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- PDB-1e7z: Crystal structure of the EMAP2/RNA binding domain of the p43 prot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e7z | ||||||
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Title | Crystal structure of the EMAP2/RNA binding domain of the p43 protein from human aminoacyl-tRNA synthetase complex | ||||||
![]() | ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II | ||||||
![]() | RNA BINDING DOMAIN / OB-FOLD / TRNA SYNTHETASE COMPLEX | ||||||
Function / homology | ![]() positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / GTPase binding / cell-cell signaling ...positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / GTPase binding / cell-cell signaling / angiogenesis / defense response to virus / tRNA binding / inflammatory response / translation / apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pasqualato, S. / Kerjan, P. / Renault, L. / Menetrey, J. / Mirande, M. / Cherfils, J. | ||||||
![]() | ![]() Title: Structure of the Emapii Domain of Human Aminoacyl-tRNA Synthetase Complex Reveals Evolutionary Dimeric Mimicry Authors: Renault, L. / Kerjan, P. / Pasqualato, S. / Menetrey, J. / Robinson, J.C. / Kawaguchi, S. / Vassylyev, D.G. / Yokoyama, S. / Mirande, M. / Cherfils, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.5 KB | Display | ![]() |
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PDB format | ![]() | 34.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1fl0SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19297.332 Da / Num. of mol.: 1 Fragment: C-TERMINAL DOMAIN/RNA BINDING DOMAIN RESIDUES 147-312 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.55 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 11716 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.042 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Rsym value: 0.183 / % possible all: 96.5 |
Reflection | *PLUS Num. measured all: 119628 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 96.5 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FL0 Resolution: 2.05→28.48 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 7632586.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.1208 Å2 / ksol: 0.344836 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→28.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.296 |