3T5G | pdb_00003t5g

Structure of fully modified farnesylated Rheb in complex with PDE6D

PDB DOI: https://doi.org/10.2210/pdb3T5G/pdb

Classification: SIGNALING PROTEIN,LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-07-27 Released: 2011-10-26
Deposition Author(s): Ismail, S.A., Chen, Y.-X., Wittinghofer, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.198 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo.

Ismail, S.A., Chen, Y.X., Rusinova, A., Chandra, A., Bierbaum, M., Gremer, L., Triola, G., Waldmann, H., Bastiaens, P.I., Wittinghofer, A.

(2011) Nat Chem Biol 7: 942-949

PubMed: 22002721 Search on PubMed
DOI: https://doi.org/10.1038/nchembio.686
Primary Citation Related Structures:
3T5G, 3T5I

PubMed Abstract:
Lipidated Rho and Rab GTP-binding proteins are transported between membranes in complex with solubilizing factors called 'guanine nucleotide dissociation inhibitors' (GDIs). Unloading from GDIs using GDI displacement factors (GDFs) has been proposed but remains mechanistically elusive. PDEδ is a putative solubilizing factor for several prenylated Ras-subfamily proteins. Here we report the structure of fully modified farnesylated Rheb-GDP in complex with PDEδ. The structure explains the nucleotide-independent binding of Rheb to PDEδ and the relaxed specificity of PDEδ. We demonstrate that the G proteins Arl2 and Arl3 act in a GTP-dependent manner as allosteric release factors for farnesylated cargo. We thus describe a new transport system for farnesylated G proteins involving a GDI-like molecule and an unequivocal GDF. Considering the importance of PDEδ for proper Ras and Rheb signaling, this study is instrumental in developing a new target for anticancer therapy.

Organizational Affiliation

Structural Biology Group, Max Planck Institute for Molecular Physiology, Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 38.51 kDa
Atom Count: 3,023
Modeled Residue Count: 318
Deposited Residue Count: 333
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Rheb	A	181	Homo sapiens	Mutation(s): 1 Gene Names: RHEB, RHEB2 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q15382 (Homo sapiens) Explore Q15382 Go to UniProtKB: Q15382
PHAROS: Q15382 GTEx: ENSG00000106615
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15382
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	B	152	Homo sapiens	Mutation(s): 0 Gene Names: PDE6D, PDED
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens) Explore O43924 Go to UniProtKB: O43924
PHAROS: O43924 GTEx: ENSG00000156973
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43924
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FAR Query on FAR 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]	FARNESYL C₁₅ H₂₆ JXBSHSBNOVLGHF-BUJBXKITSA-N		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 D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMT Query on CMT	A	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.235 (Depositor), 0.235 (DCC)
R-Value Work: 0.198 (Depositor), 0.197 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.89	α = 90
b = 57.38	β = 90
c = 134.52	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Ismail, S.A.

Chen, Y.-X.

Wittinghofer, A.

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2011-11-30
Changes: Database references
Version 1.2: 2013-09-25
Changes: Derived calculations
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description