[English] 日本語
Yorodumi- PDB-6ztl: E. coli 70S-RNAP expressome complex in collided state bound to NusG -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ztl | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | E. coli 70S-RNAP expressome complex in collided state bound to NusG | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | GENE REGULATION / Transcription / Translation / Expressome / Ribosome / RNA polymerase | ||||||||||||||||||
Function / homology | Function and homology information transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding ...transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / bacterial-type flagellum-dependent cell motility / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / nitrate assimilation / DNA-directed RNA polymerase complex / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / transcription antitermination / DNA-templated transcription initiation / response to reactive oxygen species / cell motility / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / large ribosomal subunit / ribosomal small subunit biogenesis / ribosome biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / response to heat / 5S rRNA binding / cytosolic small ribosomal subunit / protein-containing complex assembly / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / protein dimerization activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Webster, M.W. / Takacs, M. / Weixlbaumer, A. | ||||||||||||||||||
Funding support | France, 5items
| ||||||||||||||||||
Citation | Journal: Science / Year: 2020 Title: Structural basis of transcription-translation coupling and collision in bacteria. Authors: Michael William Webster / Maria Takacs / Chengjin Zhu / Vita Vidmar / Ayesha Eduljee / Mo'men Abdelkareem / Albert Weixlbaumer / Abstract: Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The ...Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo-electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ztl.cif.gz | 3.9 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ztl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ztl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ztl_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ztl_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6ztl_validation.xml.gz | 375.4 KB | Display | |
Data in CIF | 6ztl_validation.cif.gz | 590.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/6ztl ftp://data.pdbj.org/pub/pdb/validation_reports/zt/6ztl | HTTPS FTP |
-Related structure data
Related structure data | 11419MC 6ztjC 6ztmC 6ztnC 6ztoC 6ztpC 6zu1C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10846 (Title: E. coli 70S-RNAP expressome complex in collided state (with NusG, 34nt intervening mRNA) [7712 multi-frame micrographs in TIFF format] Data size: 2.3 TB Data #1: E. coli 70S-RNAP expressome complex in collided state (with NusG, 34nt intervening mRNA) [7712 multi-frame micrographs in TIFF format] [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 6 types, 6 molecules AAAVAWAXBABB
#1: RNA chain | Mass: 499888.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP054232.1 |
---|---|
#22: RNA chain | Mass: 15789.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#23: RNA chain | Mass: 24832.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: CP047127.1 |
#24: RNA chain | Mass: 24751.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: CP054236.1 |
#25: RNA chain | Mass: 941820.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP023165.1 |
#26: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP035706.1 |
-30S ribosomal protein ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
#2: Protein | Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0 |
---|---|
#3: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3 |
#4: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8 |
#5: Protein | Mass: 17617.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1 |
#6: Protein | Mass: 15197.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: W8T6F0 |
#7: Protein | Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359 |
#8: Protein | Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7 |
#9: Protein | Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3 |
#10: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5 |
#11: Protein | Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9 |
#12: Protein | Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3 |
#13: Protein | Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9 |
#14: Protein | Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59 |
#15: Protein | Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4 |
#16: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3 |
#17: Protein | Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63 |
#18: Protein | Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7 |
#19: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3 |
#20: Protein | Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7 |
#21: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679 |
+50S ribosomal protein ... , 28 types, 28 molecules BCBDBEBFBGBHBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB1B2B3B4B5B6
-DNA chain , 2 types, 2 molecules CNCT
#55: DNA chain | Mass: 12063.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#56: DNA chain | Mass: 11872.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules CACBCCCDCE
#57: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase #58: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8V2, DNA-directed RNA polymerase #59: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, Z5561, ECs4911 / Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8T8, DNA-directed RNA polymerase #60: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A800, DNA-directed RNA polymerase |
---|
-Protein , 1 types, 1 molecules CF
#61: Protein | Mass: 20560.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: nusG, A6592_25585, A6V01_22710, A8C65_22140, A9819_22730, A9P13_25180, A9R57_05240, A9X72_23950, AC067_25565, AC789_1c43770, ACN002_4069, ACN68_05355, ACN81_23140, ACU57_23215, ACU90_26230, ...Gene: nusG, A6592_25585, A6V01_22710, A8C65_22140, A9819_22730, A9P13_25180, A9R57_05240, A9X72_23950, AC067_25565, AC789_1c43770, ACN002_4069, ACN68_05355, ACN81_23140, ACU57_23215, ACU90_26230, AM270_23415, AM446_26285, AM464_13235, AML07_02765, AML35_27155, APT94_08685, APZ14_17375, ARC77_16990, AU473_00875, AUQ13_12310, AUS26_26490, AW059_24245, AW106_22725, AWB10_24980, AWG90_024840, AWP75_07120, B7C53_21495, B9M99_23250, B9T59_11605, BANRA_02652, BANRA_02965, BANRA_04868, BANRA_05054, BB545_03125, BE963_11245, BEN53_24665, BER14_24185, BHF03_13055, BHF46_22020, BHS81_23795, BHS87_22260, BIQ87_22825, BIU72_18845, BIZ41_20425, BJJ90_25150, BK248_06370, BK292_28055, BK296_22625, BK334_23885, BK373_27240, BK375_25285, BK383_27750, BMT91_03315, BN17_39461, BOH76_00570, BON63_20075, BON65_15050, BON66_14345, BON69_07640, BON71_08905, BON72_17240, BON75_02205, BON76_16185, BON83_01585, BON86_02250, BON87_25635, BON92_00555, BON94_22220, BON95_12895, BON96_11035, BTQ04_24460, BTQ06_27300, BUE81_05395, BvCms12BK_01423, BvCms2454_04763, BvCms28BK_04512, BvCms35BK_02101, BvCmsC61A_02144, BvCmsHHP001_05230, BvCmsHHP019_04457, BvCmsHHP056_02613, BvCmsKKP036_03586, BvCmsKKP061_02988, BvCmsKSNP073_02860, BvCmsKSNP081_04473, BvCmsKSNP120_03442, BvCmsKSP011_02762, BvCmsKSP024_02914, BvCmsKSP026_03368, BvCmsKSP045_04193, BvCmsKSP058_05150, BvCmsKSP067_02572, BvCmsKSP076_03394, BvCmsNSNP036_01151, BvCmsNSP006_02609, BvCmsNSP007_05025, BvCmsNSP047_00265, BvCmsNSP072_02887, BvCmsOUP014_03194, BvCmsSINP011_03926, BvCmsSINP022_04149, BvCmsSIP019_00806, BvCmsSIP044_03280, BVL39_05395, BW690_26720, BWI89_17415, BWP17_22740, BXT93_25190, BZL31_04420, BZL69_05760, C2M16_25145, C2U48_12750, C4M78_26060, C5715_03885, C5N07_24575, C5P01_26085, C5P44_24205, C6669_07630, C6B13_24055, C7235_23740, C7B02_25750, C7B06_24590, C7B07_24515, C7B08_25795, C7B18_24885, C9098_22125, C9114_22875, C9141_23580, C9160_23410, C9162_26315, C9201_22170, C9306_18330, C9E25_22050, C9E67_28690, C9Z03_20290, C9Z23_22460, C9Z28_21960, C9Z29_22205, C9Z37_20890, C9Z39_11545, C9Z68_22005, C9Z70_22895, C9Z78_23210, C9Z89_21250, CA593_06055, CDC27_21525, CDL37_18180, CF006_23900, CG692_19490, CI641_013295, CI693_09880, CI694_22430, CIG45_23855, CJU63_23510, CMR93_21685, CO706_19475, COD30_25685, COD46_23680, CQB02_21475, CQP61_26065, CR538_24245, CR539_01640, CRD98_23200, CRE06_24015, CRM83_18660, CRX46_23015, CSB64_25615, CV83915_02071, CVH05_03840, CWM24_27465, CWS33_24585, D0X26_26090, D2184_25125, D2185_24315, D2188_26625, D3821_09130, D3822_07045, D3O91_23455, D3P01_24300, D3Y67_18010, D4M06_24755, D4V08_22465, D6T60_24420, D6X76_25425, D7K63_24265, D7K66_23575, D9D20_23600, D9D31_17400, D9D43_22285, D9E34_21740, D9E35_23840, D9F17_24210, D9G11_22910, D9G42_23575, D9G48_16785, D9H36_23700, D9H53_22650, D9H68_20300, D9H70_22035, D9H94_18920, D9I18_21340, D9I87_21115, D9I88_18975, D9I97_19355, D9J03_21550, D9J11_22250, D9J44_24490, D9J60_24680, D9J78_24465, D9K48_24855, D9K54_12200, D9L89_22830, D9X97_23540, DAH18_24890, DAH26_25975, DAH30_23810, DAH32_23215, DAH34_21590, DAH37_22535, DAH43_24845, DB359_25595, DBQ99_24575, DD762_22315, DEN86_24465, DEN89_26545, DEN97_23745, DEO04_24340, DEO19_24590, DIV22_03710, DJ492_21155, DJ503_21480, DL455_22945, DL545_23715, DL800_27635, DM102_24845, DM129_21405, DMI04_23160, DN627_23120, DN700_22935, DNB37_22335, DND16_22055, DNQ45_05150, DNX30_24180, DOY56_23490, DP258_23400, DP277_21350, DQE83_24500, DQF57_23755, DQO13_23745, DS732_01515, DTL43_13735, DTL90_24565, DTM10_25890, DTM45_24265, DU309_24235, DU321_23455, DWB25_23615, DXT69_22770, DXT71_22275, DXT73_22975, DXX80_014070, E0I42_21930, E0K84_22915, E0L12_22075, E2112_20390, E2115_21525, E2116_21360, E2119_22370, E2127_20870, E2128_03155, E2129_21325, E2134_22760, E2135_19300, E2855_04995, E2863_04087, E4K55_23315, E5P22_12620, E5P28_08855, E5P37_21480, E5S42_21570, E5S46_22920, E5S47_23055, E5S58_21655, E5S61_22405, EA223_18780, EAI42_07555, EAI46_11730, EAI52_22765, EAX79_24725, EB509_19910, EB510_23015, EB515_23215, EC1094V2_4288, EC3234A_76c00020, EC3426_00293, EC382_20035, EC95NR1_03447, ECONIH1_23440, ECs4905, ECTO6_04524, ED225_22815, ED600_17570, ED607_18465, ED611_23905, ED648_18875, ED903_15555, ED944_23285, EEA45_21070, EEP23_09520, EF173_24425, EHH55_00685, EHJ36_22675, EI021_22100, EI028_22550, EI032_21280, EIA08_23380, EIA21_22555, EIZ93_16305, EJC75_19605, EKI52_13975, EL75_4207, EL79_4413, EL80_4320, ELT20_20690, ELT49_22095, ELT58_20800, ELU85_23620, ELV08_18720, ELV15_18010, ELV28_22220, ELY05_18135, EO241_25805, EPT01_21710, EPU41_22430, EQ820_22900, EQ823_21595, EQ825_24495, EQ830_22075, ERL57_22710, ERS085365_04268, ERS085366_03833, ERS085374_04594, ERS085379_04702, ERS085386_04623, ERS085404_04521, ERS085416_04255, ERS139211_00029, ERS150873_04413, ERS150876_04842, EST51_23890, EVY14_16870, EXM29_02430, ExPECSC019_03691, ExPECSC038_04333, EXX06_24555, EXX13_24135, EXX23_22335, EXX24_23200, EXX53_20975, EXX55_24470, EXX71_22285, EXX78_23980, EXX87_25010, EYD11_21620, EYX82_16660, EYY27_22340, EYY34_19835, EYY78_22630, F1E13_23780, F1E19_21855, F7F18_24025, F7F23_23365, F7F29_25900, F7G01_23380, F7G03_24045, FAF34_028990, FKO60_24845, FNJ69_19080, FNJ83_24770, FORC82_4527, FQ915_26180, FQR64_21830, FRV13_16245, FV293_23400, FV295_22235, FV438_22405, FWK02_12320, FY127_17780, FZ043_01110, GJ11_25170, HmCms184_03867, HmCmsJML074_03188, HmCmsJML079_04908, HmCmsJML204_03263, HMPREF3040_01771, HW43_01555, MJ49_09455, MS6198_46010, NCTC10082_02087, NCTC10090_02786, NCTC10429_00094, NCTC10764_02978, NCTC10766_02647, NCTC10865_05901, NCTC10974_05357, NCTC11022_04295, NCTC11112_02275, NCTC11126_05446, NCTC11181_01971, NCTC11341_02768, NCTC12950_05220, NCTC13127_06170, NCTC13148_04401, NCTC13846_04507, NCTC7922_04992, NCTC7927_05255, NCTC8009_08439, NCTC8179_05103, NCTC8450_00357, NCTC8500_05331, NCTC8622_01622, NCTC8960_02346, NCTC9007_05346, NCTC9036_04655, NCTC9044_02298, NCTC9045_05548, NCTC9050_02824, NCTC9055_01673, NCTC9058_02141, NCTC9062_03438, NCTC9077_05942, NCTC9111_04961, NCTC9117_05910, NCTC9119_05061, NCTC9701_05002, NCTC9702_05645, NCTC9703_04220, NCTC9706_02009, NCTC9777_01124, NCTC9969_04938, PGD_00616, PU06_15460, RG28_25315, RK56_017435, RX35_03749, SAMEA3472043_04873, SAMEA3472044_04880, SAMEA3472047_03493, SAMEA3472055_04940, SAMEA3472056_05316, SAMEA3472070_05100, SAMEA3472080_04808, SAMEA3472090_05013, SAMEA3472108_04978, SAMEA3472110_05075, SAMEA3472112_05160, SAMEA3472114_04960, SAMEA3472147_04113, SAMEA3484427_04977, SAMEA3484429_04980, SAMEA3484434_04732, SAMEA3485101_05504, SAMEA3485113_04488, SAMEA3752372_05072, SAMEA3752553_04898, SAMEA3752557_04837, SAMEA3752559_04862, SAMEA3752620_04706, SAMEA3753064_05336, SAMEA3753097_04838, SAMEA3753164_04793, SAMEA3753290_00011, SAMEA3753300_04891, SK85_04313, UC41_25620, UN86_14210, UN91_25475, WQ89_24645, WR15_01460, YDC107_2696 Plasmid: pSKB2_(His)6-HRV3C-NusG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3SID2 |
---|
-Non-polymers , 3 types, 445 molecules
#62: Chemical | ChemComp-MG / #63: Chemical | ChemComp-PHE / | #64: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| |||||||||||||||||||||||||||||||||||
Source (natural) |
| |||||||||||||||||||||||||||||||||||
Source (recombinant) |
| |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 684211 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45774 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE |