5C4V: Ski-like protein

Ski-like protein. Determined by X-ray diffraction at 2.6 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,835
Mol. weight: 129.14 kDa
Ligands: ZN, NI
Released: 12 Oct 2016

Explore 5C4V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C4V contains 39 α-helices and 57 β-strands across 6 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: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	322-330	9	1
β-strand	333-334	2	1
β-strand	339-342	4	1
β-strand	347-351	5	2
β-strand	358	1	2
β-strand	361-363	3	2
α-helix	374-380	7
β-strand	387-392	6	2
β-strand	396-400	5	2
β-strand	407-410	4	1
α-helix	412-417	6
β-strand	426-429	4	1
β-strand	434-438	5	2
α-helix	440-458	19
α-helix	492-496	5
α-helix	497-499	3
β-strand	500-505	6	1
α-helix	518-520	3
β-strand	524-529	6	1
α-helix	530-540	11

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	262-266	5	7
β-strand	272-276	5	7
α-helix	278-280	3
β-strand	289-291	3	7
β-strand	297-298	2	7
α-helix	300-303	4
α-helix	310-311	2
β-strand	315-318	4	1
α-helix	322-324	3
α-helix	325-328	4
β-strand	330-331	2	7
α-helix	341-352	12

Chain C: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	322-330	9	3
β-strand	333-334	2	3
α-helix	337-338	2
β-strand	339-342	4	3
β-strand	347-351	5	4
β-strand	358	1	4
β-strand	361-363	3	4
α-helix	374-380	7
β-strand	387-392	6	4
β-strand	396-400	5	4
β-strand	407-410	4	3
α-helix	412-417	6
β-strand	426-429	4	3
β-strand	434-438	5	4
α-helix	440-452	13
α-helix	493-496	4
α-helix	497-499	3
β-strand	500-505	6	3
α-helix	518-520	3
β-strand	524-529	6	3
α-helix	530-541	12

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	263-266	4	8
β-strand	272-276	5	8
α-helix	278-280	3
β-strand	289-291	3	8
β-strand	297-298	2	8
α-helix	300-303	4
α-helix	310-312	3
β-strand	315-318	4	3
α-helix	322-324	3
α-helix	325-328	4
β-strand	330-331	2	8
α-helix	341-351	11

Chain E: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	322-330	9	5
β-strand	333-334	2	5
α-helix	337-338	2
β-strand	339-342	4	5
β-strand	347-351	5	6
β-strand	358	1	6
β-strand	361-363	3	6
α-helix	374-381	8
β-strand	387-392	6	6
β-strand	396-400	5	6
β-strand	407-410	4	5
α-helix	412-417	6
β-strand	426-429	4	5
β-strand	434-438	5	6
α-helix	440-459	20
α-helix	493-497	5
β-strand	500-505	6	5
α-helix	518-520	3
β-strand	524-529	6	5
α-helix	530-540	11

Chain F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	263-266	4	9
β-strand	272-276	5	9
α-helix	278-280	3
β-strand	289-291	3	9
β-strand	297-298	2	9
α-helix	300-303	4
β-strand	315-318	4	5
α-helix	322-324	3
α-helix	325-328	4
β-strand	330-331	2	9
α-helix	341-352	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mothers against decapentaplegic homolog 4	A, C, E	protein	258	Homo sapiens	Q13485 (AlphaFold model)
Ski-like protein	B, D, F	protein	127	Homo sapiens	P12757 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>5C4V_1 Mothers against decapentaplegic homolog 4 (chains A, C, E)
MHHHHHHSSGVDLGTENLYFQSISNHPAPEYWCSIAYFEMDVQVGETFKVPSSCPIVTVD
GYVDPSGGDRFCLGQLSNVHRTEAIERARLHIGKGVQLECKGEGDVWVRCLSDHAVFVQS
YYLDREAGRAPGDAVHKIYPSAYIKVFDLRQCHRQMQQQAATAQAAAAAQAAAVAGNIPG
PGSVGGIAPAISLSAAAGIGVDDLRRLCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHR
ALQLLDEVLHTMPIADPQ

Sequence of entity 2 (B, D, F), FASTA

>5C4V_2 Ski-like protein (chains B, D, F)
MTFPQNGSVLPAKSSLAQLKETGSAFEVEHECLGKCQGLFAPQFYVQPDAPCIQCLECCG
MFAPQTFVMHSHRSPDKRTCHWGFESAKWHCYLHVNQKYLGTPEEKKLKIILEEMKEKFS
AHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
NI	Nickel (II) ion	Ni	2

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

Primary citation

SnoN Stabilizes the SMAD3/SMAD4 Protein Complex. Wallden, K., Nyman, T., Hallberg, B.M. Sci Rep (2017) 7:46370-46370. DOI 10.1038/srep46370 · PubMed

Other PDB entries of the same protein (UniProt Q13485 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YIC 1.6 Å, 14-3-3 sigma in complex with SMAD4 pS403 peptide
9HWE 1.7 Å, SMAD4 MH2, residues 314-552
9HZA 2.03 Å, SMAD4 MH2, residues 272-552
5MEY 2.05 Å, Crystal structure of Smad4-MH1 bound to the GGCGC site.
1YGS 2.1 Å, Crystal structure of the SMAD4 tumor suppressor C-terminal domain
9QE6 2.1 Å, SMAD4 MH2 domain (residues 314-552) bound by Nanobody A1 (NbA1)
5UWU 2.24 Å, Crystal Structure of SMAD4 NES Peptide in complex with CRM1-Ran-RanBP1
1U7F 2.6 Å, Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex
1DD1 2.62 Å, Crystal structure analysis of the SMAD4 active fragment
1U7V 2.7 Å, Crystal Structure of the phosphorylated Smad2/Smad4 heterotrimeric complex
1MR1 2.85 Å, Crystal Structure of a Smad4-Ski Complex
5MEZ 2.98 Å, Crystal structure of Smad4-MH1 bound to the GGCT site.

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