9QE8 | pdb_00009qe8

SMAD4 MH2 domain (residues 314-552) bound by Nanobody A7 (NbA7)

PDB DOI: https://doi.org/10.2210/pdb9QE8/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens, Lama glama
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-07 Released: 2026-09-30
Deposition Author(s): Pluta, R., Macias, M.J., Condeminas, M.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN), Generalitat de Catalunya, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.274 (Depositor), 0.237 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Characterizing two nanobodies for SMAD4.

Condeminas, M., Torner, C., Pluta, R., Ruiz, L., R de Regil, M., Khan, R.J., Pous, J., Pardon, E., Steyaert, J., Fromm, S., Martin-Malpartida, P., Macias, M.J.

(2026) FEBS Lett

PubMed: 42779504 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.70466
Primary Citation Related Structures:
9HWE, 9HZA, 9QE6, 9QE8

PubMed Abstract:
In metazoans, TGF-β signaling regulates essential cellular processes via the SMAD proteins. Many biophysical and cellular assays of SMAD-driven signaling require molecular tools that can recognize them in their native folded state. In this context, we report two nanobodies (Nbs), NbS4A1 and NbS4A7, which target the 3D structure of the human SMAD4-MH2 domain with high affinity and specificity. X-ray structures of the Nb-SMAD4 complexes reveal that each nanobody recognizes the SMAD4-MH2 domain through distinct but overlapping sites, precluding their simultaneous binding. Furthermore, NbS4A1 impedes SMAD4 binding with R-SMADs while NbS4A7 recognizes SMAD4 even when bound to R-SMADs. These distinct interaction modes will enable the study of folded SMAD complexes with cofactors and/or DNA in different experimental contexts.

Organizational Affiliation

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Spain.

Macromolecule Content

Total Structure Weight: 241.94 kDa
Atom Count: 14,014
Modeled Residue Count: 1,776
Deposited Residue Count: 2,196
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog 4	A, C, E, G, I A, C, E, G, I, K	240	Homo sapiens	Mutation(s): 0 Gene Names: SMAD4, DPC4, MADH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13485 (Homo sapiens) Explore Q13485 Go to UniProtKB: Q13485
PHAROS: Q13485 GTEx: ENSG00000141646
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13485
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody A7 (NbA7)	B, D, F, H, J B, D, F, H, J, L	126	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain N [auth A] SDF format, chain DA [auth I] SDF format, chain CA [auth H] SDF format, chain AA [auth G] MOL2 format, chain X [auth F] MOL2 format, chain N [auth A] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth F] mmCIF format, chain N [auth A] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth H] mmCIF format, chain AA [auth G]	AA [auth G], CA [auth H], DA [auth I], N [auth A], X [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain N [auth A] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain N [auth A] Focus chain X [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain GA [auth K] SDF format, chain W [auth E] SDF format, chain T [auth C] SDF format, chain P [auth A] SDF format, chain BA [auth G] MOL2 format, chain GA [auth K] MOL2 format, chain W [auth E] MOL2 format, chain T [auth C] MOL2 format, chain P [auth A] MOL2 format, chain BA [auth G] mmCIF format, chain GA [auth K] mmCIF format, chain W [auth E] mmCIF format, chain T [auth C] mmCIF format, chain P [auth A] mmCIF format, chain BA [auth G]	BA [auth G], GA [auth K], P [auth A], T [auth C], W [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain GA [auth K] Focus chain P [auth A] Focus chain T [auth C] Focus chain W [auth E] Interactions & Density Focus chain BA [auth G] Focus chain GA [auth K] Focus chain P [auth A] Focus chain T [auth C] Focus chain W [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth A] SDF format, chain FA [auth J] SDF format, chain EA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth A] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth A] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth I]	EA [auth I] FA [auth J] M [auth A] O [auth A] Q [auth C] EA [auth I], FA [auth J], M [auth A], O [auth A], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth E], Y [auth F], Z [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth I] Focus chain FA [auth J] Focus chain M [auth A] Focus chain O [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain EA [auth I] Focus chain FA [auth J] Focus chain M [auth A] Focus chain O [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.274 (Depositor), 0.237 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.126	α = 119.933
b = 147.899	β = 94.326
c = 148.856	γ = 89.308

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-30

Deposition Author(s):

Pluta, R.

Macias, M.J.

Condeminas, M.

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PDC_2021-121162-I00
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2021-122909NB-I00
Generalitat de Catalunya	Spain	2021 SGR-866
Ministerio de Ciencia e Innovacion (MCIN)	Spain	BFU2017-82675-P
Other private		BBVA