6S8S | pdb_00006s8s

Extended structure of the human DDX6 C-terminal domain in complex with an EDC3 FDF peptide

PDB DOI: https://doi.org/10.2210/pdb6S8S/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-10 Released: 2019-09-04
Deposition Author(s): Peter, D., Valkov, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.226 (Depositor), 0.231 (DCC)
R-Value Work:
0.179 (Depositor), 0.187 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2WAX

Literature

Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression.

Peter, D., Ruscica, V., Bawankar, P., Weber, R., Helms, S., Valkov, E., Igreja, C., Izaurralde, E.

(2019) Genes Dev 33: 1355-1360

PubMed: 31439631 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/gad.329219.119
Primary Citation Related Structures:
6S8R, 6S8S

PubMed Abstract:
GIGYF (Grb10-interacting GYF [glycine-tyrosine-phenylalanine domain]) proteins coordinate with 4EHP (eIF4E [eukaryotic initiation factor 4E] homologous protein), the DEAD (Asp-Glu-Ala-Asp)-box helicase Me31B/DDX6, and mRNA-binding proteins to elicit transcript-specific repression. However, the underlying molecular mechanism remains unclear. Here, we report that GIGYF contains a motif necessary and sufficient for direct interaction with Me31B/DDX6. A 2.4 Å crystal structure of the GIGYF-Me31B complex reveals that this motif arranges into a coil connected to a β hairpin on binding to conserved hydrophobic patches on the Me31B RecA2 domain. Structure-guided mutants indicate that 4EHP-GIGYF-DDX6 complex assembly is required for tristetraprolin-mediated down-regulation of an AU-rich mRNA, thus revealing the molecular principles of translational repression.

Organizational Affiliation

Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.

Macromolecule Content

Total Structure Weight: 57.05 kDa
Atom Count: 3,775
Modeled Residue Count: 415
Deposited Residue Count: 474
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX6	A, C	193	Homo sapiens	Mutation(s): 0 Gene Names: DDX6, HLR2, RCK EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P26196 (Homo sapiens) Explore P26196 Go to UniProtKB: P26196
PHAROS: P26196 GTEx: ENSG00000110367
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26196
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Enhancer of mRNA-decapping protein 3	B, D	44	Homo sapiens	Mutation(s): 0 Gene Names: EDC3, LSM16, YJDC, YJEFN2, PP844
UniProt & NIH Common Fund Data Resources
Find proteins for Q96F86 (Homo sapiens) Explore Q96F86 Go to UniProtKB: Q96F86
PHAROS: Q96F86 GTEx: ENSG00000179151
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96F86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXS Query on CXS Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	J [auth A], K [auth A], L [auth A], P [auth C], Q [auth C]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth C] Focus chain Q [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth C], N [auth C], O [auth C], R [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.226 (Depositor), 0.231 (DCC)
R-Value Work: 0.179 (Depositor), 0.187 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.425	α = 90
b = 47.878	β = 96.34
c = 65.757	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-09-04

Deposition Author(s):

Peter, D.

Valkov, E.

Revision History (Full details and data files)

Version 1.0: 2019-09-04
Type: Initial release
Version 1.1: 2019-10-09
Changes: Data collection, Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description