[English] 日本語
Yorodumi
- PDB-5gt8: Crystal Structure of apo-CASTOR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gt8
TitleCrystal Structure of apo-CASTOR1
Components(GATS-like protein 3) x 2
KeywordsSIGNALING PROTEIN / arginine binding / mTOR / CASTOR1 / GATOR2 / ACT domain / GATSL2
Function / homology
Function and homology information


cellular response to L-arginine / small molecule sensor activity / Amino acids regulate mTORC1 / arginine binding / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein sequestering activity / identical protein binding / cytosol
Similarity search - Function
CASTOR family / CASTOR1, N-terminal / : / Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain / Cytosolic arginine sensor for mTORC1 subunit 1/2, ACT-like / CASTOR, ACT domain / ACT domain / ACT-like domain
Similarity search - Domain/homology
Cytosolic arginine sensor for mTORC1 subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGuo, L. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
MOST2016YFA0502700 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structures of arginine sensor CASTOR1 in arginine-bound and ligand free states
Authors: Zhou, Y. / Wang, C. / Xiao, Q. / Guo, L.
History
DepositionAug 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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: GATS-like protein 3
B: GATS-like protein 3
C: GATS-like protein 3
D: GATS-like protein 3


Theoretical massNumber of molelcules
Total (without water)147,4454
Polymers147,4454
Non-polymers00
Water79344
1
A: GATS-like protein 3
C: GATS-like protein 3


Theoretical massNumber of molelcules
Total (without water)73,7022
Polymers73,7022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-15 kcal/mol
Surface area24490 Å2
MethodPISA
2
B: GATS-like protein 3

D: GATS-like protein 3


Theoretical massNumber of molelcules
Total (without water)73,7442
Polymers73,7442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1770 Å2
ΔGint-14 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.410, 142.600, 95.400
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein GATS-like protein 3 / Cellular arginine sensor for mTORC1 protein 1 / CASTOR1


Mass: 36850.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATSL3, CASTOR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WTX7
#2: Protein GATS-like protein 3 / Cellular arginine sensor for mTORC1 protein 1 / CASTOR1


Mass: 36892.914 Da / Num. of mol.: 1 / Fragment: UNP residues A285I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATSL3, CASTOR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WTX7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 21%(w/v) PEG3350, 0.1M Tris pH 5.0, 0.2M MgCl2, 0.2% n- dodecyl- N, N- dimethylamine-N-oxide

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→142.598 Å / Num. obs: 34540 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 54.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.7-2.860.592.110.885196.2
2.86-3.060.3553.580.957199.9
3.06-3.30.2046.510.979199.7
3.3-3.620.12110.450.992199.1
3.62-4.050.08614.670.995199.3
4.05-4.670.05422.090.997199.2
4.67-5.720.04426.420.997199.3
5.72-8.080.03927.120.998199.2
8.08-142.5980.02239.020.999198.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155: ???refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GT7

5gt7


Resolution: 2.8→47.41 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 31.27
RfactorNum. reflection% reflection
Rfree0.265 1795 5.78 %
Rwork0.243 --
obs0.244 31076 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8232 0 0 44 8276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038428
X-RAY DIFFRACTIONf_angle_d0.5911500
X-RAY DIFFRACTIONf_dihedral_angle_d16.2055004
X-RAY DIFFRACTIONf_chiral_restr0.0451384
X-RAY DIFFRACTIONf_plane_restr0.0041447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87570.34361390.29812203X-RAY DIFFRACTION100
2.8757-2.96030.34461390.30442284X-RAY DIFFRACTION99
2.9603-3.05590.35391330.31982217X-RAY DIFFRACTION100
3.0559-3.16510.36241400.2812265X-RAY DIFFRACTION100
3.1651-3.29180.28281290.28192242X-RAY DIFFRACTION100
3.2918-3.44150.28361370.26122246X-RAY DIFFRACTION100
3.4415-3.62290.3061410.24872256X-RAY DIFFRACTION100
3.6229-3.84980.29921360.24792255X-RAY DIFFRACTION100
3.8498-4.14690.27761400.23882225X-RAY DIFFRACTION99
4.1469-4.56390.2261370.20442283X-RAY DIFFRACTION100
4.5639-5.22360.18531410.19212259X-RAY DIFFRACTION100
5.2236-6.57840.27971380.24432277X-RAY DIFFRACTION100
6.5784-47.41630.22511450.23892269X-RAY DIFFRACTION99
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)
14.3391.18281.53163.5081.794510.0716-0.12480.66480.1529-0.03820.27720.2199-0.6951-0.2089-0.12560.38890.08130.03520.48520.05310.2965-17.5012-25.7813-23.4508
23.7969-0.9003-0.69211.95640.61184.3301-0.05391.0054-0.10270.07740.03770.06720.3659-0.050.01390.412-0.04240.07720.7728-0.01940.3107-14.1535-34.4496-23.4914
37.5357-0.9921-3.01052.36591.37734.3976-0.14280.5496-0.28140.12070.0782-0.26430.10210.70290.02760.33620.0083-0.04250.7515-0.03110.3207-3.0691-33.8279-24.296
45.34-0.557-2.25173.72770.99188.76-0.2524-0.4729-0.02980.02960.19320.17051.0002-0.12390.0220.4854-0.0619-0.01430.46280.05170.3105-18.1534-71.9775-15.4131
52.13811.2399-0.39691.572-0.88317.5412-0.1269-0.37010.29380.05250.1125-0.09740.39360.5696-0.04160.56950.0307-0.07990.4476-0.07960.258-11.3263-61.8951-21.4455
66.65050.68390.2572.03141.31526.26760.0023-1.087-0.0046-0.17130.0967-0.2906-0.07181.1912-0.1020.3912-0.026-0.00030.7336-0.08040.3374-3.6505-63.5757-15.6146
75.047-0.42080.15482.6966-1.98959.32790.0677-1.38760.0670.2936-0.0221-0.1845-0.91361.1590.06740.739-0.0269-0.0371.122-0.09990.352-10.0495-26.332221.8535
80.39170.0633-0.09063.38991.13335.69760.0959-0.5408-0.27110.02430.27620.34430.2829-1.2651-0.31770.81860.06150.17360.88540.15580.4332-21.4874-35.956311.6445
93.69391.2909-1.83851.6591-3.37175.91970.1774-0.9919-0.28280.3314-0.31290.0260.0624-0.49920.22680.94070.23340.08091.67070.1360.3359-26.3574-33.475525.6397
105.1434-1.06340.25282.9752-0.56197.36410.09841.1810.03940.2524-0.1764-0.03240.49730.73180.10260.6566-0.0619-0.10450.8877-0.08450.3139-10.8039-70.657734.3528
113.7674-0.40850.9011.50160.38366.73930.30610.03750.23120.1167-0.08130.2738-0.4876-1.2837-0.15140.55490.0035-0.10110.58730.08330.4125-20.8795-59.268242.2689
121.0121-1.7118-1.21265.8786-1.58933.29660.14520.8758-0.2528-0.16340.20160.18450.1926-0.1998-0.37810.4253-0.1532-0.1511.3377-0.0790.6079-26.7852-67.624327.8252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 137 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 138 THROUGH 206 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 207 THROUGH 323 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 147 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 148 THROUGH 206 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 207 THROUGH 321 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 0 THROUGH 152 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 153 THROUGH 248 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 249 THROUGH 323 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 1 THROUGH 147 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 148 THROUGH 263 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 264 THROUGH 319 )

+
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