[English] 日本語
Yorodumi
- PDB-6zy4: Cryo-EM structure of MlaFEDB in complex with ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zy4
TitleCryo-EM structure of MlaFEDB in complex with ADP
Components
  • ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
  • Toluene tolerance protein Ttg2A
  • Uncharacterized protein
  • YrbD protein
KeywordsLIPID TRANSPORT / phospholipid / phospholipid transport / ABC transporter / MlaFEDB / MlaFE / MlaD / MlaE / MlaF / MlaB / outer membrane / Mla transport pathway
Function / homology
Function and homology information


phospholipid transfer activity / intermembrane phospholipid transfer / phospholipid-translocating ATPase complex / phospholipid transport / ATP-binding cassette (ABC) transporter complex / response to antibiotic / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / cytosol
Similarity search - Function
: / Probable phospholipid ABC transporter-binding protein MlaD / ABC transport permease subunit MlaE, Proteobacteria / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain profile. / STAS domain ...: / Probable phospholipid ABC transporter-binding protein MlaD / ABC transport permease subunit MlaE, Proteobacteria / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain profile. / STAS domain / STAS domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / YrbD protein / Intermembrane phospholipid transport system permease protein MlaE / Intermembrane phospholipid transport system binding protein MlaB / Toluene tolerance protein Ttg2A / Anti-sigma factor antagonist
Similarity search - Component
Biological speciesEscherichia coli B185 (bacteria)
Escherichia coli (E. coli)
Escherichia coli 909945-2 (bacteria)
Escherichia coli 2.3916 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsDong, C.J. / Dong, H.H.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2017YFA0504803, 2018YFA0507700, 2017YFC0840100, 2017YFC00840101,31900039,81971974 China
Wellcome TrustWT106121MA United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural insights into outer membrane asymmetry maintenance in Gram-negative bacteria by MlaFEDB.
Authors: Xiaodi Tang / Shenghai Chang / Wen Qiao / Qinghua Luo / Yuejia Chen / Zhiying Jia / James Coleman / Ke Zhang / Ting Wang / Zhibo Zhang / Changbin Zhang / Xiaofeng Zhu / Xiawei Wei / ...Authors: Xiaodi Tang / Shenghai Chang / Wen Qiao / Qinghua Luo / Yuejia Chen / Zhiying Jia / James Coleman / Ke Zhang / Ting Wang / Zhibo Zhang / Changbin Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong /
Abstract: The highly asymmetric outer membrane of Gram-negative bacteria functions in the defense against cytotoxic substances, such as antibiotics. The Mla pathway maintains outer membrane lipid asymmetry by ...The highly asymmetric outer membrane of Gram-negative bacteria functions in the defense against cytotoxic substances, such as antibiotics. The Mla pathway maintains outer membrane lipid asymmetry by transporting phospholipids between the inner and outer membranes. It comprises six Mla proteins, MlaFEDBCA, including the ABC transporter MlaFEDB, which functions via an unknown mechanism. Here we determine cryo-EM structures of Escherichia coli MlaFEDB in an apo state and bound to phospholipid, ADP or AMP-PNP to a resolution of 3.3-4.1 Å and establish a proteoliposome-based transport system that includes MlaFEDB, MlaC and MlaA-OmpF to monitor the transport direction of phospholipids. In vitro transport assays and in vivo membrane permeability assays combined with mutagenesis identify functional residues that not only recognize and transport phospholipids but also regulate the activity and structural stability of the MlaFEDB complex. Our results provide mechanistic insights into the Mla pathway, which could aid antimicrobial drug development.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11549
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YrbD protein
D: YrbD protein
I: YrbD protein
J: YrbD protein
K: YrbD protein
L: YrbD protein
B: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
C: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
F: Toluene tolerance protein Ttg2A
G: Toluene tolerance protein Ttg2A
E: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,08116
Polymers255,17812
Non-polymers9034
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31850 Å2
ΔGint-275 kcal/mol
Surface area96020 Å2
MethodPISA

-
Components

-
Protein , 4 types, 12 molecules ADIJKLBCFGEH

#1: Protein
YrbD protein


Mass: 19593.133 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli B185 (bacteria) / Gene: ECDG_03382 / Production host: Escherichia coli (E. coli) / References: UniProt: D6IEA5
#2: Protein ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component / Lipid asymmetry maintenance protein MlaB / Phospholipid ABC transporter substrate-binding protein / ...Lipid asymmetry maintenance protein MlaB / Phospholipid ABC transporter substrate-binding protein / Phospholipid ABC transporter-binding protein / Putative anti-sigma factor antagonist / Putative phospholipid ABC transporter-binding protein MlaB


Mass: 11795.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: mlaB, yrbB, A6581_13415, A6592_14225, A6V01_00625, A8C65_02170, A9P13_02945, A9R57_12600, A9X72_02835, AC067_23675, ACN002_3282, ACN68_12355, ACN81_18445, ACU57_14445, ACU90_11565, AM270_15510, ...Gene: mlaB, yrbB, A6581_13415, A6592_14225, A6V01_00625, A8C65_02170, A9P13_02945, A9R57_12600, A9X72_02835, AC067_23675, ACN002_3282, ACN68_12355, ACN81_18445, ACU57_14445, ACU90_11565, AM270_15510, AM446_04320, AM464_08585, AMK83_06340, AML07_19340, APT94_23200, APZ14_04295, ARC77_12405, AU473_05735, AUQ13_03075, AUS26_18260, AW106_13275, AWB10_02850, AWG90_020620, AWP75_14100, B9M99_10250, B9T59_16250, BANRA_01811, BANRA_03804, BANRA_03999, BANRA_04207, BB545_09780, BE963_06830, BER14_09135, BHJ80_21985, BHS81_19200, BHS87_17970, BIQ87_18040, BIU72_05405, BJJ90_02770, BK292_10220, BK296_13050, BK373_10175, BK375_18740, BK383_15965, BMA87_01295, BMT49_25595, BMT91_11610, BOH76_04915, BON63_14235, BON66_12205, BON69_26555, BON71_25170, BON72_13935, BON75_23145, BON76_05525, BON83_09240, BON86_01565, BON87_18195, BON92_11035, BON94_12335, BON95_22020, BON96_06355, BTQ04_16475, BTQ06_11870, BUE81_19690, BvCms2454_04822, BvCms28BK_03527, BvCms35BK_01543, BvCmsHHP001_01202, BvCmsHHP019_05314, BvCmsKKP061_00888, BvCmsKSNP073_02163, BvCmsKSNP081_00287, BvCmsKSP011_02050, BvCmsKSP024_00283, BvCmsKSP026_00502, BvCmsKSP045_01650, BvCmsKSP067_01464, BvCmsNSNP036_02151, BvCmsNSP006_04640, BvCmsNSP047_04118, BvCmsNSP072_03187, BvCmsOUP014_03632, BvCmsSINP011_04458, BvCmsSIP019_00407, BvCmsSIP044_00137, BVL39_10130, BW690_19360, BWI89_22070, BWP17_10155, BXT93_02550, BZL31_05925, BZL69_07715, C2M16_04215, C5715_22795, C5N07_18070, C5P01_18835, C6669_12020, C7235_03225, C7B02_15875, C7B08_03565, C7B18_13830, C9098_07790, C9114_15455, C9141_00390, C9160_02340, C9162_04110, C9201_13875, C9306_00415, C9E25_11270, C9E67_03375, C9Z03_07490, C9Z28_00385, C9Z29_07190, C9Z37_14660, C9Z39_14275, C9Z43_00380, C9Z68_06245, C9Z69_11175, C9Z70_06765, C9Z78_03315, C9Z89_09065, CA593_10345, CDL37_12215, CF006_16665, CG692_07300, CI641_009255, CI693_03675, CI694_20835, CIG45_16045, CJU63_19140, CJU64_19020, CMR93_08835, CO706_14630, COD30_12915, COD46_10760, CQP61_03650, CR538_03070, CR539_21250, CRD98_04715, CRE06_06830, CRM83_23500, CRX46_03745, CVH05_10780, CWM24_22870, CWS33_08375, D0X26_09090, D2184_10505, D2185_00445, D2188_02580, D3821_08325, D3822_14575, D3O91_07625, D3P01_09160, D3Y67_18290, D4011_13725, D4074_02435, D4628_02655, D4636_02890, D4638_00790, D4660_02830, D4718_09085, D4L91_11950, D4M06_11225, D4U85_14330, D5H35_09780, D5I97_10670, D6004_08125, D6C36_14160, D6D43_15510, D6T60_15390, D6T98_02410, D6W00_14015, D6X36_05360, D6X63_01430, D6X76_04335, D7K33_12855, D7K63_12220, D7K66_04495, D7W70_15855, D7Z75_02945, D8Y65_13475, D9610_07810, D9C99_05120, D9D20_06275, D9D31_14515, D9D43_03615, D9D44_04410, D9E19_10400, D9E34_11740, D9E49_09595, D9F17_07200, D9F32_01240, D9F87_05870, D9G29_07025, D9G48_11290, D9G69_01100, D9G95_17085, D9H53_01195, D9H68_07560, D9I18_07175, D9I88_07240, D9J03_05150, D9J11_01130, D9J44_07850, D9J52_07915, D9J58_06110, D9J60_11185, D9J63_16910, D9J78_05130, D9K02_06080, D9K48_12255, D9L89_05370, D9S45_00255, D9X77_02330, D9X97_03120, D9Z28_03370, DAH18_20610, DAH26_17315, DAH30_12875, DAH32_13975, DAH34_01980, DAH37_04255, DAH43_16780, DBQ99_04040, DD762_13125, DEN86_08060, DEN89_09405, DEN97_16135, DEO04_19605, DEO19_06430, DIV22_02975, DJ503_19040, DK132_07375, DL257_05650, DL292_05795, DL326_06060, DL455_12700, DL479_06590, DL530_10055, DL705_01300, DL800_23275, DLT82_02655, DLU50_08550, DLU67_08375, DLU82_10330, DLW60_07490, DLW88_04795, DLY41_08155, DM102_15165, DM155_07645, DM267_03265, DM280_09055, DM296_04835, DM382_07360, DM820_04625, DM962_02640, DM973_04650, DMI04_04270, DMI53_12715, DMO02_15405, DMY83_09920, DN660_01330, DN700_04595, DN703_01080, DN808_01890, DNB37_13705, DNC98_07160, DND16_06535, DND79_01330, DNI21_03635, DNJ62_12070, DNK12_02835, DNQ45_01620, DNW42_05405, DNX19_05580, DNX30_11365, DOE35_12610, DOS18_13030, DOT81_04255, DOU81_12375, DOY22_14085, DOY56_12245, DOY61_04695, DOY67_01285, DP265_06555, DP277_10105, DQE83_16545, DQE91_01265, DQF36_08635, DQF57_03615, DQF71_07160, DQF72_06460, DQG35_02830, DQO13_01295, DQP61_01770, DRP48_13910, DRW19_01295, DS143_06770, DS721_11090, DS732_23695, DT034_01270, DTL43_04295, DTM10_06985, DTM45_14510, DTZ20_12090, DU309_11135, DU321_08670, DVB38_07395, DXT69_05520, DXT71_00440, DXX80_009590, E0I42_14340, E0K84_17700, E0L12_03915, E2119_05870, E2127_02575, E2128_02495, E2129_05760, E2134_15595, E2135_08080, E2855_04145, E2863_03970, E4K55_06660, E4K61_09280, E5P22_07075, E5P28_12910, E5P37_13135, E5S42_17100, E5S46_15725, E5S47_16890, E5S58_02935, E5S61_19420, EA214_08600, EA223_04825, EA225_07080, EA233_06175, EAI42_05495, EAI52_09890, EAM59_01020, EAN70_10745, EAX79_13230, EB476_09250, EB509_07200, EB510_12405, EB515_07025, EBA84_05830, EBJ06_06135, EBM08_05455, EC1094V2_454, EC3234A_53c00700, EC3426_04342, EC95NR1_02575, ECTO6_00563, ED225_04270, ED307_11785, ED600_09400, ED607_10425, ED611_04280, ED903_04655, ED944_07260, EEA45_06940, EEP23_06300, EF082_03990, EF173_17005, EG075_10110, EG599_06165, EG796_01190, EG808_04845, EGC26_04915, EGU87_04215, EH186_08760, EH412_00995, EHD45_17860, EHD63_05275, EHD79_13055, EHJ36_00995, EHJ66_06090, EHV81_00555, EHV90_06170, EHW09_05600, EHX09_11795, EI021_04065, EI028_15050, EI032_12380, EI041_02000, EIZ86_06785, EIZ93_11790, EJ366_25995, EJC75_15225, EKI52_18235, EL75_0496, EL79_0518, EL80_0509, ELT20_05045, ELU85_06925, ELV05_02275, ELV08_02985, ELV15_01830, ELV28_06345, EPT01_00415, EQ820_11545, EQ823_05050, EQ830_04520, ERL57_13435, ERS085365_00538, ERS085366_00551, ERS085374_01930, ERS085379_00371, ERS085383_00695, ERS085404_02185, ERS085406_02933, ERS085416_00356, ERS139211_02331, ERS150873_02331, ERS150876_01029, EST51_02745, EVY14_07725, EXM29_19995, ExPECSC019_00712, ExPECSC038_02702, EXX71_13400, EXX78_16730, EYD11_02645, EYX82_02455, EYY34_10615, F1E19_20375, F7F00_12170, F7F11_09035, F7F18_01205, F7F23_11445, F7F26_00405, F7F29_05115, F7G01_13980, F7G03_16150, F9Z74_11630, FAF34_018885, FE846_13735, FKO60_06240, FNJ69_14865, FNJ83_20565, FORC82_0569, FQ022_08190, FQ915_12490, FQR64_03035, FQZ46_16130, FTV92_21230, FV293_08375, FVB16_04440, FWK02_19645, FY127_07380, FZ043_22035, GHR40_07595, GII67_12750, GIY13_09305, GIY19_08335, GJ11_20810, GJD97_02885, GKE15_04665, GKE22_12205, GKE24_04655, GKE26_04130, GKE29_02675, GKE31_04620, GKE39_10535, GKE46_11210, GKE58_04575, GKE60_04100, GKE64_10535, GKE77_05005, GKE87_00910, GKE93_06185, GKF00_03235, GKF03_05520, GKF28_12045, GKF34_04640, GKF47_04635, GKF74_09220, GKF86_04260, GKF89_14375, GKG12_08325, GN312_06640, GNZ00_05080, GNZ02_01290, GNZ03_06110, GP654_17710, GP661_13045, GP664_12080, GP666_12960, GP689_13875, GP712_11385, GP935_13340, GP946_08670, GP950_18225, GQE30_02570, GQE34_13735, GQE51_04670, GQE64_09725, GQE68_06200, GQE88_20265, GQE93_14850, GQM06_05785, GQM09_11065, GQM13_09420, GQM17_12885, GQN16_09500, GRW42_15935, GRW80_12045, HmCmsJML074_04878, HmCmsJML079_04444, HmCmsJML204_02250, HMPREF3040_00351, HW43_20915, MJ49_14345, NCTC10082_02946, NCTC10090_03637, NCTC10418_00837, NCTC10764_03982, NCTC10766_02903, NCTC10865_00786, NCTC10963_00565, NCTC10974_00682, NCTC11022_03358, NCTC11341_01768, NCTC12650_00838, NCTC12950_00597, NCTC13127_00906, NCTC13216_01244, NCTC7922_03906, NCTC7927_00668, NCTC8179_06070, NCTC8500_00486, NCTC8622_00353, NCTC8960_03188, NCTC8985_05122, NCTC9007_04416, NCTC9044_01237, NCTC9050_03718, NCTC9055_02489, NCTC9062_02576, NCTC9077_00732, NCTC9111_00974, NCTC9117_00877, NCTC9701_00685, NCTC9702_00649, NCTC9703_05076, NCTC9706_02844, NCTC9777_02009, PGD_03924, RG28_21075, RK56_014610, RX35_04279, SAMEA3472043_01825, SAMEA3472047_01897, SAMEA3472055_00376, SAMEA3472070_01148, SAMEA3472080_00969, SAMEA3472090_00572, SAMEA3472110_01519, SAMEA3472112_01503, SAMEA3472114_00459, SAMEA3472147_01902, SAMEA3484427_00584, SAMEA3484429_00758, SAMEA3484434_03617, SAMEA3752372_01803, SAMEA3752553_01163, SAMEA3752557_01851, SAMEA3752559_03249, SAMEA3752620_02365, SAMEA3753064_02960, SAMEA3753164_02324, SAMEA3753290_00124, SAMEA3753300_02107, SK85_03504, UC41_09935, UN86_15380, WQ89_06640, WR15_24440, YDC107_1864
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: W8T4U6, UniProt: P64602*PLUS
#3: Protein Toluene tolerance protein Ttg2A


Mass: 29128.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 909945-2 (bacteria) / Gene: HMPREF1620_02486
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: V0AC37
#4: Protein Uncharacterized protein


Mass: 27885.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2.3916 (bacteria) / Gene: EC23916_1052
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I2X585

-
Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / 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
1MlaFEDBCOMPLEX#1-#40MULTIPLE SOURCES
2YrbD proteinCOMPLEX#11RECOMBINANT
3ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS componentCOMPLEX#21RECOMBINANT
4Toluene tolerance protein Ttg2ACOMPLEX#31RECOMBINANT
5Uncharacterized proteinCOMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli B185 (bacteria)550676
33Escherichia coli (E. coli)562
44Escherichia coli 909945-2 (bacteria)1269007
55Escherichia coli 2.3916 (bacteria)869688
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
44Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
55Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 7.8 / Details: 20 mM Tris-Cl, pH 7.8, 150 mM NaCl and 0.05% LMNG
Buffer component
IDConc.FormulaBuffer-ID
120 mMTris-HClTris1
2150 mMNaClSodium chloride1
30.05 %LMNG1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

-
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
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 2364885
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91690 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL

+
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