7BTC

Crystal structure of Rheb Y35N mutant bound to GDP

PDB DOI: https://doi.org/10.2210/pdb7BTC/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-04-01 Released: 2020-06-17
Deposition Author(s): Zhang, C., Zhang, T., Ding, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.233
R-Value Work: 0.187
R-Value Observed: 0.189

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.

Literature

Molecular basis for the functions of dominantly active Y35N and inactive D60K Rheb mutants in mTORC1 signaling.

Zhang, C., Liu, Y., Zhang, Y., Wang, X., Zhang, T., Ding, J.

(2020) J Mol Cell Biol 12: 741-744

PubMed: 32470140 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/jmcb/mjaa025
Primary Citation of Related Structures:
7BTA, 7BTC, 7BTD

Organizational Affiliation

State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Macromolecule Content

Total Structure Weight: 82.17 kDa
Atom Count: 5,577
Modelled Residue Count: 662
Deposited Residue Count: 708
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Rheb	A, B, C, D	177	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15382
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.233
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.426	α = 90
b = 78.656	β = 90
c = 117.398	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Zhang, C.

Zhang, T.

Ding, J.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870722

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
Version 1.1: 2020-12-30
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Refinement description