+Open data
-Basic information
Entry | Database: PDB / ID: 4xej | ||||||
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Title | IRES bound to bacterial Ribosome | ||||||
Components |
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Keywords | RIBOSOME / Internal Ribosome Entry Site / IRES / 70S / bacterial initiation | ||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plautia stali intestine virus Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Zhu, J. / Korostelev, A. / Noller, H.F. / Donohue, J.P. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Authors: Colussi, T.M. / Costantino, D.A. / Zhu, J. / Donohue, J.P. / Korostelev, A.A. / Jaafar, Z.A. / Plank, T.D. / Noller, H.F. / Kieft, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xej.cif.gz | 14.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4xej.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4xej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/4xej ftp://data.pdbj.org/pub/pdb/validation_reports/xe/4xej | HTTPS FTP |
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-Related structure data
Related structure data | 4v83S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
+50S ribosomal protein ... , 29 types, 58 molecules AL02BL02AL03BL03AL04BL04AL05BL05AL06BL06AL09BL09AL11BL11AL13BL13AL14BL14AL15BL15AL16BL16AL17BL17AL18BL18AL19BL19AL20BL20...
-30S ribosomal protein ... , 20 types, 40 molecules AS02BS02AS03BS03AS04BS04AS05BS05AS06BS06AS07BS07AS08BS08AS09BS09AS10BS10AS11BS11AS12BS12AS13BS13AS14BS14AS15BS15AS16BS16...
#29: Protein | Mass: 26987.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62662 #30: Protein | Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62663 #31: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62664 #32: Protein | Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62665 #33: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62666 #34: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62667 #35: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62668 #36: Protein | Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62669 #37: Protein | Mass: 11299.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62653 #38: Protein | Mass: 12014.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62654 #39: Protein | Mass: 13604.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P61941 #40: Protein | Mass: 13308.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62655 #41: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62656 #42: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62657 #43: Protein | Mass: 9924.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62238 #44: Protein | Mass: 11721.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62658 #45: Protein | Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62659 #46: Protein | Mass: 8949.435 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62660 #47: Protein | Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62661 #48: Protein/peptide | Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62613 |
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-RNA chain , 4 types, 8 molecules A16SB16SA23SB23SA5SB5SAIREBIRE
#50: RNA chain | Mass: 489042.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #51: RNA chain | Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #52: RNA chain | Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919 #53: RNA chain | Mass: 62739.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plautia stali intestine virus / Production host: Escherichia coli (E. coli) / References: GenBank: 2344756 |
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-Non-polymers , 1 types, 4 molecules
#54: Chemical | ChemComp-ZN / |
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-Details
Sequence details | THE AUTHORS BELIEVE THAT THE C1161U CONFLICT IS AN ERROR IN THE SEQUENCE DATABASE. G2808U CHANGE IS ...THE AUTHORS BELIEVE THAT THE C1161U CONFLICT IS AN ERROR IN THE SEQUENCE DATABASE. G2808U CHANGE IS A SUBSTITUTI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.19 % |
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Initial crystallization screening was performed around conditions previously reported (31, 48) by dispensing 0.2 + 0.2 mL sitting drops with a Phoenix robotic liquid handling system (Art ...Details: Initial crystallization screening was performed around conditions previously reported (31, 48) by dispensing 0.2 + 0.2 mL sitting drops with a Phoenix robotic liquid handling system (Art Robbins) on 96-well plates. Once optimal crystallization conditions were determined, crystals were grown by the sitting-drop vapor-diffusion method using drops dispensed by the Phoenix with 1- to 2-mL ribosome complexes mixed with 1-2 mL of reservoir solution [100 mM Tris-OAc, pH 7.0, 200 mM potassium thiocyanate (KSCN), 3.6-5% PEG 20,000, 6-14% 2-methyl-2,4-pentanediol (MPD)] at 22.5C. Crystals emerged after 5-7 d and matured between 2-3 wk. Crystals were then subjected to cryoprotection by gradually replacing the mother liquor with cryoprotection buffer I (100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 5% PEG 20,000, 25% MPD, 14% PEG 200, and 10 mM Mg(OAc)2). The crystals then were flash-frozen by plunging into liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→60 Å / Num. obs: 555726 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.995 / Rrim(I) all: 0.2 / Net I/σ(I): 8.28 |
Reflection shell | Resolution: 3.8→4 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.998 / Rrim(I) all: 1.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4V83 Resolution: 3.8→60 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.8→60 Å
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