9Q72 | pdb_00009q72

Trypanosoma brucei EIF4E5 translation initiation factor in complex with cap-4

PDB DOI: https://doi.org/10.2210/pdb9Q72/pdb

Classification: TRANSLATION
Organism(s): Trypanosoma brucei brucei TREU927
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-22 Released: 2025-11-26
Deposition Author(s): Penteado, R.F., Guimaraes, B.G.
Funding Organization(s): Pasteur Institute, Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.169 (Depositor), 0.190 (DCC)
R-Value Work:
0.139 (Depositor), 0.163 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Selective eIF4E-eIF4G Pairing and Cap-4 Recognition Mechanisms in Trypanosomatids: Insights From EIF4E5-EIF4G1 and EIF4E6-EIF4G5 Complexes.

Penteado, R.F., Vichier-Guerre, S., da Silva Pereira, B.M., Dugue, L., Guerra Slompo, E.P., Assuncao de Matos, T.R., Pochet, S., Zanchin, N.I.T., Guimaraes, B.G.

(2026) J Mol Biology 438: 169550-169550

PubMed: 41265746 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2025.169550
Primary Citation Related Structures:
9Q72, 9Q73, 9Q74, 9Q75, 9Q78, 9Q79

PubMed Abstract:
Translation initiation in eukaryotes is a highly regulated process involving the assembly of several transient protein complexes. A key step in this process is recognition of the mRNA 5' cap structure by the initiation factor eIF4E, a core component of the eIF4F complex. In trypanosomatids, this mechanism diverges from canonical eukaryotic systems, featuring five distinct eIF4F-like complexes formed through specific pairings of eIF4E and eIF4G homologs. Additionally, trypanosomatid mRNAs exhibit a unique hypermethylated cap-4 structure at the 5' end. To elucidate the molecular basis of selective eIF4E-eIF4G interactions and the modulation of cap binding upon eIF4G engagement, we determined high-resolution crystal structures of EIF4E5-EIF4G1 complexes from Trypanosoma brucei and T. cruzi, and the EIF4E6-EIF4G5 complex from T. cruzi. These structural studies, supported by biophysical analyses in the presence and absence of a cap-4 analog, reveal key determinants of cap recognition associated with cap-4 structural flexibility and plasticity in the cap-binding pockets. We observe conformational rearrangements upon eIF4G binding and propose a relationship between these structural changes and increased cap-4 affinity. In addition, comparative structural analysis of the EIF4E5-EIF4G1 and EIF4E6-EIF4G5 complexes offers atomic-level insights into the molecular determinants of specificity that govern selective eIF4E-eIF4G pairings in trypanosomatids.

Organizational Affiliation

Carlos Chagas Institute, Oswaldo Cruz Foundation, Rua Prof. Algacyr Munhoz Mader, 3775, 81350-010 Curitiba, PR, Brazil.

Macromolecule Content

Total Structure Weight: 26.24 kDa
Atom Count: 2,088
Modeled Residue Count: 187
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E type 5	A	215	Trypanosoma brucei brucei TREU927	Mutation(s): 0 Gene Names: Tb10.70.2180
UniProt
Find proteins for Q38B99 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38B99 Go to UniProtKB: Q38B99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q38B99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LRM (Subject of Investigation/LOI) Query on LRM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-3H-purin-7-ium C₅₆ H₇₉ N₂₀ O₃₈ P₆ LXUOPLSSKHEGET-DYPPLJCPSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]