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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | NMT1-NAC bound human ribosome (combined translational states) | |||||||||
Map data | NMT1-NAC bound human ribosome (combined translational states) - Homogeneous refinement - local resolution filtered | |||||||||
Sample |
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Keywords | myristoylation / NMT1 / co-translational / NAC / ribosome / RNC | |||||||||
| Function / homology | Function and homology informationSynthesis of diphthamide-EEF2 / negative regulation of striated muscle cell apoptotic process / myristoyltransferase activity / regulation of skeletal muscle fiber development / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / Late Phase of HIV Life Cycle / N-terminal protein myristoylation / positive regulation of skeletal muscle tissue growth ...Synthesis of diphthamide-EEF2 / negative regulation of striated muscle cell apoptotic process / myristoyltransferase activity / regulation of skeletal muscle fiber development / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / Late Phase of HIV Life Cycle / N-terminal protein myristoylation / positive regulation of skeletal muscle tissue growth / ketone metabolic process / translation at postsynapse / regulation of opsin-mediated signaling pathway / PML body organization / positive regulation of protein localization to mitochondrion / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cardiac ventricle development / Activation, myristolyation of BID and translocation to mitochondria / ribosome hibernation / translation elongation factor binding / heart trabecula morphogenesis / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / response to folic acid / SUMO binding / skeletal muscle tissue regeneration / translation at presynapse / positive regulation of cytoplasmic translation / optic nerve development / response to insecticide / alpha-beta T cell differentiation / exit from mitosis / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / axial mesoderm development / retinal ganglion cell axon guidance / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / middle ear morphogenesis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / 90S preribosome assembly / protein localization to membrane / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of ubiquitin-protein transferase activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of DNA-templated transcription initiation / nucleolus organization / TNFR1-mediated ceramide production / negative regulation of formation of translation preinitiation complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / PD-L1(CD274) glycosylation and translocation to plasma membrane / GAIT complex / negative regulation of RNA splicing / Enterobacterial factors antagonize host defense / TORC2 complex binding / G1 to G0 transition / supercoiled DNA binding / negative regulation of DNA repair / erythrocyte homeostasis / blastocyst development / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / NF-kappaB complex / cytoplasmic translational initiation / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of myoblast fusion / Uptake and function of diphtheria toxin / cytoplasmic side of rough endoplasmic reticulum membrane / lncRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ion channel inhibitor activity / positive regulation of natural killer cell proliferation / Maturation of DENV proteins / protein kinase A binding / homeostatic process / laminin receptor activity / skeletal muscle cell differentiation / lung morphogenesis / Dengue Virus Genome Translation and Replication / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / macrophage chemotaxis Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||
Authors | Denk T / Berninghausen O / Beckmann R | |||||||||
| Funding support | Germany, 1 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_52582.map.gz | 32.3 MB | EMDB map data format | |
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| Header (meta data) | emd-52582-v30.xml emd-52582.xml | 118.9 KB 118.9 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_52582_fsc.xml | 14.9 KB | Display | FSC data file |
| Images | emd_52582.png | 119.7 KB | ||
| Filedesc metadata | emd-52582.cif.gz | 22.7 KB | ||
| Others | emd_52582_additional_1.map.gz emd_52582_additional_2.map.gz emd_52582_half_map_1.map.gz emd_52582_half_map_2.map.gz | 175.2 MB 328.5 MB 322.8 MB 322.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-52582 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-52582 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9i2eMC ![]() 9i2dC ![]() 9qloC ![]() 9qlpC ![]() 9qlqC ![]() 9s3bC ![]() 9s3cC ![]() 9s3dC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_52582.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | NMT1-NAC bound human ribosome (combined translational states) - Homogeneous refinement - local resolution filtered | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.049 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: NMT1-NAC bound human ribosome (combined translational states) -...
| File | emd_52582_additional_1.map | ||||||||||||
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| Annotation | NMT1-NAC bound human ribosome (combined translational states) - Homogeneous refinement | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Additional map: NMT1-NAC bound human ribosome (combined translational states) -...
| File | emd_52582_additional_2.map | ||||||||||||
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| Annotation | NMT1-NAC bound human ribosome (combined translational states) - Homogeneous refinement - sharpened | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: NMT1-NAC bound human ribosome (combined translational states) -...
| File | emd_52582_half_map_1.map | ||||||||||||
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| Annotation | NMT1-NAC bound human ribosome (combined translational states) - Homogeneous refinement - half map A | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: NMT1-NAC bound human ribosome (combined translational states) -...
| File | emd_52582_half_map_2.map | ||||||||||||
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| Annotation | NMT1-NAC bound human ribosome (combined translational states) - Homogeneous refinement - half map B | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : NMT1-NAC bound human ribosome (combined translational states)
+Supramolecule #1: NMT1-NAC bound human ribosome (combined translational states)
+Macromolecule #1: Elongation factor 2
+Macromolecule #3: Isoform 2 of SERPINE1 mRNA-binding protein 1
+Macromolecule #7: 60S ribosomal protein L8
+Macromolecule #8: 60S ribosomal protein L3
+Macromolecule #9: 60S ribosomal protein L4
+Macromolecule #10: 60S ribosomal protein L5
+Macromolecule #11: Large ribosomal subunit protein eL6
+Macromolecule #12: Large ribosomal subunit protein uL30
+Macromolecule #13: 60S ribosomal protein L7a
+Macromolecule #14: 60S ribosomal protein L9
+Macromolecule #15: Ribosomal protein uL16-like
+Macromolecule #16: 60S ribosomal protein L11
+Macromolecule #17: 60S ribosomal protein L13
+Macromolecule #18: 60S ribosomal protein L14
+Macromolecule #19: 60S ribosomal protein L15
+Macromolecule #20: 60S ribosomal protein L13a
+Macromolecule #21: 60S ribosomal protein L17
+Macromolecule #22: 60S ribosomal protein L18
+Macromolecule #23: 60S ribosomal protein L19
+Macromolecule #24: 60S ribosomal protein L18a
+Macromolecule #25: 60S ribosomal protein L21
+Macromolecule #26: 60S ribosomal protein L22
+Macromolecule #27: 60S ribosomal protein L23
+Macromolecule #28: 60S ribosomal protein L24
+Macromolecule #29: 60S ribosomal protein L23a
+Macromolecule #30: 60S ribosomal protein L26
+Macromolecule #31: 60S ribosomal protein L27
+Macromolecule #32: 60S ribosomal protein L27a
+Macromolecule #33: 60S ribosomal protein L29
+Macromolecule #34: 60S ribosomal protein L30
+Macromolecule #35: 60S ribosomal protein L31
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L35a
+Macromolecule #38: 60S ribosomal protein L34
+Macromolecule #39: 60S ribosomal protein L35
+Macromolecule #40: 60S ribosomal protein L36
+Macromolecule #41: 60S ribosomal protein L37
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: Ubiquitin-60S ribosomal protein L40
+Macromolecule #45: 60S ribosomal protein L41
+Macromolecule #46: 60S ribosomal protein L36a
+Macromolecule #47: 60S ribosomal protein L37a
+Macromolecule #48: 60S ribosomal protein L28
+Macromolecule #49: 60S ribosomal protein L10a
+Macromolecule #50: Nascent polypeptide-associated complex subunit alpha
+Macromolecule #51: Isoform 2 of Transcription factor BTF3
+Macromolecule #52: Glycylpeptide N-tetradecanoyltransferase 1
+Macromolecule #54: 40S ribosomal protein SA
+Macromolecule #55: 40S ribosomal protein S3a
+Macromolecule #56: 40S ribosomal protein S2
+Macromolecule #57: 40S ribosomal protein S3
+Macromolecule #58: 40S ribosomal protein S4, X isoform
+Macromolecule #59: 40S ribosomal protein S5
+Macromolecule #60: 40S ribosomal protein S6
+Macromolecule #61: 40S ribosomal protein S7
+Macromolecule #62: 40S ribosomal protein S8
+Macromolecule #63: 40S ribosomal protein S9
+Macromolecule #64: 40S ribosomal protein S10
+Macromolecule #65: 40S ribosomal protein S11
+Macromolecule #66: 40S ribosomal protein S12
+Macromolecule #67: 40S ribosomal protein S13
+Macromolecule #68: 40S ribosomal protein S14
+Macromolecule #69: 40S ribosomal protein S15
+Macromolecule #70: 40S ribosomal protein S16
+Macromolecule #71: 40S ribosomal protein S17
+Macromolecule #72: 40S ribosomal protein S18
+Macromolecule #73: 40S ribosomal protein S19
+Macromolecule #74: 40S ribosomal protein S20
+Macromolecule #75: 40S ribosomal protein S21
+Macromolecule #76: 40S ribosomal protein S15a
+Macromolecule #77: 40S ribosomal protein S23
+Macromolecule #78: 40S ribosomal protein S24
+Macromolecule #79: 40S ribosomal protein S25
+Macromolecule #80: 40S ribosomal protein S26
+Macromolecule #81: 40S ribosomal protein S27
+Macromolecule #82: 40S ribosomal protein S28
+Macromolecule #83: 40S ribosomal protein S29
+Macromolecule #84: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #85: Ubiquitin
+Macromolecule #86: Receptor of activated protein C kinase 1
+Macromolecule #2: E-site tRNA
+Macromolecule #4: 28S rRNA
+Macromolecule #5: 5S rRNA
+Macromolecule #6: 5.8S rRNA
+Macromolecule #53: 18S rRNA
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.6 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
Germany, 1 items
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Z (Sec.)
Y (Row.)
X (Col.)




















































Processing
FIELD EMISSION GUN

