2XNS

Crystal Structure Of Human G alpha i1 Bound To A Designed Helical Peptide Derived From The Goloco Motif Of RGS14

PDB DOI: https://doi.org/10.2210/pdb2XNS/pdb

Classification: HYDROLASE/PEPTIDE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-08-05 Released: 2011-06-08
Deposition Author(s): Bosch, D., Sammond, D.W., Butterfoss, G.L., Machius, M., Siderovski, D.P., Kuhlman, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.41 Å
R-Value Free: 0.244
R-Value Work: 0.223
R-Value Observed: 0.223

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Computational Design of the Sequence and Structure of a Protein-Binding Peptide.

Sammond, D.W., Bosch, D.E., Butterfoss, G.L., Purbeck, C., Machius, M., Siderovski, D.P., Kuhlman, B.

(2011) J Am Chem Soc 133: 4190

PubMed: 21388199 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ja110296z
Primary Citation of Related Structures:
2XNS

PubMed Abstract:
The de novo design of protein-binding peptides is challenging because it requires the identification of both a sequence and a backbone conformation favorable for binding. We used a computational strategy that iterates between structure and sequence optimization to redesign the C-terminal portion of the RGS14 GoLoco motif peptide so that it adopts a new conformation when bound to Gα(i1). An X-ray crystal structure of the redesigned complex closely matches the computational model, with a backbone root-mean-square deviation of 1.1 Å.

Organizational Affiliation

Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.

Macromolecule Content

Total Structure Weight: 85.52 kDa
Atom Count: 5,862
Modelled Residue Count: 710
Deposited Residue Count: 734
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GUANINE NUCLEOTIDE-BINDING PROTEIN G(I) SUBUNIT ALPHA-1	A, B	327	Homo sapiens	Mutation(s): 0 EC: 3.6.5.1 (PDB Primary Data), 3.6.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATOR OF G-PROTEIN SIGNALING 14	C, D	40	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43566 (Homo sapiens) Explore O43566 Go to UniProtKB: O43566
PHAROS: O43566 GTEx: ENSG00000169220
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43566
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 E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
SRT Query on SRT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	I [auth C], J [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain I [auth C] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.41 Å
R-Value Free: 0.244
R-Value Work: 0.223
R-Value Observed: 0.223
Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 265.261	α = 90
b = 265.261	β = 90
c = 265.261	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description