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- EMDB-73595: Structure of the long chain acyl-CoA carboxylase complex from Myc... -

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Entry
Database: EMDB / ID: EMD-73595
TitleStructure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA
Map data
Sample
  • Complex: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
    • Protein or peptide: Acetyl-/propionyl-coenzyme A carboxylase AccE5
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
  • Ligand: BIOTIN
  • Ligand: BICARBONATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name)
  • Ligand: propionyl Coenzyme A
KeywordsCarboxylase / transferase / lipid synthesis / mycolic acid synthesis / LIGASE
Function / homology
Function and homology information


propionyl-CoA carboxylase / biotin carboxylase / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / biotin carboxylase activity / acetyl-CoA carboxylase activity / carbon fixation / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain ...Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit / Acetyl-/propionyl-coenzyme A carboxylase AccE5 / Propionyl-CoA carboxylase beta chain / Propionyl-CoA carboxylase beta chain
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsLiang Y / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis for substrate specificity and MSMEG_0435-0436 binding by the mycobacterial long-chain acyl-CoA carboxylase complex.
Authors: Yingke Liang / Stephanie A Bueler / John L Rubinstein /
Abstract: The presence of mycolic acid is a defining feature of the mycobacterial cell wall, which provides a highly impermeable barrier to many antibiotics. Biosynthesis of this fatty acid, as well as ...The presence of mycolic acid is a defining feature of the mycobacterial cell wall, which provides a highly impermeable barrier to many antibiotics. Biosynthesis of this fatty acid, as well as tuberculostearic acid, requires precursor molecules produced by the essential long-chain acyl-coenzyme A (CoA) carboxylase (LCC) complex. The LCC complex catalyzes carboxylation of the α-carbon of long-chain acyl-CoA, but also short-chain acetyl-CoA and propionyl-CoA. The complex includes the subunits AccA3, which contains a biotin carboxylase (BC) domain and a biotin carboxyl carrier protein (BCCP) domain, the long-chain acyl-CoA carboxyltransferase AccD4, the short-chain acyl-CoA carboxyltransferase AccD5, and the incompletely characterized protein AccE. We used electron cryomicroscopy (cryo-EM) to determine structures of the LCC complex from . In the structures, two AccE subunits tether eight AccA3 subunits to an AccD4AccD5 heterohexamer core. Cryo-EM of the enzyme during catalysis reveals how AccD4 and AccD5 achieve substrate specificity, with AccD5 binding tightly to CoA and AccD4 binding long acyl chains. The BCCP domains of AccA3 undergo long-distance translocation to transfer a carboxyl group from the BC domain of AccA3 to the acyl-CoA substrate bound in AccD5. Further, we find that two copies of a protein complex formed from MSMEG_0435 and MSMEG_0436 can bind the LCC complex, sequestering the biotin moiety of BCCP domains near AccD5 and decreasing propionyl-CoA carboxylase activity. Rv0263c, the ortholog of MSMEG_0435, has a role in bacterial survival during transmission, suggesting that these proteins may regulate production of branched fatty acid precursors for the mycobacterial cell wall.
History
DepositionOct 26, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73595.png

Downloads & links

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Map

FileDownload / File: emd_73595.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.056640565 - 1.2988142
Average (Standard dev.)0.011497654 (±0.03174834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 446.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Structure of the long chain acyl-CoA carboxylase complex from Myc...

EntireName: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA
Components
  • Complex: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
    • Protein or peptide: Acetyl-/propionyl-coenzyme A carboxylase AccE5
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
  • Ligand: BIOTIN
  • Ligand: BICARBONATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name)
  • Ligand: propionyl Coenzyme A

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Supramolecule #1: Structure of the long chain acyl-CoA carboxylase complex from Myc...

SupramoleculeName: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 870 KDa

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Macromolecule #1: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit

MacromoleculeName: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 63.215176 KDa
SequenceString: MANHASSKIS KVLVANRGEI AVRVIRAAKD AGLASVAVYA EPDADAPHVR LADEAFALGG QTSAESYLVF EKILDAAEKS GANAIHPGY GFLSENADFA QAVIDAGLIW IGPSPQSIRD LGDKVTARHI AARAKAPLVP GTPDPVKDAD EVVAFAKEHG V PVAIKAAF ...String:
MANHASSKIS KVLVANRGEI AVRVIRAAKD AGLASVAVYA EPDADAPHVR LADEAFALGG QTSAESYLVF EKILDAAEKS GANAIHPGY GFLSENADFA QAVIDAGLIW IGPSPQSIRD LGDKVTARHI AARAKAPLVP GTPDPVKDAD EVVAFAKEHG V PVAIKAAF GGGGRGMKVA RTLEEIPELF ESATREAIAA FGRGECFVER YLDKPRHVEA QVIADQHGNV VVAGTRDCSL QR RFQKLVE EAPAPFLTDA QRKEIHESAK RICKEAGYYG AGTVEYLVGQ DGLISFLEVN TRLQVEHPVT EETSGIDLVR QQF KIANGE PLDITEDPTP RGHSFEFRIN GEDAGRGFLP APGPVTKFVA PTGPGVRMDS GVETGSVIGG QFDSMLAKLI VTGA TREEA LERSRRALAE FTVEGLATVI PFHRAVVSDP AFIGDGEKFD VHTRWIETEW NNTVEPFTGG DPIEEEDTVP RQTVV VEVG GRRLEVSLPG DLAIGGGGGA AAPGVVRKKP KPRKRGGGGA KAASGDAVTA PMQGTVVKVA VEEGQEVSAG DLVVVL EAM KMENPVTAHK DGTITGLAVE AGAAITQGTV IAEIK

UniProtKB: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit

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Macromolecule #2: Acetyl-/propionyl-coenzyme A carboxylase AccE5

MacromoleculeName: Acetyl-/propionyl-coenzyme A carboxylase AccE5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 10.357693 KDa
SequenceString:
MSGANDSTTV SGEVQADVTD EAKADHEAHI KVLRGEPTPE EMAALMAVLA SAGGGPAEPV KKERNMWGHP VDKLRYSVFS WQRVTLLER THMRR

UniProtKB: Acetyl-/propionyl-coenzyme A carboxylase AccE5

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Macromolecule #3: Propionyl-CoA carboxylase beta chain

MacromoleculeName: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 56.23407 KDa
SequenceString: MTNKTTAELL AELREKLELA KEPGGEKAVA KREKKGIPSA RARINALLDP GSFIEIGALA KTPGDPNALY GDGVVTGRGT IDGRPVGVF SHDQTVFQGS VGEMFGRKVA RLMEWVAMVG CPIIGINDSA GARIQDAVTS LAWYAELGRR HEMLRGLVPE I SLIFGKCA ...String:
MTNKTTAELL AELREKLELA KEPGGEKAVA KREKKGIPSA RARINALLDP GSFIEIGALA KTPGDPNALY GDGVVTGRGT IDGRPVGVF SHDQTVFQGS VGEMFGRKVA RLMEWVAMVG CPIIGINDSA GARIQDAVTS LAWYAELGRR HEMLRGLVPE I SLIFGKCA GGAVYSPIQT DLLVAVRDQG YMFITGPDVI KDVTGEDVTF DELGGADEQA KRGNIHKVVN SEAEAYQYVR DY LSFLPSN HFDNPPIVNP GMEPEITPHD LELDSIVPDA DNMAYDMHEI LLRIFDDGDV FEIAEQRGPA MITAFARVDG HPV GVIANQ PMVLSGAIDN EASDKAASFI RFCDSYNLPL VFVVDTPGAM PGVAEEKGGI IKRGGRFFNA IVEADVPKVT VIIR KAYGG GYAVMGSKQL SADLNFAWPT ARIAVIGAEG AAQLLVKRFP DPNAPEVQKI RDDFIEGYNL NMATPWIAAE RGYID AVIQ PHETRLLLRK SLRLLRDKQN GPKVQRKHGL LPL

UniProtKB: Propionyl-CoA carboxylase beta chain

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Macromolecule #4: Propionyl-CoA carboxylase beta chain

MacromoleculeName: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 58.488074 KDa
SequenceString: MTSVTEPSAE HQVDIHTTAG KLADLKRRTE ETLHPVGEAA VDKVHAKGKL TARERILALL DEGSFVELDA LAKHRSTNFG LEKNRPLGD GVITGYGTID GRDVCIFSQD ATVFGGSLGE VYGEKIVKVQ ELAIKTGRPL IGINDGAGAR IQEGVVSLGL Y SRIFHNNI ...String:
MTSVTEPSAE HQVDIHTTAG KLADLKRRTE ETLHPVGEAA VDKVHAKGKL TARERILALL DEGSFVELDA LAKHRSTNFG LEKNRPLGD GVITGYGTID GRDVCIFSQD ATVFGGSLGE VYGEKIVKVQ ELAIKTGRPL IGINDGAGAR IQEGVVSLGL Y SRIFHNNI KASGVIPQIS LIMGAAAGGH VYSPALTDFV VMVDQTSQMF ITGPDVIKTV TGEDVTMEEL GGAHTHMAKS GT AHYVASG EQDAFDYVRD LLSYLPPNNY ADPPLYPVAI PEGSIEETLT DEDLELDTLI PDSPNQPYDM HEVITRILDD DEF LEVQAG YAGNIVVGFG RVEGRPVGIV ANQPTQFAGC LDINASEKAA RFIRTCDCFN IPIVLLVDVP GFLPGTDQEY NGII RRGAK LLYAYGEATV AKVTVITRKS YGGAYCVMGS KDMGADVVVA WPTAQIAVMG ASGAVGFVYR QQLKEAAKNG EDVDA LRLE LQQTYEDTLV NPYIAAERGY VDAVIPPSHT RGYVANALRL LERKIVQMPP KKHGNIPL

UniProtKB: Propionyl-CoA carboxylase beta chain

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Macromolecule #5: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 5 / Number of copies: 6 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Macromolecule #6: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydrox...

MacromoleculeName: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~- ...Name: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name)
type: ligand / ID: 9 / Number of copies: 2 / Formula: A1CZD
Molecular weightTheoretical: 1.056002 KDa

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Macromolecule #10: propionyl Coenzyme A

MacromoleculeName: propionyl Coenzyme A / type: ligand / ID: 10 / Number of copies: 4 / Formula: 1VU
Molecular weightTheoretical: 823.597 Da
Chemical component information

ChemComp-191:
PROPIONYL COENZYME A

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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: 6
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 8000 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.0-privatebeta) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Composite map from initial maps generated ab initio in cryoSPARC v5.0.0-privatebeta
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta)
Details: Resolution estimated from constituent consensus and locally refined maps
Number images used: 124481
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta)

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