[English] 日本語
Yorodumi
- PDB-3lq9: Crystal structure of human REDD1, a hypoxia-induced regulator of mTOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lq9
TitleCrystal structure of human REDD1, a hypoxia-induced regulator of mTOR
ComponentsDNA-damage-inducible transcript 4 protein
KeywordsSIGNALING PROTEIN / REDD1 DDIT4 mTOR / hypoxia / cancer
Function / homology
Function and homology information


protein-containing complex disassembly / negative regulation of glycolytic process / negative regulation of TOR signaling / neurotrophin TRK receptor signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to dexamethasone stimulus / 14-3-3 protein binding / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / brain development ...protein-containing complex disassembly / negative regulation of glycolytic process / negative regulation of TOR signaling / neurotrophin TRK receptor signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to dexamethasone stimulus / 14-3-3 protein binding / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / brain development / neuron migration / neuron differentiation / defense response to virus / response to hypoxia / intracellular signal transduction / apoptotic process / mitochondrion / cytosol / cytoplasm
Similarity search - Function
RTP801-like / RTP801-like / RTP801-like, C-terminal domain superfamily / RTP801 C-terminal region / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA damage-inducible transcript 4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsVega-Rubin-de-Celis, S. / Abdallah, Z. / Brugarolas, J. / Zhang, X.
CitationJournal: Biochemistry / Year: 2010
Title: Structural analysis and functional implications of the negative mTORC1 regulator REDD1.
Authors: Vega-Rubin-de-Celis, S. / Abdallah, Z. / Kinch, L. / Grishin, N.V. / Brugarolas, J. / Zhang, X.
History
DepositionFeb 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-damage-inducible transcript 4 protein
B: DNA-damage-inducible transcript 4 protein


Theoretical massNumber of molelcules
Total (without water)29,6622
Polymers29,6622
Non-polymers00
Water3,657203
1
A: DNA-damage-inducible transcript 4 protein


Theoretical massNumber of molelcules
Total (without water)14,8311
Polymers14,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-damage-inducible transcript 4 protein


Theoretical massNumber of molelcules
Total (without water)14,8311
Polymers14,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.331, 36.586, 47.970
Angle α, β, γ (deg.)77.56, 89.08, 86.18
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein DNA-damage-inducible transcript 4 protein / Protein regulated in development and DNA damage response 1 / REDD-1 / HIF-1 responsive protein RTP801


Mass: 14830.898 Da / Num. of mol.: 2 / Fragment: C-terminal functional domain / Mutation: deletion of residues 200-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDIT4, REDD1, RTP801 / Plasmid: modified pET28 with a His6-Sumo tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NX09
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaF, 20-26% PEG3350, 0.05 mM C12E9, vapor diffusion, hanging drop, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97926
SYNCHROTRONAPS 19-BM21.28288
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJan 1, 2008
CUSTOM-MADE2CCDJan 1, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
21.282881
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 25.34 / Number: 55284 / Rmerge(I) obs: 0.079 / Χ2: 1.93 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 11682 / % possible obs: 96
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745097.110.0653.9134.9
3.764.7497.810.0552.6044.9
3.293.7698.510.0672.3075
2.993.2998.110.0861.9095
2.772.9997.810.111.5855
2.612.7797.710.1421.5175
2.482.6197.210.1561.314.8
2.372.4895.910.1721.274.6
2.282.3792.910.2051.2294.1
2.22.2887.210.2321.1153.9
ReflectionResolution: 2→50 Å / Num. obs: 14319 / % possible obs: 95.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Χ2: 1.859 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.40.25913922.251,292.5
2.07-2.153.80.21413781.7681,294
2.15-2.253.90.15914131.6591,294.9
2.25-2.3740.13114351.7861,295.5
2.37-2.524.10.10914381.661,296.3
2.52-2.714.10.09614451.811,296.7
2.71-2.994.20.0814652.0051,296.9
2.99-3.424.20.06414452.0911,297.8
3.42-4.314.10.0514551.7971,297.7
4.31-5040.04514531.8051,297

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→27.096 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.851 / SU ML: 0.28 / σ(F): 1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.214 708 5.07 %
Rwork0.177 --
obs0.179 13975 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.587 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 90.6 Å2 / Biso mean: 30.4 Å2 / Biso min: 11.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.806 Å21.177 Å21.635 Å2
2--6.712 Å2-1.821 Å2
3----2.906 Å2
Refinement stepCycle: LAST / Resolution: 2→27.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 203 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031942
X-RAY DIFFRACTIONf_angle_d0.772618
X-RAY DIFFRACTIONf_chiral_restr0.051319
X-RAY DIFFRACTIONf_plane_restr0.002332
X-RAY DIFFRACTIONf_dihedral_angle_d15.69733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.1530.2611250.1982441256686
2.153-2.370.2151380.1772641277993
2.37-2.7120.2311420.182678282095
2.712-3.4160.251430.1792756289997
3.416-27.0980.1791600.1682751291197

+
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