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- EMDB-23708: ATP-bound AMP-activated protein kinase -

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Basic information

Entry
Database: EMDB / ID: EMD-23708
TitleATP-bound AMP-activated protein kinase
Map data
Sample
  • Complex: MBP-fused ATP bound AMPK in complex with C-compound stabilized by Fab and a nanobody
    • Protein or peptide: x 7 types
  • Ligand: x 4 types
Function / homology
Function and homology information


AMPK inhibits chREBP transcriptional activation activity / Lipophagy / import into nucleus / cAMP-dependent protein kinase regulator activity / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / nucleotide-activated protein kinase complex / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process ...AMPK inhibits chREBP transcriptional activation activity / Lipophagy / import into nucleus / cAMP-dependent protein kinase regulator activity / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / nucleotide-activated protein kinase complex / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process / cAMP-dependent protein kinase activity / Macroautophagy / AMP binding / cellular response to nutrient levels / carbohydrate transmembrane transporter activity / positive regulation of protein kinase activity / Activation of AMPK downstream of NMDARs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ADP binding / TP53 Regulates Metabolic Genes / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / periplasmic space / protein kinase activity / protein phosphorylation / positive regulation of gene expression / protein kinase binding / signal transduction / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Maltodextrin-binding protein / 5'-AMP-activated protein kinase subunit beta-2 / 5'-AMP-activated protein kinase subunit gamma-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsYan Y / Mukherjee S / Harikumar KG / Strutzenberg T / Zhou XE / Powell SK / Xu T / Sheldon R / Lamp J / Brunzelle JS ...Yan Y / Mukherjee S / Harikumar KG / Strutzenberg T / Zhou XE / Powell SK / Xu T / Sheldon R / Lamp J / Brunzelle JS / Radziwon K / Ellis A / Novick SJ / Vega IE / Jones R / Miller LJ / Xu HE / Griffin PR / Kossiakoff AA / Melcher K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM129436 United States
CitationJournal: Science / Year: 2021
Title: Structure of an AMPK complex in an inactive, ATP-bound state.
Authors: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna ...Authors: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna Radziwon / Abigail Ellis / Scott J Novick / Irving E Vega / Russell G Jones / Laurence J Miller / H Eric Xu / Patrick R Griffin / Anthony A Kossiakoff / Karsten Melcher /
Abstract: Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in ...Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in which the kinase activation loop (AL) is protected from protein phosphatases, thus keeping the AL in its active, phosphorylated state. At low AMP:ATP (adenosine triphosphate) ratios, ATP inhibits AMPK by increasing AL dynamics and accessibility. We developed conformation-specific antibodies to trap ATP-bound AMPK in a fully inactive, dynamic state and determined its structure at 3.5-angstrom resolution using cryo-electron microscopy. A 180° rotation and 100-angstrom displacement of the kinase domain fully exposes the AL. On the basis of the structure and supporting biophysical data, we propose a multistep mechanism explaining how adenine nucleotides and pharmacological agonists modulate AMPK activity by altering AL phosphorylation and accessibility.
History
DepositionMar 26, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.009
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  • Surface view with fitted model
  • Atomic models: PDB-7m74
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23708.png

Downloads & links

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Map

FileDownload / File: emd_23708.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.011854566 - 0.03116666
Average (Standard dev.)0.00021865858 (±0.0013628452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 231.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8280.8280.828
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z231.840231.840231.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0120.0310.000

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Supplemental data

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Sample components

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Entire : MBP-fused ATP bound AMPK in complex with C-compound stabilized by...

EntireName: MBP-fused ATP bound AMPK in complex with C-compound stabilized by Fab and a nanobody
Components
  • Complex: MBP-fused ATP bound AMPK in complex with C-compound stabilized by Fab and a nanobody
    • Protein or peptide: 5'-AMP-activated protein kinase catalytic subunit alpha-1
    • Protein or peptide: 5'-AMP-activated protein kinase subunit beta-2
    • Protein or peptide: 5'-AMP-activated protein kinase subunit gamma-1
    • Protein or peptide: Maltose/maltodextrin ABC transporter substrate-binding protein MalE
    • Protein or peptide: Fab light chainFragment antigen-binding
    • Protein or peptide: Fab heavy chainFragment antigen-binding
    • Protein or peptide: NanobodySingle-domain antibody
  • Ligand: 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: MBP-fused ATP bound AMPK in complex with C-compound stabilized by...

SupramoleculeName: MBP-fused ATP bound AMPK in complex with C-compound stabilized by Fab and a nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: 5'-AMP-activated protein kinase catalytic subunit alpha-1

MacromoleculeName: 5'-AMP-activated protein kinase catalytic subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.004395 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VKIGHYILGD TLGVGTFGKV KVGKHELTGH KVAVKILNRQ KIRSLDVVGK IRREIQNLKL FRHPHIIKLY QVISTPSDIF MVMEYVSGG ELFDYICKNG RLDEKESRRL FQQILSGVDY CHRHMVVHRD LKPENVLLDA HMNAKIADFG LSNMMSDGEF L RTSCGSPN ...String:
VKIGHYILGD TLGVGTFGKV KVGKHELTGH KVAVKILNRQ KIRSLDVVGK IRREIQNLKL FRHPHIIKLY QVISTPSDIF MVMEYVSGG ELFDYICKNG RLDEKESRRL FQQILSGVDY CHRHMVVHRD LKPENVLLDA HMNAKIADFG LSNMMSDGEF L RTSCGSPN YAAPEVISGR LYAGPEVDIW SSGVILYALL CGTLPFDDDH VPTLFKKICD GIFYTPQYLN PSVISLLKHM LQ VDPMKRA TIKDIREHEW FKQDLPKYLF PEDPSYSSTM IDDEALKEVC EKFECSEEEV LSCLYNRNHQ DPLAVAYHLI IDN RRIMNE AKDFYLATSP PDSFLDDHHL TRPHPERVPF LVAETPRARH TLDELNPQKS KHQGVRKAKW HLGIRSQSRP NDIM AEVCR AIKQLDYEWK VVNPYYLRVR RKNPVTSTYS KMSLQLYQVD SRTYLLDFRS IDDELTPRPG SHTIEFFEMC ANLIK ILAQ

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Macromolecule #2: 5'-AMP-activated protein kinase subunit beta-2

MacromoleculeName: 5'-AMP-activated protein kinase subunit beta-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.38465 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MARPTVIRWS EGGKEVFISG SFNNWSTKIP LIKSHNDFVA ILDLPEGEHQ YKFFVDGQWV HDPSEPVVTS QLGTINNLIH VKKSDFEVF DALKLDSMES SETSCRDLSS SPPGPYGQEM YAFRSAARFK SPPILPPHLL QVILNKDTNI SCDPALLPEP N HVMLNHLY ...String:
MARPTVIRWS EGGKEVFISG SFNNWSTKIP LIKSHNDFVA ILDLPEGEHQ YKFFVDGQWV HDPSEPVVTS QLGTINNLIH VKKSDFEVF DALKLDSMES SETSCRDLSS SPPGPYGQEM YAFRSAARFK SPPILPPHLL QVILNKDTNI SCDPALLPEP N HVMLNHLY ALSIKDSVMV LSATHRYKKK YVTTLLYKPI

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Macromolecule #3: 5'-AMP-activated protein kinase subunit gamma-1

MacromoleculeName: 5'-AMP-activated protein kinase subunit gamma-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.833359 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSNNSVYTS FMKSHRCYDL IPTSSKLVVF DTSLQVKKAF FALVTNGVRA APLWDSKKQS FVGMLTITDF INILHRYYKS ALVQIYELE EHKIETWREV YLQDSFKPLV CISPNASLFD AVSSLIRNKI HRLPVIDPES GNTLYILTHK RILKFLKLFI T EFPKPEFM ...String:
MGSNNSVYTS FMKSHRCYDL IPTSSKLVVF DTSLQVKKAF FALVTNGVRA APLWDSKKQS FVGMLTITDF INILHRYYKS ALVQIYELE EHKIETWREV YLQDSFKPLV CISPNASLFD AVSSLIRNKI HRLPVIDPES GNTLYILTHK RILKFLKLFI T EFPKPEFM SKSLEELQIG TYANIAMVRT TTPVYVALGI FVQHRVSALP VVDEKGRVVD IYSKFDVINL AAEKTYNNLD VS VTKALQH RSHYFEGVLK CYLHETLETI INRLVEAEVH RLVVVDENDV VKGIVSLSDI LQALVLTGG

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Macromolecule #4: Maltose/maltodextrin ABC transporter substrate-binding protein MalE

MacromoleculeName: Maltose/maltodextrin ABC transporter substrate-binding protein MalE
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 40.827125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPAAAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL MFNLQEPYFT W PLIAADGG ...String:
MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPAAAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL MFNLQEPYFT W PLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NGPWAWSNID TS AVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYEEELAKDP RIA ATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTNAAEF

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Macromolecule #5: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.794248 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QMTQSPSSLS ASVGDRVTIT CRASQSVSSA VAWYQQKPGK APKLLIYSAS SLYSGVPSRF SGSRSGTDFT LTISSLQPED FATYYCQQS SSGPITFGQG TKVEIKRTVA APSVFIFPPS DSQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD ...String:
QMTQSPSSLS ASVGDRVTIT CRASQSVSSA VAWYQQKPGK APKLLIYSAS SLYSGVPSRF SGSRSGTDFT LTISSLQPED FATYYCQQS SSGPITFGQG TKVEIKRTVA APSVFIFPPS DSQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGE

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Macromolecule #6: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.466369 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFNIY YYSIHWVRQA PGKGLEWVAS IYPYSGSTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARY YPYFISYYSK MEAMDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFNIY YYSIHWVRQA PGKGLEWVAS IYPYSGSTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARY YPYFISYYSK MEAMDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS

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Macromolecule #7: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.159438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGRTIS RYAMSWFRQA PGKEREFVAV ARRSGDGAFY ADSVQGRFTV SRDDAKNTVY LQMNSLKPE DTAVYYCAID SDTFYSGSYD YWGQGTQVTV S

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Macromolecule #9: 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a...

MacromoleculeName: 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine
type: ligand / ID: 9 / Number of copies: 1 / Formula: TAK
Molecular weightTheoretical: 399.488 Da
Chemical component information

ChemComp-TAK:
6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #12: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

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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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING
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 / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3918314
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4rer

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 569379

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