPD
LQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKH
DLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPA
DKNKGKYGQFSGLNPGGRPITPPRNSAKAKK

Sequence of entity 3 (C), FASTA

>7UPI_3 Leucine-rich repeat protein SHOC-2 (chains C)
GMSSSLGKEKDSKEKDPKVPSAKEREKEAKASGGFGKESKEKEPKTKGKDAKDGKKDSSA
AQPGVAFSVDNTIKRPNPAPGTRKKSSNAEVIKELNKCREENSMRLDLSKRSIHILPSSI
KELTQLTELYLYSNKLQSLPAEVGCLVNLMTLALSENSLTSLPDSLDNLKKLRMLDLRHN
KLREIPSVVYRLDSLTTLYLRFNRITTVEKDIKNLSKLSMLSIRENKIKQLPAEIGELCN
LITLDVAHNQLEHLPKEIGNCTQITNLDLQHNELLDLPDTIGNLSSLSRLGLRYNRLSAI
PRSLAKCSALEELNLENNNISTLPESLLSSLVKLNSLTLARNCFQLYPVGGPSQFSTIYS
LNMEHNRINKIPFGIFSRAKVLSKLNMKDNQLTSLPLDFGTWTSMVELNLATNQLTKIPE
DVSGLVSLEVLILSNNLLKKLPHGLGNLRKLRELDLEENKLESLPNEIAYLKDLQKLVLT
NNQLTTLPRGIGHLTNLTHLGLGENLLTHLPEEIGTLENLEELYLNDNPNLHSLPFELAL
CSKLSIMSIENCPLSHLPPQIVAGGPSFIIQFLKMQGPYRAMV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
MN	Manganese (II) ion	Mn	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

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

Primary citation

Structure-function analysis of the SHOC2-MRAS-PP1C holophosphatase complex. Kwon, J.J., Hajian, B., Bian, Y. et al. Nature (2022) 609:408-415. DOI 10.1038/s41586-022-04928-2 · PubMed

Other PDB entries of the same protein (UniProt O14807 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9O0P 1.5 Å, Crystal structure of GDP-bound mutant MRAS in complex with MRTX1133
9O0Q 1.9 Å, Crystal structure of GMPPNP-bound mutant MRAS in complex with MRTX1133
7TXH 1.95 Å, Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca
9C1A 1.96 Å, Crystal structure of GDP-bound human M-RAS protein in crystal form I
9B4R 2.1 Å, Crystal structure of MRAS bound to GMPPNP
7TVF 2.17 Å, Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom
9C1B 2.27 Å, Crystal structure of GDP-bound human M-RAS protein in crystal form II
9B4T 2.75 Å, Crystal structure of the MRAS-p110alpha complex
9MEZ 2.8 Å, Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain)
7SD0 2.95 Å, Cryo-EM structure of the SHOC2:PP1C:MRAS complex

Browse structure collections

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