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- PDB-7t6d: CryoEM structure of the YejM/LapB complex -

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Basic information

Entry
Database: PDB / ID: 7t6d
TitleCryoEM structure of the YejM/LapB complex
Components
  • Inner membrane protein YejM
  • Lipopolysaccharide assembly protein B
KeywordsMEMBRANE PROTEIN / YejM / YciM / regulation / lipopolysaccharide synthesis / LpxC
Function / homology
Function and homology information


: / lipopolysaccharide metabolic process / regulation of lipid biosynthetic process / membrane => GO:0016020 / iron ion binding / plasma membrane
Similarity search - Function
Lipopolysaccharide assembly protein B / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / : / Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily ...Lipopolysaccharide assembly protein B / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / : / Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Chem-LPP / Chem-PGV / Inner membrane protein YejM / Lipopolysaccharide assembly protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMi, W. / Shu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli.
Authors: Sheng Shu / Wei Mi /
Abstract: Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH- ...Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH-mediated degradation of LpxC, which catalyzes the first committed step in LPS synthesis. FtsH is a membrane-bound AAA+ protease, and its protease activity toward LpxC is regulated by essential membrane proteins LapB and YejM. However, the regulatory mechanisms are elusive. We establish an in vitro assay to analyze the kinetics of LpxC degradation and demonstrate that LapB is an adaptor protein that utilizes its transmembrane helix to interact with FtsH and its cytoplasmic domains to recruit LpxC. Our YejM/LapB complex structure reveals that YejM is an anti-adaptor protein, competing with FtsH for LapB to inhibit LpxC degradation. Structural analysis unravels that LapB and LPS have overlapping binding sites in YejM. Thus, LPS levels control formation of the YejM/LapB complex to determine LpxC protein levels.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide assembly protein B
B: Lipopolysaccharide assembly protein B
C: Inner membrane protein YejM
D: Inner membrane protein YejM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,2216
Polymers225,8234
Non-polymers1,3982
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11020 Å2
ΔGint-88 kcal/mol
Surface area61550 Å2

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Components

#1: Protein Lipopolysaccharide assembly protein B


Mass: 45546.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: lapB, lapB_1, lapB_2, yciM, A6519_003392, A8499_002320, A8W81_000860, A8X68_001918, A9X72_14480, AAG43_002492, ABE90_026530, ABT96_002964, ACN002_1742, ACN68_13760, ACU57_02830, ACW72_002916, ...Gene: lapB, lapB_1, lapB_2, yciM, A6519_003392, A8499_002320, A8W81_000860, A8X68_001918, A9X72_14480, AAG43_002492, ABE90_026530, ABT96_002964, ACN002_1742, ACN68_13760, ACU57_02830, ACW72_002916, AM270_04715, AM464_24460, AMK64_001197, AML23_13785, AO169_003132, AT335_001728, AT845_003561, AUQ29_06870, AW059_17045, B2D52_003072, B5N24_003363, B6L15_002768, B6R12_000713, B6R15_001447, B7C15_002578, B9T59_25470, BANRA_00913, BANRA_01922, BANRA_02272, BANRA_04238, BE930_07195, BF481_003525, BFL24_11350, BHF52_04915, BHS81_08140, BHS87_06805, BIZ41_06440, BJI68_16000, BK272_18185, BKD45_002476, BMC34_002615, BMT50_25160, BMT91_09485, BN17_11291, BOH76_12790, BON63_08380, BON65_11400, BON70_13430, BON72_10370, BON73_23360, BON76_22345, BON86_26965, BON87_00675, BON91_05790, BON93_04810, BON94_23115, BON95_24295, BON96_11840, BON98_20550, BTQ06_01755, BUE81_21790, BvCms2454_02783, BvCmsC61A_00867, BvCmsHHP019_01251, BvCmsHHP056_05185, BvCmsKKP005_01617, BvCmsKKP036_02977, BvCmsKKP057_02775, BvCmsKKP061_04930, BvCmsKSNP073_02552, BvCmsKSP011_00507, BvCmsKSP067_03395, BvCmsNSNP036_02647, BvCmsSIP082_03266, BVL39_21785, C2121_001848, C2U48_01890, C3F40_05575, C5F72_14800, C5N07_15420, C5Y87_08390, C6B13_16180, C6B22_15545, C6L19_000308, C6N50_002146, C7B02_10605, C9114_03730, C9160_12100, C9E67_15785, C9Z62_12310, CA593_21440, CBT22_000243, CCS08_27640, CCZ91_000907, CDL36_22330, CDL37_04200, CDL57_24010, CF32_002531, CG692_05225, CG831_002162, CIG67_22415, CLG78_002326, CN875_001332, CO706_02845, COD50_12455, CQP61_13055, CS116_002344, CT143_17675, D0X26_18180, D2183_20380, D3G36_18000, D3O91_23240, D3Y67_04030, D4U49_17205, D4V09_13060, D5H22_10790, D6T60_03370, D9D77_16425, D9E49_04245, D9F92_17650, D9H13_01425, D9H94_11055, D9J11_07075, D9K17_12190, DAH18_14065, DAH23_15505, DAH34_16510, DAH50_11685, DB282_08780, DEN89_18990, DEO15_14770, DIV22_30895, DM968_19040, DRW19_11270, DS732_11480, DS966_14175, DTL43_11095, DTL90_01335, DXB10_15580, DXB10_16775, DXT69_00360, DXT71_10990, DXT73_13915, E0I42_06310, E2112_02885, E2123_11980, E2127_03390, E2128_00455, E2129_00375, E3N34_18830, E4K51_14885, E4K54_14850, E5P52_03605, E5S34_10145, E5S35_09160, E5S38_11225, E5S43_08140, E5S47_06570, E5S52_03675, E5S61_07790, EAI46_04695, EAN77_13100, EBP16_17290, EC1094V2_2484, EC3234A_230c01430, EC95NR1_00326, ECs1853, ED648_03900, EGC08_11645, EH88_003316, EHD79_11840, EHH55_10950, EI021_13605, EI041_15605, EIA08_16130, EIA13_10710, EIZ93_19170, EKI52_01585, EL79_2487, EL80_2488, ELT21_12950, ELT31_16165, ELT33_13755, ELT49_21030, ELT58_08985, ELU83_12175, ELU95_16765, ELV08_11905, ELV10_01715, ELX76_20405, ELY05_10955, EO241_12655, EQO00_13740, ERS085358_00939, ERS085386_02975, ERS085406_00731, Esc0902E_14650, ETECE1373_02637, ETECE36_03510, EVY14_13400, EWK56_17840, ExPECSC038_05182, EXX13_01995, EYX47_09350, EYX55_08745, F6U69_15745, F9400_07670, F9407_04140, F9S76_06015, F9V07_00360, F9V24_11000, F9X20_015225, F9X20_15355, FC554_07815, FDM60_05915, FE587_04450, FEJ01_09950, FFF58_19650, FGG80_24000, FKO60_08750, FMP09_02050, FOI11_006585, FOI11_13555, FPI65_07590, FPS82_10375, FQE77_10850, FQF29_23035, FV293_10890, FY127_08365, G4A38_11915, G5603_19860, G5632_16960, G5696_03530, G6Z99_13635, G7635_000932, G9448_04240, GAJ26_07165, GBE29_13210, GF147_07410, GF646_08560, GF699_11645, GFY34_05975, GFZ60_14750, GIB53_11460, GKF86_18860, GKF89_20570, GKG12_03945, GLW94_11560, GNZ05_13290, GOP20_20825, GP662_03380, GQA06_04230, GQE42_15065, GQE64_13610, GQE87_12585, GQF58_06905, GQF59_08575, GQM06_04685, GQM10_06545, GQW07_00450, GQW76_09945, GRO95_01570, GRQ19_03720, GRW05_11530, GRW57_13825, GRW80_12460, GRW81_07680, GUB08_18980, H0O72_03640, H4P50_08895, H4P51_14150, HH411_001987, HH795_004427, HHG09_004014, HHH44_001843, HIE44_002503, HIF90_001390, HIR12_001593, HJN04_001209, HJO75_002524, HJS41_002779, HL425_08705, HL601_11520, HLZ20_07505, HLZ50_09210, HMJ82_13920, HMS79_05245, HMU48_18525, HMV41_16070, HMV95_10465, HNC38_13520, HNC52_13050, HND12_15785, HND24_14400, HNO08_14040, HNV65_09995, HNV94_15550, HNY50_11855, HNY54_14470, HV109_13370, HVV39_23985, HVV53_02660, HVW04_04200, HVW11_24340, HVY77_14595, HVZ33_13530, HVZ71_13670, HZ71_002608, I6H00_07305, I6H01_24000, I6H02_25750, JE86ST02C_16760, JE86ST05C_16890, NCTC10089_02682, NCTC10090_00861, NCTC10418_04179, NCTC10429_05120, NCTC10764_02333, NCTC10767_05193, NCTC10865_03455, NCTC11022_01072, NCTC11112_05334, NCTC11181_04717, NCTC13127_03637, NCTC13216_03875, NCTC4450_04325, NCTC7927_03033, NCTC8008_02211, NCTC8500_03093, NCTC8960_05553, NCTC8985_01499, NCTC9036_02890, NCTC9045_03196, NCTC9048_03637, NCTC9050_00806, NCTC9073_01700, NCTC9081_03892, NCTC9117_03545, NCTC9434_03952, NCTC9706_00177, NCTC9777_04051, NCTC9969_02938, PGD_01970, PU06_14205, RG28_16120, SAMEA3472043_03563, SAMEA3472056_02600, SAMEA3472080_01068, SAMEA3484427_01617, SAMEA3484429_01482, SAMEA3485101_02085, SAMEA3485110_04597, SAMEA3751407_01252, SAMEA3752386_00749, SAMEA3752557_02954, SAMEA3753064_00168, SAMEA3753290_01068, SAMEA3753300_03507, THOESC010_24410, TUM18780_23450, UN91_04670, WP2S18E08_26240, WP4S18E08_25230, WQ89_18230, WR15_00725
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star pLysS / References: UniProt: C3TC27
#2: Protein Inner membrane protein YejM


Mass: 67364.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yejM, pbgA, yejM_2, A6583_09370, A6592_11615, A8499_001072, A8C65_16830, A8W81_001303, A9X72_08400, ACN002_2250, ACU57_09240, ADS93_002353, AM340_15765, AM464_02270, APX88_05005, AUQ29_19365, ...Gene: yejM, pbgA, yejM_2, A6583_09370, A6592_11615, A8499_001072, A8C65_16830, A8W81_001303, A9X72_08400, ACN002_2250, ACU57_09240, ADS93_002353, AM340_15765, AM464_02270, APX88_05005, AUQ29_19365, AW086_07975, AW118_16940, AWP47_24265, AZZ83_002338, B6R12_000845, B6R15_004238, B6R17_002480, B6R27_005186, B6R48_001484, B6R87_001451, B9T59_22870, BANRA_00752, BANRA_04871, BE930_28735, BER14_18270, BF271_000946, BFL24_16505, BG821_000075, BH692_09340, BHS87_12530, BIQ87_13040, BJI68_13215, BJJ90_08330, BK272_02805, BK373_07505, BM922_001699, BMC79_000422, BMT49_13905, BMT91_00115, BN17_14751, BO068_002744, BON72_16040, BON73_18350, BON76_17375, BON86_23915, BON87_08430, BON92_16815, BON93_21655, BON94_17700, BON96_18625, BON98_04460, BOY03_001080, BUE81_18280, BUE82_07615, BvCms2454_04584, BvCmsHHP019_05090, BvCmsSIP024_01508, BWI89_02190, BZL69_09245, C4952_001182, C4M78_17535, C5715_06575, C5F72_09155, C5Y87_12800, C6B13_00290, C6B22_01615, C7B02_03025, C9E67_09155, C9Z43_08610, C9Z68_16250, CA593_16265, CCS08_24350, CCV12_002491, CD42_001250, CDL36_01005, CDL37_14785, CDL57_04530, CG692_11165, CG831_003323, CQP61_10000, CT143_04215, D0X26_21125, D1912_29500, D2183_09840, D3822_12865, D3G36_02140, D3O91_01050, D3Y67_09165, D4U49_06490, D4V09_19965, D9F92_03905, D9H13_11200, D9J11_19635, D9J61_06525, DAH23_00425, DAH34_05185, DAH37_09170, DEN86_03840, DLW88_13930, DM968_07875, DNX30_05665, DS732_17010, DS966_01280, DTM10_09095, DTM45_08440, DU321_11480, DXB10_11805, E0N24_08640, E2119_00760, E2123_11275, E2127_01995, E2128_04195, E2129_08825, E3N34_20700, E4K51_00800, E4K54_03780, E5P52_00935, EA239_06720, EA435_00905, EC3234A_43c00110, ECs3080, EI021_01330, EI041_05800, EIA08_04310, ELT17_13065, ELT21_02385, ELT33_04940, ELT48_05200, ELT49_19620, ELT58_04240, ELT72_00755, ELV10_04545, ELV13_02810, ELV22_00720, ELV24_08035, ELX56_00815, ELX68_00770, ELX69_02045, ELX70_02545, ELX76_00500, ELX79_03840, ELX83_15305, ELY05_14680, ELY23_08830, ELY24_08630, ELY50_02880, EO241_01170, EPS76_06925, EQO00_09055, ERS085386_00298, ETECE925_01624, EWK56_07190, ExPECSC038_02216, EXX79_04640, F2N27_23515, F2N28_23660, F3N40_00740, F6U69_01695, F7F11_05890, F9386_09630, F9571_15145, F9S83_16100, F9V24_17745, FFF58_08555, FGG80_10995, FHR00_02145, FJQ51_21990, FKO60_02570, FMP09_00770, FNJ67_09010, FOI11_001990, FOI11_18055, FPI65_13810, FQF29_23785, FZN30_10900, G3565_00930, G3813_002500, G4A38_04620, G5603_04965, G6P89_08200, GF147_03470, GFY48_00705, GKF52_07460, GKG12_01680, GKZ24_12255, GLW94_00250, GNO40_04250, GP711_04060, GQE64_02255, GQE87_19270, GQW07_05465, GQW68_08245, GQW76_18825, GQW80_04770, GRC73_01825, GRO95_13145, GRQ19_15575, GRW05_06845, GRW80_02890, GRW81_01115, GTP88_01785, GUB92_18760, GUI33_19260, GW978_00750, GXU05_002919, GXV26_001787, H5C78_15085, HH411_001705, HH795_001884, HHG09_004071, HI055_001135, HIE29_002609, HIE44_001815, HIT56_002195, HJM92_004122, HJO75_003640, HJQ60_001849, HJS37_000913, HJS41_002956, HJU54_002487, HL425_00735, HL601_00640, HLU10_10190, HLU56_15835, HLV18_10515, HLZ20_01885, HmCms169_00898, HMJ82_13430, HMS79_06405, HMU06_05650, HMU48_06105, HMV95_16605, HMV95_25940, HNC30_04745, HNC36_11220, HNC38_05860, HNC52_14840, HNC59_05410, HNC66_16020, HNC99_03425, HND12_03865, HND24_03720, HNO08_17220, HNV94_03750, HNY50_05155, HNY54_04060, HPE39_17300, HVV39_02785, HVV53_07965, HVW04_24015, HVW43_25590, HVX16_08400, HVZ33_08545, HX136_08025, HZ71_001224, MJ49_19865, MS7163_02295, NCTC10082_04105, NCTC10089_01672, NCTC10764_00976, NCTC10767_02951, NCTC11022_02170, NCTC11126_04042, NCTC12950_01951, NCTC13127_02131, NCTC13216_04902, NCTC8008_01090, NCTC8500_01909, NCTC8959_02126, NCTC9001_02081, NCTC9044_05974, NCTC9045_01997, NCTC9048_01750, NCTC9073_01555, NCTC9081_05148, NCTC9434_01706, NCTC9702_01992, NCTC9706_04975, SAMEA3472064_00873, SAMEA3472080_00462, SAMEA3472112_02618, SAMEA3472117_02395, SAMEA3472120_00721, SAMEA3484427_01505, SAMEA3484429_01356, SAMEA3751407_04919, SAMEA3752312_00374, SAMEA3752386_04909, SAMEA3752557_00509, SAMEA3753064_00496, SAMEA3753290_01284, SAMEA3753300_00187, SM09_02308, WP2S18E08_17110, WP4S18E07_15720, WP4S18E08_15980, WQ89_02845
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star pLysS / References: UniProt: C3T3G2
#3: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: complex of YejM and YciM / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 225.556 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8.84 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092 / Movie frames/image: 82

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.27data extraction
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARC3.2CTF correction
9cryoSPARC3.2initial Euler assignment
10cryoSPARC3.2final Euler assignment
12cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1181379 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 137.57 Å2 / Biso mean: 49.2648 Å2 / Biso min: 20.65 Å2

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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

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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

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