[English] 日本語
Yorodumi
- PDB-7bta: Crystal structure of Rheb D60K mutant bound to GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bta
TitleCrystal structure of Rheb D60K mutant bound to GDP
ComponentsGTP-binding protein Rheb
KeywordsSIGNALING PROTEIN / mTORC1 / small GTPase / Rheb
Function / homology
Function and homology information


regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / protein kinase activator activity / oligodendrocyte differentiation ...regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / protein kinase activator activity / oligodendrocyte differentiation / mTORC1-mediated signalling / cellular response to nutrient levels / positive regulation of TOR signaling / regulation of macroautophagy / endomembrane system / positive regulation of TORC1 signaling / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / TP53 Regulates Metabolic Genes / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spliceosomal complex / GDP binding / postsynaptic density / regulation of cell cycle / lysosomal membrane / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / protein kinase binding / magnesium ion binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, C. / Zhang, T. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870722 China
CitationJournal: J Mol Cell Biol / Year: 2020
Title: Molecular basis for the functions of dominantly active Y35N and inactive D60K Rheb mutants in mTORC1 signaling.
Authors: Zhang, C. / Liu, Y. / Zhang, Y. / Wang, X. / Zhang, T. / Ding, J.
History
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP-binding protein Rheb
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4026
Polymers40,3262
Non-polymers1,0764
Water21612
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7013
Polymers20,1631
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area8100 Å2
MethodPISA
2
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7013
Polymers20,1631
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-6 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.860, 47.800, 61.070
Angle α, β, γ (deg.)90.000, 112.750, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein GTP-binding protein Rheb / Ras homolog enriched in brain


Mass: 20163.057 Da / Num. of mol.: 2 / Fragment: GTPase domain / Mutation: D60K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHEB, RHEB2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15382
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.3 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 8 / Details: 0.2 M NaH2PO4: 16% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→31.852 Å / Num. obs: 9007 / % possible obs: 97.8 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 679 / CC1/2: 0.881

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTQ

1xtq


Resolution: 2.6→31.852 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.2559 423 4.72 %
Rwork0.1905 --
obs0.1936 8967 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.02 Å2 / Biso mean: 51.4272 Å2 / Biso min: 19.63 Å2
Refinement stepCycle: final / Resolution: 2.6→31.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 66 12 2489
Biso mean--46.6 36.82 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092514
X-RAY DIFFRACTIONf_angle_d1.1653398
X-RAY DIFFRACTIONf_chiral_restr0.059399
X-RAY DIFFRACTIONf_plane_restr0.006408
X-RAY DIFFRACTIONf_dihedral_angle_d18.291496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6005-2.97650.33541370.2327278497
2.9765-3.74920.24731390.19862842100
3.7492-31.8520.24031470.1743291899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.739-1.8206-0.22813.4499-0.44133.7992-0.1237-0.0196-0.1913-0.03990.27110.26420.0064-0.16890.08130.2826-0.0611-0.03720.2030.02930.3843108.1341-9.734729.9765
21.2951-1.2580.55711.6858-1.0710.855-0.7853-0.4493-0.63841.56780.7631.30980.3508-0.9484-0.02460.4626-0.02640.2150.7831-0.07790.9513105.0207-12.341239.5828
35.4137-1.5539-0.7444.9316-0.44544.48750.23960.07360.47020.4579-0.1680.2292-0.5987-0.6053-0.02360.3798-0.0167-0.08230.24040.01140.3716105.8428-0.253928.338
41.10990.75140.39167.3811-0.76183.3432-0.15661.2369-1.1282-1.58490.09691.52420.5647-0.86790.22150.7314-0.1926-0.09420.6788-0.14821.2388104.6954-23.879822.6943
51.55191.0661-0.8962.65710.87271.87680.14290.1179-1.5248-1.05710.78252.10910.7615-1.85820.11610.4823-0.0375-0.0981-0.094-0.07310.6906109.4999-14.311323.4257
64.6045-1.9563-0.18095.7799-0.47624.61110.07140.4861-0.4807-0.7046-0.25250.32390.3721-0.25190.05890.3436-0.0389-0.0710.2441-0.07770.449113.6305-18.0819.2882
73.3812-2.0512-0.48264.12140.28983.1429-0.118-0.06210.29870.08820.0462-0.2321-0.08780.40910.1520.2626-0.0416-0.05520.19260.00830.3463120.6656-11.083928.507
84.22472.2079-0.24993.1330.95133.7914-0.02370.29970.2166-0.7080.04570.4098-0.6213-0.55610.07260.45890.0832-0.06170.24340.01840.3311102.6383-36.234743.3461
94.57061.41290.152.69071.49733.7020.0340.5262-0.0383-0.52230.2959-0.0073-0.1405-0.39480.01360.45720.0248-0.02340.3079-0.03350.4891102.5853-44.228541.2022
104.73181.66140.46064.96271.95433.4567-0.1297-0.67410.9569-0.5237-0.22491.1419-0.9463-0.59250.17690.52380.1801-0.07510.3368-0.08070.467599.4702-28.383152.7304
113.79852.02060.09643.90461.45553.15260.2509-0.2418-0.1911-0.2397-0.1778-0.0525-0.19450.005-0.04040.39710.0381-0.02360.1986-0.00150.3513109.8255-35.019353.4722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 27 )A4 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 40 )A28 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 60 )A41 - 60
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 71 )A61 - 71
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 89 )A72 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 119 )A90 - 119
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 170 )A120 - 170
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 27 )B4 - 27
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 60 )B28 - 60
10X-RAY DIFFRACTION10chain 'B' and (resid 61 through 113 )B61 - 113
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 170 )B114 - 170

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more