[English] 日本語
Yorodumi
- PDB-7afr: Ribosome maturation factor RimP (apo) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7afr
TitleRibosome maturation factor RimP (apo)
ComponentsRibosome maturation factor RimP
KeywordsRNA BINDING PROTEIN / solution state NMR / 30S biogenesis / ribosome assembly / RimP.
Function / homology
Function and homology information


ribosomal small subunit assembly / translation / cytosol
Similarity search - Function
Ribosome maturation factor RimP, C-terminal domain / RimP-like superfamily, N-terminal / Ribosome maturation factor RimP / Ribosome maturation factor RimP, N-terminal / Ribosome maturation factor RimP, C-terminal / RimP, N-terminal domain superfamily / Ribosome maturation factor RimP, C-terminal domain superfamily / RimP N-terminal domain / RimP C-terminal SH3 domain / GMP Synthetase; Chain A, domain 3 ...Ribosome maturation factor RimP, C-terminal domain / RimP-like superfamily, N-terminal / Ribosome maturation factor RimP / Ribosome maturation factor RimP, N-terminal / Ribosome maturation factor RimP, C-terminal / RimP, N-terminal domain superfamily / Ribosome maturation factor RimP, C-terminal domain superfamily / RimP N-terminal domain / RimP C-terminal SH3 domain / GMP Synthetase; Chain A, domain 3 / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosome maturation factor RimP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsSchedlbauer, A. / Iturrioz, I. / Ochoa-Lizarralde, B. / Diercks, T. / Fucini, P. / Connell, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)CTQ2017-82222-R Spain
European CommissionPCIG14-GA-2013-632072 Spain
CitationJournal: Sci Adv / Year: 2021
Title: A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de ...Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de Astigarraga / David Gil-Carton / Paola Fucini / Sean R Connell /
Abstract: While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high- ...While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30 ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16 ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
History
DepositionSep 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Ribosome maturation factor RimP


Theoretical massNumber of molelcules
Total (without water)16,7381
Polymers16,7381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10980 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Ribosome maturation factor RimP


Mass: 16737.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rimP, yhbC, A6581_13520, A6592_14330, A6V01_00515, A8C65_02275, A9819_18200, A9P13_03050, A9R57_12705, A9X72_02945, AC067_23780, AC789_1c35400, ACN002_3263, ACU57_14550, ACU90_11670, AJ318_ ...Gene: rimP, yhbC, A6581_13520, A6592_14330, A6V01_00515, A8C65_02275, A9819_18200, A9P13_03050, A9R57_12705, A9X72_02945, AC067_23780, AC789_1c35400, ACN002_3263, ACU57_14550, ACU90_11670, AJ318_05135, AM270_15615, AM446_04425, AM464_08475, AM465_07740, AMK83_06445, AML07_19235, AML35_13990, APT94_23095, APU18_16510, APZ14_04190, ARC77_12300, AU473_05840, AUQ13_02970, AUS26_18365, AW059_15280, AW106_13165, AWB10_02960, AWE53_007750, AWF59_011795, AWG78_015830, AWG90_020515, AZZ83_001444, B6V57_17915, B7C53_06465, B9M99_10360, B9N33_16975, B9T59_16360, BANRA_01790, BANRA_03978, BANRA_04186, BB545_09885, BEN53_19595, BFD68_02460, BHF03_08615, BHF46_07210, BHS81_19095, BHS87_17860, BIQ87_17930, BIU72_05300, BIZ41_14495, BJJ90_02875, BK248_21925, BK292_10325, BK296_12945, BK334_09665, BK373_10280, BK375_17180, BK383_15860, BMA87_01190, BMT49_25700, BMT91_09135, BvCms12BK_01026, BvCms2454_04843, BvCms28BK_03353, BvCms35BK_01522, BvCmsC61A_01482, BvCmsHHP019_03132, BvCmsHHP056_02505, BvCmsKKP036_00265, BvCmsKKP061_00867, BvCmsKSNP073_02141, BvCmsKSNP081_00265, BvCmsKSNP120_03551, BvCmsKSP011_02071, BvCmsKSP024_00304, BvCmsKSP026_00481, BvCmsKSP045_01629, BvCmsKSP058_01861, BvCmsKSP067_01443, BvCmsKSP076_01609, BvCmsNSNP036_02130, BvCmsNSP006_04619, BvCmsNSP007_02230, BvCmsNSP047_04139, BvCmsNSP072_03166, BvCmsOUP014_03611, BvCmsSINP011_04479, BvCmsSINP022_03542, BvCmsSIP019_00386, BvCmsSIP044_00116, BWI89_22175, C2M16_04320, C2U48_17655, C4K41_03675, C4M78_03215, C5715_22690, C5N07_18175, C5P01_18940, C5P44_00535, C6669_12125, C6B13_18120, C7235_03330, C7B02_15770, C7B06_16695, C7B07_10705, C7B08_03460, C7B18_13725, C9098_07895, C9114_15350, C9141_00495, C9160_02445, C9162_04215, C9201_13770, C9306_00520, C9E25_11375, C9E67_03480, C9Z03_07385, C9Z23_02310, C9Z28_00490, C9Z29_07085, C9Z37_14765, C9Z39_14380, C9Z43_00485, C9Z69_11070, C9Z70_06870, C9Z78_03420, C9Z89_09170, CA593_10450, CCZ14_12150, CCZ17_15250, CDC27_16980, CDL37_12105, CF006_16775, CG692_07190, CI641_009150, CI693_03565, CI694_20945, CIG45_16155, CJU63_19030, CJU64_18910, CMR93_08945, CO706_14525, COD30_12805, COD46_10650, CQB02_14455, CQP61_03755, CR538_03180, CR539_21140, CRD98_04820, CRE06_06720, CRJUMX01_260087, CRM83_23605, CRT43_19210, CRX46_03850, CSB64_06490, CT146_02950, CUB99_16240, CVH05_10885, CWM24_22975, CWS33_08270, D0X26_08985, D1912_12210, D2184_10400, D2185_00550, D2188_02685, D3821_08430, D3822_14680, D3M98_06670, D3O91_07730, D3P01_09055, D3P02_05570, D3Y67_18395, D4011_13620, D4074_02330, D4628_02550, D4636_02785, D4638_00685, D4660_02725, D4718_08975, D4L91_11845, D4M06_11120, D4U49_10465, D4U85_14225, D4V08_01260, D5H35_09675, D5I97_10565, D6004_08020, D6C36_14055, D6D43_15405, D6T60_15285, D6T98_02305, D6W00_13910, D6X36_05255, D6X63_01325, D6X76_04230, D7K33_12750, D7K63_12115, D7K66_04390, D7W70_15750, D7Y10_03485, D7Z75_02840, D8Y65_13370, D9610_07705, D9C99_05015, D9D31_09850, D9D33_00515, D9D43_03510, D9D44_04305, D9D94_03385, D9E13_09760, D9E19_10295, D9E34_10730, D9E49_09490, D9E73_12375, D9F17_07095, D9F32_01135, D9G11_02975, D9G29_06920, D9G42_16795, D9G48_22395, D9G69_00995, D9G95_16980, D9H10_06565, D9H36_12500, D9H53_01090, D9H68_07455, D9H70_01525, D9H94_03415, D9I18_07070, D9I20_02730, D9I37_14605, D9I87_04955, D9I88_16545, D9I97_11395, D9J11_01025, D9J44_07745, D9J46_20545, D9J52_07810, D9J58_06005, D9J60_11080, D9J63_16805, D9J78_05025, D9K02_05975, D9K48_12150, D9K54_17935, D9L89_05265, D9L99_02555, D9S45_00150, D9X77_02225, D9X97_03015, D9Z28_03265, DAH18_20505, DAH26_17210, DAH30_12980, DAH32_14080, DAH34_01875, DAH37_04360, DAH43_16675, DB359_10675, DBQ99_04145, DD762_19135, DEN86_08165, DEN89_09300, DEN97_16030, DEO04_19500, DEO19_06325, DEO20_07555, DIV22_03080, DJ487_12870, DJ492_21815, DJ503_10870, DK132_15395, DL251_15040, DL257_05545, DL292_14605, DL326_05955, DL455_12595, DL479_06485, DL530_21135, DL545_03765, DL705_01195, DL800_23160, DL979_03350, DLT82_02550, DLU50_08445, DLU67_08270, DLU82_10225, DLW60_07385, DLW88_04690, DLX38_07775, DLY41_08050, DLY44_02205, DM102_15060, DM129_03900, DM155_07540, DM267_13960, DM272_02325, DM280_08950, DM296_04730, DM382_07255, DM820_04520, DM962_02535, DM973_04545, DMC44_07025, DMI04_04165, DMI53_12610, DMO02_15300, DMY83_09815, DMZ50_12315, DN660_01225, DN700_04490, DN703_00975, DN808_01785, DNB37_13600, DNC98_07055, DND16_06430, DND79_01225, DNI21_14825, DNJ62_11965, DNK12_02730, DNQ45_19755, DNR35_05290, DNR41_11080, DNW42_05300, DNX19_05475, DNX30_11260, DOE35_12505, DOM23_01535, DOS18_12925, DOT81_04150, DOU81_12270, DOY22_13980, DOY56_12140, DOY61_04590, DOY67_01180, DP265_06450, DP277_10000, DQE91_01160, DQF36_20850, DQF57_03510, DQF71_07055, DQF72_06355, DQG35_02725, DQO13_01190, DQP61_01665, DRP48_13805, DRW19_01190, DS143_06665, DS721_10985, DS732_23590, DS966_19175, DT034_01165, DTL43_04190, DTM10_07090, DTM45_14405, DTZ20_11985, DU309_11240, DU321_08565, DU333_16815, DVB38_07290, DW236_11980, DWB25_03315, DXT69_05625, DXT71_00545, DXT73_13265, DXX80_009485, E0I42_14235, E0K84_20585, E0L04_19770, E0L12_03810, E2112_05640, E2114_08285, E2115_05735, E2119_05765, E2127_02470, E2128_02600, E2129_05655, E2134_15700, E2135_07975, E2148_12390, E2855_04121, E2863_03946, E4K55_06555, E4K60_03320, E4K61_09175, E5P22_12890, E5P28_13015, E5P37_13240, E5S42_11910, E5S46_04245, E5S47_02865, E5S56_15530, E5S58_02830, E5S61_05810, EA159_13410, EA167_07035, EA189_10710, EA191_13025, EA198_19520, EA200_07260, EA203_14945, EA213_02390, EA214_08705, EA218_15110, EA222_06430, EA225_06975, EA231_14825, EA232_14625, EA233_06070, EA242_07640, EA245_09665, EA250_06530, EA410_15875, EA429_03180, EA434_19670, EA435_15260, EA834_14920, EAI42_15040, EAI46_15085, EAI52_09995, EAM59_00915, EAN70_10640, EAN77_10380, EAX79_13125, EB476_09145, EB509_07095, EB510_12300, EB515_06920, EBA46_01560, EBA84_05725, EBJ06_06030, EBM08_05350, EC3234A_53c00490, EC3426_04319, EC382_14550, EC95NR1_02552, ECONIH1_18750, ECTO124_00619, ECTO6_00586, ED225_04165, ED307_11680, ED600_09295, ED607_10320, ED611_04175, ED648_02810, ED903_04550, ED944_07155, EEA45_06835, EEP23_06195, EF082_03885, EF173_16900, EG075_10005, EG599_06060, EG796_01085, EG808_04740, EGC26_04810, EGT48_12345, EGU87_04110, EH186_10365, EH412_00890, EHD45_09310, EHD63_05170, EHD79_19375, EHH55_24255, EHJ36_00890, EHJ66_05985, EHV81_00450, EHV90_06065, EHW09_05495, EHX09_11690, EI021_03960, EI028_15155, EI032_08700, EI041_02105, EIA08_12605, EIA21_02775, EIZ93_15760, EJ366_26100, EJC75_15120, EKI52_18340, ELT17_03400, ELT20_05150, ELT22_04740, ELT23_06870, ELT33_08790, ELT48_07015, ELT49_04545, ELT58_00540, ELU82_09410, ELU85_07030, ELU96_15070, ELV05_02170, ELV08_03090, ELV13_06450, ELV15_01725, ELV22_10740, ELV24_06460, ELV28_06240, ELX56_11845, ELX70_11310, ELX76_04020, ELX79_02845, ELX83_01980, ELY05_03155, ELY23_12930, ELY24_06190, ELY41_02060, ELY48_01080, ELY50_10975, EO241_09475, EPS76_01470, EPS91_00535, EPS94_08350, EPT01_00520, EPU41_18025, EQ823_04945, EQ825_16430, EQ830_04625, ERL57_13330, ERS085365_00561, ERS085366_00575, ERS085374_01907, ERS085379_00394, ERS085383_00718, ERS085386_00509, ERS085404_02208, ERS085406_02910, ERS085416_00333, ERS139211_00574, ERS150873_04325, ERS150876_01006, EST51_02850, EVY14_07620, EWK56_02880, EXM29_19890, ExPECSC019_00733, ExPECSC038_02681, ExPECSC065_00152, EXX06_09585, EXX13_07220, EXX23_07435, EXX24_06255, EXX53_05215, EXX55_08940, EXX71_13295, EXX78_16835, EXX87_04485, EYD11_02750, EYX82_02350, EYX99_26670, EYY27_17450, EYY34_08680, EYY78_15515, F1E13_04755, F1E19_22160, F7F00_12275, F7F11_09140, F7F18_01100, F7F23_11550, F7F26_00510, F7F29_05220, F7G01_14085, F7G03_16255, F9059_01215, F9Z74_11735, FAF34_018990, FE846_13840, FKO60_06135, FNJ67_03680, FNJ69_14760, FNJ83_20460, FQ022_08085, FQ915_16575, FQR64_03140, FQU83_04615, FQZ46_16235, FRV13_20650, FV293_08480, FV295_10420, FV438_11005, FVB16_12900, FWK02_30950, FY127_14860, FZ043_21930, GFU40_08290, GFU45_16445, GFU47_23645, GHR40_07700, GII67_12855, GII91_02620, GIY13_09410, GIY19_08440, GJ11_20705, GJ638_05280, GJD97_02990, GKE15_04560, GKE22_12100, GKE24_04550, GKE26_04235, GKE29_02570, GKE31_04515, GKE39_10640, GKE46_11105, GKE58_04470, GKE60_04205, GKE64_10430, GKE77_04900, GKE87_00805, GKE92_01045, GKE93_06080, GKF00_04240, GKF03_05185, GKF28_11940, GKF34_04535, GKF47_04530, GKF74_09325, GKF86_04155, GKF89_14480, GKG08_09990, GKG09_10130, GKG11_10335, GKG12_08430, GKG22_10250, GKG29_10290, GN312_06535, GNZ00_04975, GNZ02_01185, GNZ03_06215, GP654_17605, GP661_13150, GP664_11975, GP666_12855, GP689_13980, GP700_08285, GP712_11280, GP720_14900, GP727_07890, GP912_13015, GP935_13235, GP946_08565, GP950_18120, GQA06_13100, GQE22_11445, GQE30_02675, GQE34_11815, GQE42_06055, GQE47_10010, GQE51_04775, GQE58_09360, GQE64_09830, GQE68_06305, GQE88_18540, GQE93_14745, GQL64_21185, GQM06_01810, GQM09_10960, GQM13_09315, GQM17_12990, GQN16_09395, GQN33_10425, GQS26_10800, GRW42_15825, GRW80_12150, HmCms169_01197, HmCms184_00230, HmCmsJML074_04857, HmCmsJML079_04423, HmCmsJML146_01154, HmCmsJML204_02229, HmCmsJML236_03431, HW43_20810, MJ49_14450, MS6198_36560, MS8345_03519, NCTC10082_02969, NCTC10089_00628, NCTC10090_03661, NCTC10764_04007, NCTC10766_02930, NCTC10767_01659, NCTC10865_00812, NCTC10963_00588, NCTC11022_03335, NCTC11181_02870, NCTC12650_00863, NCTC13216_01221, NCTC13846_00637, NCTC7927_00693, NCTC7928_02343, NCTC8009_01696, NCTC8179_06096, NCTC8621_00648, NCTC8959_03135, NCTC8960_03211, NCTC9001_05629, NCTC9007_04393, NCTC9036_00679, NCTC9044_01214, NCTC9045_00716, NCTC9050_03744, NCTC9055_02513, NCTC9058_01245, NCTC9062_02553, NCTC9111_00997, NCTC9119_00654, NCTC9434_00565, NCTC9701_00708, NCTC9703_05099, NCTC9706_02867, NCTC9777_02133, NCTC9969_00790, PGD_03946, PU06_19955, RG28_20970, RK56_014715, RX35_04257, SAMEA3472043_01802, SAMEA3472044_03331, SAMEA3472047_01873, SAMEA3472055_00399, SAMEA3472056_03073, SAMEA3472070_01171, SAMEA3472080_00946, SAMEA3472090_00549, SAMEA3472108_00101, SAMEA3472110_01542, SAMEA3472112_01526, SAMEA3472114_00482, SAMEA3472147_01879, SAMEA3484427_00607, SAMEA3484429_00735, SAMEA3484434_03594, SAMEA3485101_01711, SAMEA3752372_01780, SAMEA3752553_01186, SAMEA3752557_01874, SAMEA3752559_03272, SAMEA3752620_02342, SAMEA3753064_02937, SAMEA3753097_03303, SAMEA3753164_02301, SAMEA3753290_00147, SAMEA3753300_02130, SK85_03483, SY51_18280, U12A_03406, U14A_03403, UC41_24430, UN86_15485, UN91_15510, WQ89_06745, WR15_24545, YDC107_1843
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J3VRH1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 15N TROSY
121isotropic23D HNCO
131isotropic23D HNCA
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH
1131isotropic23D HN(CO)CA
1121isotropic23D HN(CA)CO
1111isotropic13D (H)CCH-TOCSY
1101isotropic13D HNCAHA
191anisotropic13D HN(CO)CAHA
181isotropic23D CNH NOESY
171isotropic23D HNH NOESY
161isotropic23D CCH NOESY

-
Sample preparation

DetailsType: solution
Contents: 600 uM [U-99% 13C; U-99% 15N] RimP, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP, 90% H2O/10% D2O
Label: sample1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMRimP[U-99% 13C; U-99% 15N]1
10 mMHEPESnone1
6 mMMgCl2none1
30 mMNH4Clnone1
75 uMTCEPnone1
Sample conditionsIonic strength: 40 mM / Label: condition_1 / pH: 7.6 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
GROMACSEmile Apol, Rossen Apostolov, Paul Bauer, Herman J.C. Berendsen, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Rudi van Drunen, Anton Feenstra, Alan Gray, Gerrit Groenhof, Anca Hamuraru, Vincent Hindriksen M. Eric Irrgang, Aleksei Iupinov, Christoph Junghans, Joe Jordan, Dimitrios Karkoulis, Peter Kasson,, Jiri Kraus, Carsten Kutzner, Per Larsson, Justin A. Lemkul, Viveca Lindahl, Magnus Lundborg, Erik Marklund, Pascal Merz, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alexey Shvetsov, Alfons Sijbers, Peter Tieleman, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov.refinement
Refinement
MethodSoftware ordinal
simulated annealing3
molecular dynamics4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

+
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