[English] 日本語
Yorodumi
- PDB-7yla: Cryo-EM structure of 50S-HflX complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yla
TitleCryo-EM structure of 50S-HflX complex
Components
  • (50S ribosomal protein ...) x 29
  • 5S rRNA
  • Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, complete genome
  • GTPase HflX
KeywordsRIBOSOME / HflX
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation ...ribosome disassembly / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / translation repressor activity / rescue of stalled cytosolic ribosome / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / transferase activity / ribosome binding / response to heat / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / GTPase activity / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
HflX, C-terminal domain / HflX C-terminal domain / GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. ...HflX, C-terminal domain / HflX C-terminal domain / GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / EF-G domain III/V-like / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / : / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9 / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Large ribosomal subunit protein uL24, C-terminal domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / GTPase HflX / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsDamu, W. / Ning, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31725007 China
CitationJournal: Biorxiv / Year: 2022
Title: Cryo-EM Structure of the 50S-HflX Complex Reveals a Novel Mechanism of Antibiotic Resistance in E. coli
Authors: Wu, D. / Dai, Y. / Gao, N.
History
DepositionJul 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
6: GTPase HflX
I: Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, complete genome
J: 5S rRNA
K: 50S ribosomal protein L2
L: 50S ribosomal protein L3
M: 50S ribosomal protein L4
N: 50S ribosomal protein L5
O: 50S ribosomal protein L6
P: 50S ribosomal protein L9
Q: 50S ribosomal protein L11
R: 50S ribosomal protein L13
S: 50S ribosomal protein L14
T: 50S ribosomal protein L15
U: 50S ribosomal protein L16
V: 50S ribosomal protein L17
W: 50S ribosomal protein L18
X: 50S ribosomal protein L19
Y: 50S ribosomal protein L20
Z: 50S ribosomal protein L21
a: 50S ribosomal protein L22
b: 50S ribosomal protein L23
c: 50S ribosomal protein L24
d: 50S ribosomal protein L25
e: 50S ribosomal protein L27
f: 50S ribosomal protein L28
g: 50S ribosomal protein L29
h: 50S ribosomal protein L30
i: 50S ribosomal protein L32
j: 50S ribosomal protein L33
k: 50S ribosomal protein L34
l: 50S ribosomal protein L35
m: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,400,14938
Polymers1,399,46532
Non-polymers6846
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 1 types, 1 molecules 6

#1: Protein GTPase HflX / GTP-binding protein HflX


Mass: 48362.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hflX, b4173, JW4131 / Production host: Escherichia coli (E. coli) / References: UniProt: P25519

-
RNA chain , 2 types, 2 molecules IJ

#2: RNA chain Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, complete genome / 23S rRNA


Mass: 941612.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 937521852
#3: RNA chain 5S rRNA


Mass: 38177.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1727529157

+
50S ribosomal protein ... , 29 types, 29 molecules KLMNOPQRSTUVWXYZabcdefghijklm

#4: Protein 50S ribosomal protein L2


Mass: 29663.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplB, EAZG_04115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LPI5
#5: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rplC, rplC_1, A5U30_004554, A6592_25805, A8499_003334, A8502_004021, A9X72_02175, AAG43_004444, AAS29_002160, ACN68_01905, ACN81_25530, ACU57_20950, AF998_005044, AM464_09230, APX88_16065, ...Gene: rplC, rplC_1, A5U30_004554, A6592_25805, A8499_003334, A8502_004021, A9X72_02175, AAG43_004444, AAS29_002160, ACN68_01905, ACN81_25530, ACU57_20950, AF998_005044, AM464_09230, APX88_16065, AT335_004245, AT845_004376, AW118_24910, AW119_26720, AWP47_12635, B6R12_002805, B6R15_004067, B6R31_004966, B6R48_005033, B6R87_004943, BANRA_04330, BANRA_04478, BEA19_23435, BER14_25200, BF481_004928, BG944_001135, BGM66_003591, BHS81_19845, BJI68_08665, BJJ90_02115, BK292_20515, BK383_24635, BKL28_004541, BLM69_000042, BMC79_004417, BMT49_24970, BMT50_12205, BMT91_20080, BN17_32541, BO068_004021, BOB65_004252, BOH76_10300, BON63_16650, BON64_02020, BON65_18050, BON66_26160, BON67_18880, BON68_24750, BON69_09885, BON70_00130, BON71_23175, BON72_13515, BON73_23855, BON74_04615, BON75_18755, BON76_15795, BON77_05670, BON78_22665, BON79_17330, BON80_14605, BON81_00485, BON82_23230, BON83_10090, BON84_09820, BON86_14480, BON87_22970, BON88_17700, BON89_16080, BON90_18925, BON91_16820, BON92_01280, BON93_00960, BON94_10910, BON95_01970, BON96_04520, BON97_10055, BON98_13405, BR158_003792, BR331_19070, BRV02_004595, BRV34_003968, BRV41_004356, BSR05_22800, BTB68_004354, BTQ06_10700, BUO55_004695, BvCmsF30A_00536, BvCmsHHP019_04150, BvCmsHHP056_02722, BvCmsKKP036_04791, BvCmsKKP061_03032, BvCmsKSNP073_02074, BVL39_09465, BXT93_05465, BZL69_26040, C0P57_002670, C1Q91_004902, C2121_004160, C2M16_25395, C2R31_004635, C2U48_16885, C3F40_19710, C5N07_23480, C5Y87_24355, C9114_23900, C9160_24410, C9E67_02715, C9Z68_22645, CA593_09640, CCS08_00225, CCV12_002919, CDC27_17755, CDL36_25500, CDL37_18685, CF22_004847, CG831_003651, CHM61_002989, CIG67_10665, CO706_15295, CQ986_004879, CQB02_00720, CR538_02410, CR539_21910, CR628_001368, CSE52_004332, CTR35_003632, CV83915_02778, CWS33_24950, CX938_003833, CXJ73_004407, CY655_21330, D0X26_24590, D1H34_002944, D3822_13385, D3C88_31160, D3G36_23040, D3Y67_24485, D4N09_20265, D4U49_16240, D9D43_22540, D9D77_24765, D9E34_23515, D9E49_05250, D9H94_20740, D9J03_20145, D9J61_16745, DAH17_20625, DAH18_25830, DAH19_23775, DAH20_24960, DAH21_04325, DAH22_07570, DAH23_26045, DAH24_26530, DAH25_10220, DAH26_26195, DAH27_08515, DAH28_09130, DAH29_12635, DAH30_24525, DAH31_24575, DAH32_04050, DAH33_05990, DAH34_23375, DAH35_26770, DAH36_23945, DAH37_14780, DAH38_04660, DAH40_11295, DAH41_02685, DAH42_05785, DAH43_07620, DAH45_06625, DAH46_07610, DAH47_06860, DAH48_25915, DAH49_06250, DAH50_22825, DD762_23640, DEN86_25710, DEN87_25115, DEN88_25025, DEN89_26920, DEN90_26120, DEN91_25670, DEN92_25260, DEN93_25395, DEN94_25060, DEN95_25535, DEN96_24490, DEN97_24555, DEN98_24370, DEN99_24050, DEO00_23745, DEO01_24140, DEO02_24550, DEO03_23465, DEO04_24850, DEO05_24720, DEO06_25035, DEO07_25275, DEO08_24815, DEO09_24800, DEO10_24835, DEO11_24485, DEO12_25760, DEO13_24900, DEO14_24930, DEO15_25560, DEO17_25290, DEO19_25310, DEO20_25430, DIV22_15165, DKP82_26155, DM870_23850, DN627_24275, DNQ45_03850, DNX30_25385, DRW19_24990, DS732_24355, DTL43_20905, DTL90_24785, DTM45_24460, DU321_12095, DXT69_23845, DXT70_20105, DXT71_20625, DXT73_21180, E0I42_22285, E2112_22050, E2113_03705, E2114_23425, E2115_22225, E2116_22695, E2117_23015, E2118_22205, E2119_19545, E2120_23465, E2121_21545, E2122_18945, E2123_21645, E2124_22245, E2125_23050, E2127_22005, E2128_19230, E2129_22280, E2130_23045, E2131_16935, E2132_21170, E2133_20125, E2134_21975, E2135_06090, E2136_22520, E2646_17875, E3N34_07255, E3O05_13890, E4K51_21585, E4T14_17190, E4T84_22775, E5H86_24430, E5M02_22195, E5P22_10575, E5P23_18270, E5P24_20790, E5P25_23480, E5P26_15700, E5P27_18105, E5P28_20780, E5P29_17690, E5P30_23040, E5P31_16840, E5P32_11705, E5P33_08980, E5P34_20380, E5P35_16020, E5P36_06820, E5P37_20795, E5P39_20305, E5P40_15190, E5P41_17280, E5P42_07455, E5P43_17755, E5P44_19020, E5P45_14030, E5P46_16940, E5P47_16665, E5P48_15985, E5P49_19740, E5P50_20825, E5P51_15750, E5P52_20390, E5S34_21770, E5S35_22550, E5S36_21060, E5S38_21955, E5S39_21710, E5S42_21790, E5S43_21540, E5S44_22800, E5S45_22935, E5S46_21670, E5S47_23275, E5S48_23215, E5S51_20910, E5S52_23140, E5S53_22850, E5S54_24660, E5S55_22910, E5S56_23115, E5S57_20250, E5S58_20935, E5S59_22515, E5S61_22770, E5S62_22400, E6C80_04260, E6D34_21665, EA239_22885, EA435_23125, EAI46_07570, EAN77_23430, EAX79_10805, EBP16_21780, EC1094V2_335, EC95NR1_02711, ECs4185, ED648_20425, EHD79_24145, EI021_21125, EIA08_24050, EIZ93_12375, EKI52_17570, EL79_0396, EL80_0388, ELT16_22425, ELT17_22345, ELT20_19075, ELT21_19060, ELT22_22590, ELT23_23200, ELT24_21815, ELT25_21770, ELT26_21745, ELT27_21655, ELT28_22740, ELT29_23005, ELT30_21030, ELT31_10320, ELT32_22730, ELT33_23515, ELT34_21725, ELT35_21180, ELT36_21870, ELT38_22650, ELT39_22215, ELT40_22100, ELT41_20840, ELT44_23170, ELT45_22690, ELT46_22780, ELT48_23015, ELT49_22970, ELT50_22965, ELT51_23840, ELT52_22220, ELT54_08510, ELT55_20145, ELT56_22890, ELT58_22145, ELT59_22310, ELT60_23010, ELT61_22580, ELT63_20870, ELT72_22275, ELU07_18705, ELU82_21805, ELU83_22925, ELU85_15865, ELU88_22880, ELU89_17475, ELU90_22325, ELU91_21450, ELU94_19155, ELU95_22685, ELU96_23485, ELU97_23540, ELU98_18150, ELU99_24045, ELV00_23405, ELV01_23770, ELV02_22800, ELV03_22315, ELV04_22810, ELV05_20095, ELV07_23660, ELV08_15755, ELV09_19390, ELV10_17970, ELV11_24730, ELV12_18320, ELV13_17640, ELV15_19655, ELV16_22775, ELV20_22490, ELV21_17705, ELV22_19090, ELV23_23300, ELV26_24050, ELV28_23020, ELV29_21190, ELV40_23840, ELX48_21575, ELX61_21805, ELX66_23305, ELX68_21395, ELX69_24375, ELX76_23035, ELX79_21270, ELX85_16835, ELX96_16900, ELY02_08085, ELY31_21655, ELY32_12770, ELY36_23250, ELY39_19505, ELY41_18815, ELY48_23255, EN85_004347, EPS76_07120, ERS085406_04388, ERS139208_04336, EWK56_25090, ExPECSC038_03638, EXX13_24635, EYV17_11500, EYV18_18495, EYX47_21135, F0L67_25410, F2N20_22060, F2N31_23540, F3N40_22270, F7F11_22630, F7N46_23915, F9413_21140, F9461_25560, F9B07_24590, F9S83_19085, F9V24_19050, F9X20_02055, FA849_13265, FA868_22840, FDM60_20745, FE584_05435, FE587_06325, FEJ01_22420, FEL34_20830, FFF58_25360, FGG80_25040, FHD44_21360, FHO90_04645, FHQ91_21910, FIJ20_21100, FJQ40_18400, FJQ51_22090, FJQ53_22820, FKO60_25730, FOI11_019165, FOI11_04015, FPI65_20400, FPJ29_20960, FPS11_25335, FQF29_19275, FV293_22370, FVB16_04965, FY127_21635, FZC17_14865, FZN31_02540, FZU14_21915, G3565_26410, G3813_004621, G3V95_19940, G3W53_21050, G4A38_21605, G4A47_20875, G5603_24680, G7630_004348, G9448_16980, GAI66_20425, GAI89_24735, GAJ12_24625, GAJ26_22105, GF147_24610, GF699_19830, GFY34_22805, GIB53_19305, GJ11_21480, GJO56_22830, GKF66_21640, GKF89_18565, GNW61_16725, GNZ05_25890, GOP25_22800, GP711_23400, GP944_18885, GP954_00850, GP965_04390, GP975_01280, GP979_01910, GQA06_03855, GQM04_10660, GQM13_25295, GQM21_11325, GQN34_23360, GQW07_21455, GQW68_22815, GQW80_23060, GRC73_21655, GRO95_20720, GRW05_09155, GRW24_04660, GRW56_00390, GRW57_03445, GSM54_23235, GSY44_20095, GTP88_23085, GUC01_21275, GUI33_20140, H0O37_13895, H0O39_19195, H0O51_24830, H0O53_20735, H0O72_19510, HCQ42_003930, HEP30_018730, HEP34_004752, HHH44_004517, HI055_004158, HIE29_005205, HIN64_004180, HJ942_004420, HJQ60_004993, HJS37_004719, HJU54_004673, HKA49_005017, HL563_21455, HL601_22260, HLV18_23245, HLX92_09980, HLZ50_22085, HmCms169_03512, HMJ82_26095, HMU06_24615, HMV95_19700, HMW38_23200, HNC36_20285, HNC59_23020, HNC66_24755, HNC99_22445, HND12_26325, HV109_02095, HV146_21765, HV209_14620, HVV39_09360, HVW04_17440, HVW19_19380, HVW43_18575, HVX31_01875, HVX32_19140, HVY77_02080, HVZ29_19190, HVZ30_01960, HVZ71_02265, HX136_02100, I6H00_20830, I6H01_10815, IA00_004106, IFB95_004824, IH768_14175, IH772_23920, IT029_004935, J0541_004415, J4S20_004784, J5U05_004069, JE86ST02C_37880, JE86ST05C_37910, JFD_03731, JNP96_25400, NCTC10082_02821, NCTC10089_00484, NCTC10090_03509, NCTC10418_00672, NCTC10429_01075, NCTC10764_03845, NCTC10767_01498, NCTC10865_00640, NCTC10974_00531, NCTC11126_02752, NCTC11341_01907, NCTC12950_00461, NCTC13127_00766, NCTC13148_03458, NCTC13216_01370, NCTC4450_02457, NCTC7927_00533, NCTC7928_02535, NCTC8008_05364, NCTC8009_01491, NCTC8179_05923, NCTC8333_00471, NCTC8450_04919, NCTC8500_00315, NCTC8621_00490, NCTC8959_03279, NCTC8960_03052, NCTC8985_04963, NCTC9036_00521, NCTC9037_00645, NCTC9044_01378, NCTC9077_00586, NCTC9081_00899, NCTC9111_00849, NCTC9117_00738, NCTC9702_00519, NCTC9706_02719, NCTC9775_03984, NCTC9777_01873, NCTC9962_06779, ND22_005138, RG28_21705, SAMEA3472044_01144, SAMEA3472056_05429, SAMEA3472147_04274, SAMEA3751407_00042, SAMEA3752557_01970, SAMEA3753106_04616, TUM18780_04180, WP4S18E07_04240, WR15_19700, XU56_003421
Production host: Escherichia coli (E. coli) / References: UniProt: C3SQU2
#6: Protein 50S ribosomal protein L4 / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplD, eryA, b3319, JW3281 / Production host: Escherichia coli (E. coli) / References: UniProt: P60723
#7: Protein 50S ribosomal protein L5 / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplE, b3308, JW3270 / Production host: Escherichia coli (E. coli) / References: UniProt: P62399
#8: Protein 50S ribosomal protein L6


Mass: 18801.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplF / Production host: Escherichia coli (E. coli) / References: UniProt: C3SR17
#9: Protein 50S ribosomal protein L9 / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplI, b4203, JW4161 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R1
#10: Protein 50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14020.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplK, relC, b3983, JW3946 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7J7
#11: Protein 50S ribosomal protein L13 / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplM, b3231, JW3200 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA10
#12: Protein 50S ribosomal protein L14


Mass: 13451.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplN / Production host: Escherichia coli (E. coli) / References: UniProt: C3SQZ2
#13: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplO / Production host: Escherichia coli (E. coli) / References: UniProt: P02413
#14: Protein 50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#15: Protein 50S ribosomal protein L17


Mass: 13721.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplQ, EAXG_02993 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LC97
#16: Protein 50S ribosomal protein L18 / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplR, b3304, JW3266 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C018
#17: Protein 50S ribosomal protein L19 / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplS, b2606, JW2587 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7K6
#18: Protein 50S ribosomal protein L20 / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplT, pdzA, b1716, JW1706 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L3
#19: Protein 50S ribosomal protein L21 / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplU, b3186, JW3153 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG48
#20: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplV, eryB, b3315, JW3277 / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#21: Protein 50S ribosomal protein L23 / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplW, b3318, JW3280 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#22: Protein 50S ribosomal protein L24


Mass: 11078.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplX, ECJG_02968 / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL32
#23: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplY, b2185, JW2173 / Production host: Escherichia coli (E. coli) / References: UniProt: P68919
#24: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 8174.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmA, b3185, JW3152 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L8
#25: Protein 50S ribosomal protein L28 / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmB, b3637, JW3612 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M2
#26: Protein 50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7155.267 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmC, b3312, JW3274 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M6
#27: Protein 50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmD, b3302, JW3264 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG51
#28: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmF, HMPREF9536_00655 / Production host: Escherichia coli (E. coli) / References: UniProt: D7XI28
#29: Protein/peptide 50S ribosomal protein L33 / Large ribosomal subunit protein bL33


Mass: 5814.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmG, b3636, JW3611 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7N9
#30: Protein/peptide 50S ribosomal protein L34 / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmH, rimA, ssaF, b3703, JW3680 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7P5
#31: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmI, b1717, JW1707 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#32: Protein/peptide 50S ribosomal protein L36 / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmJ, b3299, JW3261 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q6

-
Non-polymers , 4 types, 6 molecules

#33: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of 50S-HflXCOMPLEX#1-#320RECOMBINANT
250S ribosomeCOMPLEX#2-#321NATURAL
3GTPase HflXCOMPLEX#11RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 1200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 1.8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93913 / Symmetry type: POINT

+
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