[English] 日本語
Yorodumi
- PDB-2rg8: Crystal Structure of Programmed for Cell Death 4 Middle MA3 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rg8
TitleCrystal Structure of Programmed for Cell Death 4 Middle MA3 domain
ComponentsProgrammed cell death protein 4
KeywordsAPOPTOSIS / TRANSLATION / MA3 domain / HEAT repeats / Anti-oncogene / Cell cycle / Cytoplasm / Nucleus / Phosphorylation / Polymorphism / RNA-binding
Function / homology
Function and homology information


epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / negative regulation of JUN kinase activity / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cytokine production involved in inflammatory response / BMP signaling pathway ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / negative regulation of JUN kinase activity / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cytokine production involved in inflammatory response / BMP signaling pathway / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / response to hormone / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / negative regulation of DNA-templated transcription / apoptotic process / negative regulation of apoptotic process / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 4 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsGarces, R. / Suzuki, C. / Wagner, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: PDCD4 inhibits translation initiation by binding to eIF4A using both its MA3 domains.
Authors: Suzuki, C. / Garces, R.G. / Edmonds, K.A. / Hiller, S. / Hyberts, S.G. / Marintchev, A. / Wagner, G.
History
DepositionOct 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death protein 4
B: Programmed cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1437
Polymers36,0042
Non-polymers1405
Water7,746430
1
A: Programmed cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0603
Polymers18,0021
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Programmed cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0834
Polymers18,0021
Non-polymers813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.680, 70.060, 110.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Programmed cell death protein 4 / / Nuclear antigen H731-like / Neoplastic transformation inhibitor protein / Protein 197/15a


Mass: 18001.789 Da / Num. of mol.: 2 / Fragment: MA3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD4, H731 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53EL6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200mM sodium acetate, 28%-30% PEG4000, 8% Jeffamine M-600, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9793
SYNCHROTRONAPS 24-ID-C20.8551
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 8, 2007mirrors
ADSC QUANTUM 3152CCDApr 8, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryo-Si MonochromatorSINGLE WAVELENGTHMx-ray1
2Cryo-Si MonochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.85511
ReflectionResolution: 1.8→35.68 Å / Num. all: 34183 / Num. obs: 34012 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.095

-
Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.68 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 85310.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2675 9.7 %RANDOM
Rwork0.202 ---
all0.202 34012 --
obs0.202 27452 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1428 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2---1.29 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 5 430 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.822.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 421 9.7 %
Rwork0.201 3902 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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