9QE6: Mothers against decapentaplegic homolog 4

SMAD4 MH2 domain (residues 314-552) bound by Nanobody A1 (NbA1). Determined by X-ray diffraction at 2.1 Å resolution. Released 30 Sept 2026.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Lama glama
Chains: 4
Atoms: 4,970
Mol. weight: 82.64 kDa
Released: 30 Sept 2026

Explore 9QE6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QE6 contains 17 α-helices and 45 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.

Chain A: 7 helices, 12 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	361-363	3	2
α-helix	374-381	8
β-strand	387-392	6	2
β-strand	396-401	6	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	440-452	13
α-helix	492-495	4
α-helix	496-499	4
β-strand	500-505	6	1
α-helix	518-520	3
β-strand	524-529	6	1
α-helix	530-540	11

Chain B: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	18-25	8	3
β-strand	30-39	10	4
β-strand	46-51	6	4
β-strand	57-59	3	4
β-strand	67-72	6	3
β-strand	77-82	6	3
α-helix	87-89	3
β-strand	91-100	10	4
α-helix	106-107	2
β-strand	108-111	4	4
β-strand	115-117	3	4

Chain C: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	322-330	9	5
β-strand	333-334	2	5
β-strand	339-342	4	5
β-strand	347-351	5	6
β-strand	361-363	3	6
α-helix	374-381	8
β-strand	387-392	6	6
β-strand	396-401	6	6
β-strand	407-410	4	5
α-helix	412-418	7
β-strand	427-429	3	5
β-strand	434-438	5	6
α-helix	440-450	11
α-helix	495-499	5
β-strand	500-505	6	5
α-helix	518-520	3
β-strand	524-529	6	5
α-helix	530-542	13

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	7
β-strand	10-13	4	8
β-strand	18-25	8	7
β-strand	30-39	10	8
β-strand	46-51	6	8
β-strand	57-59	3	8
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-100	10	8
α-helix	106-107	2
β-strand	108-111	4	8
β-strand	115-120	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mothers against decapentaplegic homolog 4	A, C	protein	240	Homo sapiens	Q13485 (AlphaFold model)
Nanobody A1 (NbA1)	B, D	protein	131	Lama glama

Sequence of entity 1 (A, C), FASTA

>9QE6_1 Mothers against decapentaplegic homolog 4 (chains A, C)
GISNHPAPEYWCSIAYFEMDVQVGETFKVPSSCPIVTVDGYVDPSGGDRFCLGQLSNVHR
TEAIERARLHIGKGVQLECKGEGDVWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYPS
AYIKVFDLRQCHRQMQQQAATAQAAAAAQAAAVAGNIPGPGSVGGIAPAISLSAAAGIGV
DDLRRLCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVLHTMPIADPQPLD

Sequence of entity 2 (B, D), FASTA

>9QE6_2 Nanobody A1 (NbA1) (chains B, D)
QVQLVESGGGLVQAEGSLRLSCAASGRFFSINAMRWYRQVPGKQREWVAGITSGGITDYA
DSVKGRFTISRDNGKNTVYLQMNSLKPEDTAVYYCNAHLREKQYDAPGNYWGQGTQVTVS
SHHHHHHEPEA

Primary citation

(RUNNING TITLE:) Nanobodies for SMAD4 Structural and Functional Studies. Condeminas, M., Torner, C., Pluta, R. et al. To be published.

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
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
5C4V 2.6 Å, Ski-like protein
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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