3Q85 | pdb_00003q85

Crystal Structure of Rem2 G-domain -GTP Analog Complex

PDB DOI: https://doi.org/10.2210/pdb3Q85/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-01-06 Released: 2011-09-21
Deposition Author(s): Navon-Perry, L., Hirsch, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.235 (Depositor), 0.231 (DCC)
R-Value Work:
0.208 (Depositor), 0.203 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Literature

RGK Family G-Domain:GTP Analog Complex Structures and Nucleotide-Binding Properties.

Sasson, Y., Navon-Perry, L., Huppert, D., Hirsch, J.A.

(2011) J Mol Biology 413: 372-389

PubMed: 21903096 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2011.08.017
Primary Citation Related Structures:
3Q72, 3Q7P, 3Q7Q, 3Q85

PubMed Abstract:
The RGK family of small G-proteins, including Rad, Gem, Rem1, and Rem2, is inducibly expressed in various mammalian tissues and interacts with voltage-dependent calcium channels and Rho kinase. Many questions remain regarding their physiological roles and molecular mechanism. Previous crystallographic studies reported RGK G-domain:guanosine di-phosphate structures. To test whether RGK proteins undergo a nucleotide-induced conformational change, we determined the crystallographic structures of Rad:GppNHp and Rem2:GppNHp to 1.7 and 1.8 Å resolutions, respectively. Also, we characterized the nucleotide-binding properties and conformations for Gem, Rad, and several structure-based mutants using fluorescence spectroscopy. The results suggest that RGK G-proteins may not behave as Ras-like canonical nucleotide-induced molecular switches. Further, the RGK proteins have differing structures and nucleotide-binding properties, which may have implications for their varied action on effectors.

Organizational Affiliation

Department of Biochemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.

Macromolecule Content

Total Structure Weight: 39.1 kDa
Atom Count: 2,866
Modeled Residue Count: 300
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein REM 2	A, B	169	Mus musculus	Mutation(s): 0 Gene Names: Rem2
UniProt
Find proteins for Q8VEL9 (Mus musculus) Explore Q8VEL9 Go to UniProtKB: Q8VEL9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8VEL9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.235 (Depositor), 0.231 (DCC)
R-Value Work: 0.208 (Depositor), 0.203 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.525	α = 90
b = 59.08	β = 101.26
c = 56.144	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Navon-Perry, L.

Hirsch, J.A.

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2011-10-26
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description