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- EMDB-30219: Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferas... -

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Basic information

Entry
Database: EMDB / ID: EMD-30219
TitleCryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.
Map data
Sample
  • Complex: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose
    • Complex: EmbA and EmbB
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbA
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
    • Complex: AcpM
      • Protein or peptide: Meromycolate extension acyl carrier protein
  • Ligand: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
  • Ligand: CARDIOLIPIN
  • Ligand: CALCIUM IONCalcium
  • Ligand: PHOSPHATE IONPhosphate
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
KeywordsMycobacterium smegmatis / cell wall synthesis / drug target / ethambutol / arabinosyltransferase / EmbA / EmbB / EmbC / acyl carrier protein / arabinogalactan / lipoarabinomannan / drug resistance / TRANSFERASE
Function / homology
Function and homology information


indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / acyl carrier activity / Transferases; Glycosyltransferases; Pentosyltransferases / cell wall organization / plasma membrane / cytoplasm
Similarity search - Function
Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site ...Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Meromycolate extension acyl carrier protein / Probable arabinosyltransferase B / Probable arabinosyltransferase A / Integral membrane indolylacetylinositol arabinosyltransferase EmbB
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang L / Zhao Y
Funding support China, United Kingdom, 4 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29020000 China
National Natural Science Foundation of China (NSFC)81520108019 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
Medical Research Council (MRC, United Kingdom)MR/S000542/1 United Kingdom
CitationJournal: Science / Year: 2020
Title: Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol.
Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang ...Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang / Manfu Wang / Yan Zhu / Bing Zhang / Lijun Bi / Xian'en Zhang / Haitao Yang / Luke W Guddat / Wenqing Xu / Quan Wang / Jun Li / Gurdyal S Besra / Zihe Rao /
Abstract: The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo- ...The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents.
History
DepositionApr 10, 2020-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bvg
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30219.png

Downloads & links

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Map

FileDownload / File: emd_30219.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.28
Minimum - Maximum-1.2339691 - 2.203403
Average (Standard dev.)0.0000927995 (±0.059921596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z295.200295.200295.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.2342.2030.000

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Supplemental data

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Mask #1

Fileemd_30219_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30219_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30219_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in ...

EntireName: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose
Components
  • Complex: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose
    • Complex: EmbA and EmbB
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbA
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
    • Complex: AcpM
      • Protein or peptide: Meromycolate extension acyl carrier protein
  • Ligand: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
  • Ligand: CARDIOLIPIN
  • Ligand: CALCIUM IONCalcium
  • Ligand: PHOSPHATE IONPhosphate
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine

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Supramolecule #1: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in ...

SupramoleculeName: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: EmbA and EmbB

SupramoleculeName: EmbA and EmbB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Supramolecule #3: AcpM

SupramoleculeName: AcpM / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Integral membrane indolylacetylinositol arabinosyltransferase EmbA

MacromoleculeName: Integral membrane indolylacetylinositol arabinosyltransferase EmbA
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Pentosyltransferases
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 116.561898 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: DYKDDDDKMT EPSRIARLIA VVAGIAGVLL CGLVPLLPVE ETTATVLWPQ GVGADGNVTE LTAPLVAGAP RALDVTIPCR AVAELPADG GVVFSTNPAG GIEAGRNGMF IRANADVVYV AFRDTVAAVA PREAVDSGAC SEIHVWADVS AVGADFAGIP D ASGTLPVD ...String:
DYKDDDDKMT EPSRIARLIA VVAGIAGVLL CGLVPLLPVE ETTATVLWPQ GVGADGNVTE LTAPLVAGAP RALDVTIPCR AVAELPADG GVVFSTNPAG GIEAGRNGMF IRANADVVYV AFRDTVAAVA PREAVDSGAC SEIHVWADVS AVGADFAGIP D ASGTLPVD KRPQVSGVFT DLKVPAQPGL AARIDIDTRF ITSPTLLKTA VMVLGLACVI GSIVALALLD RGWRRRPPRT RG RAGLWTW ITDTGVIGGL LIWHIVGAPT SDDGYNMTIA RVASEAGYTT NYYRYFGASE APFDWYQSVL SHLASISTAG VWM RLPATA AAIATWLIIS RCVLPRIGRR VAANRVAMLT AGATFLAAWL PFNNGLRPEP LIAFAVITVW MLVENSIGTR RLWP AAVAI VIAMFSVTLA PQGLIALAPL LVGARAIGRV VTARRAGTGI LASLAPLAAS VAVVFVIIFR DQTLATVAES VRIKY VVGP TIPWYQEFLR YYFLTVEDSV DGSLTRRFAV LVLLLCLFGL IMVLLRRGRV PGAVSGPLWR LCGSTAIGLL LLILTP TKW AIQFGAFAGL AGALGGVTAF AFARVGLHSR RNLALYVTAL LFILAWATSG LNGWFYVGNY GVPWFDKQPV IAHYPVT TI FLVLAIVGGL LAGWLHFRMD YAGHTEVADT GRNRALASTP LLIVATIMVV LELGSMVKAT VGRYPVYTVG SANIAALR S AGDSCAMADA VLVEADPNEG MLQPVPGQRF GEYGPLGGED PVGFTPNGVS DTLEPAEPVA ANPGTPNSDG PVDKPNIGI GYAAGTGGGY GPEGVNGSRV FLPFGLDPSR TPVMGSYGEN KLAAKATSAW YQLPPRTPDR PLVTVAAAGA IWYYEEDGSF NYGQSLKLQ WGVHRPDGTY QALSEVQPID IFQQKAWRNL RFPLAWAPPE ANVARIVADD PNLSEDQWFA FTPPRVPVLQ T AQQFLGSQ TPVLMDIATA ANFPCQRPFA ERLGVAELPE YRIIPNFKQM VVSSNQWQSA ADGGPFLFIQ ALLRTEAIPT YL RDDWYRD WGSIERYIRV VPQEQAPTAA IEEGSTRVFG WSRGGPIRAL P

UniProtKB: Probable arabinosyltransferase B

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Macromolecule #2: Integral membrane indolylacetylinositol arabinosyltransferase EmbB

MacromoleculeName: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: indolylacetylinositol arabinosyltransferase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 119.077672 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSGNMDEAVS GNMDEAVSAG KDVRIARWVA TIAGLLGFVL SVSIPLLPVT QTTATLNWPQ QGRLDNVTAP LISQAPLELT ATVPCSVVR DLPPEGGLVF GTAPAEGRDA ALNAMLVNVT ETRVDVIVRN VVVASVNRDR VAGPDCQRIE ITSNLDGTYA D FVGLTQIS ...String:
MSGNMDEAVS GNMDEAVSAG KDVRIARWVA TIAGLLGFVL SVSIPLLPVT QTTATLNWPQ QGRLDNVTAP LISQAPLELT ATVPCSVVR DLPPEGGLVF GTAPAEGRDA ALNAMLVNVT ETRVDVIVRN VVVASVNRDR VAGPDCQRIE ITSNLDGTYA D FVGLTQIS GEDAGKLQRT GYPDPNLRPA IVGVFTDLTG PAPQGLSVSA EIDTRFTTHP TALKLAAMLL AIVSTVIALL AL WRLDRLD GRRMHRLIPT RWRTVTAVDG VVVGGMAIWY VIGANSSDDG YILQMARTAE HAGYMANYFR WFGSPEDPFG WYY NVLALM TKVSDASIWI RLPDLICALI CWLLLSREVL PRLGPAVAGS RAAMWAAGLV LLGAWMPFNN GLRPEGQIAT GALI TYVLI ERAVTSGRLT PAALAITTAA FTLGIQPTGL IAVAALLAGG RPILRIVMRR RRLVGTWPLI APLLAAGTVI LAVVF ADQT IATVLEATRI RTAIGPSQEW WTENLRYYYL ILPTTDGAIS RRVAFVFTAM CLFPSLFMML RRKHIAGVAR GPAWRL MGI IFATMFFLMF TPTKWIHHFG LFAAVGGAMA ALATVLVSPT VLRSARNRMA FLSLVLFVLA FCFASTNGWW YVSNFGA PF NNSVPKVGGV QISAIFFALS AIAALWAFWL HLTRRTESRV VDRLTAAPIP VAAGFMVVVM MASMAIGVVR QYPTYSNG W ANIRAFAGGC GLADDVLVEP DSNAGFLTPL PGAYGPLGPL GGEDPQGFSP DGVPDRIIAE AIRLNNPQPG TDYDWNRPI KLDEPGINGS TVPLPYGLDP KRVPVAGTYS TEAQQESRLS SAWYELPARD ETERAAHPLV VITAAGTITG ESVANGLTTG QTVDLEYAT RGPDGTLVPA GRVTPYDVGP TPSWRNLRYP RSEIPDDAVA VRVVAEDLSL SQGDWIAVTP PRVPELQSVQ E YVGSDQPV LMDWAVGLAF PCQQPMLHAN GVTEVPKFRI SPDYYAKLQS TDTWQDGING GLLGITDLLL RASVMSTYLS QD WGQDWGS LRKFDTVVEA TPAELDFGSQ THSGLYSPGP LRIRPHLGGI KAFHHHHHHH HHH

UniProtKB: Integral membrane indolylacetylinositol arabinosyltransferase EmbB

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Macromolecule #3: Meromycolate extension acyl carrier protein

MacromoleculeName: Meromycolate extension acyl carrier protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 10.743876 KDa
SequenceString:
MAATQEEIIA GLAEIIEEVT GIEPSEVTPE KSFVDDLDID SLSMVEIAVQ TEDKYGVKIP DEDLAGLRTV GDVVAYIQKL EEENPEAAA ALREKFAADQ

UniProtKB: Meromycolate extension acyl carrier protein

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Macromolecule #5: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decameth...

MacromoleculeName: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
type: ligand / ID: 5 / Number of copies: 1 / Formula: F8L
Molecular weightTheoretical: 911.28 Da
Chemical component information

ChemComp-F8L:
[(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate

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Macromolecule #6: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 6 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION / Phosphate

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Macromolecule #9: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 9 / Number of copies: 1 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE / Phosphopantetheine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 209894

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7bvg:
Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.

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