[English] 日本語
Yorodumi
- EMDB-71550: Structure of beta-1,3-glucan synthase in complex with caspofungin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71550
TitleStructure of beta-1,3-glucan synthase in complex with caspofungin, Rho1 and long glucan
Map data
Sample
  • Complex: Structure of beta-1,3-glucan synthase from Saccharomyces cerevisiae (ScFks1) in CHAPS/CHS at the CFN-Rho1-long-glucan-bound state with UDP bound
    • Protein or peptide: x 3 types
  • Protein or peptide: x 1 types
  • Ligand: x 7 types
KeywordsEnzyme / glucan synthesis / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of secondary cell septum biogenesis / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / RHO GTPases activate PKNs / RND3 GTPase cycle / cellular bud neck septin ring organization / G alpha (12/13) signalling events / RHOF GTPase cycle / RND1 GTPase cycle / positive regulation of mitotic actomyosin contractile ring assembly ...regulation of secondary cell septum biogenesis / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / RHO GTPases activate PKNs / RND3 GTPase cycle / cellular bud neck septin ring organization / G alpha (12/13) signalling events / RHOF GTPase cycle / RND1 GTPase cycle / positive regulation of mitotic actomyosin contractile ring assembly / regulation of cell wall (1->3)-beta-D-glucan biosynthetic process / regulation of exocyst localization / : / RND2 GTPase cycle / budding cell bud growth / RHOC GTPase cycle / regulation of fungal-type cell wall organization / spore wall / fungal-type cell wall polysaccharide biosynthetic process / 1,3-beta-glucan synthase / 1,3-beta-D-glucan synthase activity / regulation of vacuole fusion, non-autophagic / (1->3)-beta-D-glucan biosynthetic process / : / 1,3-beta-D-glucan synthase complex / RHOA GTPase cycle / fungal-type cell wall biogenesis / cellular bud / ascospore wall assembly / incipient cellular bud site / actin cortical patch / cellular bud tip / fungal-type cell wall / cellular bud neck / mating projection tip / fungal-type vacuole membrane / peroxisomal membrane / regulation of cell size / small GTPase-mediated signal transduction / positive regulation of endocytosis / Neutrophil degranulation / small monomeric GTPase / actin filament organization / cell periphery / regulation of actin cytoskeleton organization / enzyme activator activity / peroxisome / regulation of protein localization / G-protein beta-subunit binding / actin cytoskeleton organization / G protein activity / mitochondrial outer membrane / endosome membrane / GTPase activity / protein kinase binding / GTP binding / endoplasmic reticulum / Golgi apparatus / signal transduction / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Protein of unknown function DUF2406 / Uncharacterised protein (DUF2406) / : / 1,3-beta-glucan synthase component FKS1, second domain / Glycosyl transferase, family 48 / 1,3-beta-glucan synthase subunit FKS1-like, domain-1 / 1,3-beta-glucan synthase component / 1,3-beta-glucan synthase subunit FKS1, domain-1 / 1,3-beta-glucan synthase subunit FKS1 / Small GTPase Rho ...Protein of unknown function DUF2406 / Uncharacterised protein (DUF2406) / : / 1,3-beta-glucan synthase component FKS1, second domain / Glycosyl transferase, family 48 / 1,3-beta-glucan synthase subunit FKS1-like, domain-1 / 1,3-beta-glucan synthase component / 1,3-beta-glucan synthase subunit FKS1, domain-1 / 1,3-beta-glucan synthase subunit FKS1 / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GTP-binding protein RHO1 / 1,3-beta-glucan synthase component FKS1 / Uncharacterized protein YMR295C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsRen Z / Lee SY
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI170906 United States
CitationJournal: Nature / Year: 2026
Title: Structural basis of fungal β-1,3-glucan synthase inhibition by caspofungin.
Authors: Zhenning Ren / Abhishek Chhetri / Chang Liu / ShuYu Offner / Kedar Sharma / Mario J Borgnia / Wonpil Im / Kenichi Yokoyama / Seok-Yong Lee /
Abstract: Invasive fungal infections pose life-threatening risks to the increasing population of immunocompromised patients. Treatment remains challenging due to limited antifungal drugs and increasing ...Invasive fungal infections pose life-threatening risks to the increasing population of immunocompromised patients. Treatment remains challenging due to limited antifungal drugs and increasing resistance. β-1,3-D-glucan synthase (GS), comprising the catalytic Fks1 and the regulatory small GTPase, Rho1 (refs. ), is the target of clinically important echinocandin antifungals. Despite recent studies, the mechanisms of GS catalysis, Rho1 regulation and echinocandin inhibition and resistance remain elusive. Here we present cryo-electron microscopy structures of native Saccharomyces cerevisiae Fks1 (ScFks1) solved under catalytically relevant conditions, revealing its interactions with the antifungal caspofungin (CFN), glucan product from the translocation channel and Rho1. CFN forms a ternary complex with nascent glucan and Fks1 at the membrane-protein interface, suggesting an unexpected role of CFN in stalling polymer translocation. Our echinocandin-resistant S643P structure suggests a resistance mechanism: the substitution destabilizes CFN and glucan binding through both allosteric structural perturbation and direct steric clash. Rho1 binding induces active site rearrangements essential for catalysis, including that of the 'latch loop' for donor substrate coordination. Furthermore, we identify YMR295C as an auxiliary subunit. These findings elucidate the mechanisms of GS-mediated glucan synthesis and its inhibition and resistance by echinocandins, laying the groundwork for rational antifungal design.
History
DepositionJul 1, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71550.png

Downloads & links

-
Map

FileDownload / File: emd_71550.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0792
Minimum - Maximum-0.42468038 - 0.86682606
Average (Standard dev.)0.0049462286 (±0.028664999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_71550_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_71550_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_71550_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Structure of beta-1,3-glucan synthase from Saccharomyces cerevisi...

EntireName: Structure of beta-1,3-glucan synthase from Saccharomyces cerevisiae (ScFks1) in CHAPS/CHS at the CFN-Rho1-long-glucan-bound state with UDP bound
Components
  • Complex: Structure of beta-1,3-glucan synthase from Saccharomyces cerevisiae (ScFks1) in CHAPS/CHS at the CFN-Rho1-long-glucan-bound state with UDP bound
    • Protein or peptide: 1,3-beta-glucan synthase component FKS1
    • Protein or peptide: GTP-binding protein RHO1
    • Protein or peptide: Gsr1p
  • Protein or peptide: Caspofungin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: (10R,12S)-10,12-dimethyltetradecanoic acid
  • Ligand: water

+
Supramolecule #1: Structure of beta-1,3-glucan synthase from Saccharomyces cerevisi...

SupramoleculeName: Structure of beta-1,3-glucan synthase from Saccharomyces cerevisiae (ScFks1) in CHAPS/CHS at the CFN-Rho1-long-glucan-bound state with UDP bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: 1,3-beta-glucan synthase component FKS1

MacromoleculeName: 1,3-beta-glucan synthase component FKS1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 1,3-beta-glucan synthase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 221.252484 KDa
SequenceString: MNTDQQPYQG QTDYTQGPGN GQSQEQDYDQ YGQPLYPSQA DGYYDPNVAA GTEADMYGQQ PPNESYDQDY TNGEYYGQPP NMAAQDGEN FSDFSSYGPP GTPGYDSYGG QYTASQMSYG EPNSSGTSTP IYGNYDPNAI AMALPNEPYP AWTADSQSPV S IEQIEDIF ...String:
MNTDQQPYQG QTDYTQGPGN GQSQEQDYDQ YGQPLYPSQA DGYYDPNVAA GTEADMYGQQ PPNESYDQDY TNGEYYGQPP NMAAQDGEN FSDFSSYGPP GTPGYDSYGG QYTASQMSYG EPNSSGTSTP IYGNYDPNAI AMALPNEPYP AWTADSQSPV S IEQIEDIF IDLTNRLGFQ RDSMRNMFDH FMVLLDSRSS RMSPDQALLS LHADYIGGDT ANYKKWYFAA QLDMDDEIGF RN MSLGKLS RKARKAKKKN KKAMEEANPE DTEETLNKIE GDNSLEAADF RWKAKMNQLS PLERVRHIAL YLLCWGEANQ VRF TAECLC FIYKCALDYL DSPLCQQRQE PMPEGDFLNR VITPIYHFIR NQVYEIVDGR FVKRERDHNK IVGYDDLNQL FWYP EGIAK IVLEDGTKLI ELPLEERYLR LGDVVWDDVF FKTYKETRTW LHLVTNFNRI WVMHISIFWM YFAYNSPTFY THNYQ QLVD NQPLAAYKWA SCALGGTVAS LIQIVATLCE WSFVPRKWAG AQHLSRRFWF LCIIFGINLG PIIFVFAYDK DTVYST AAH VVAAVMFFVA VATIIFFSIM PLGGLFTSYM KKSTRRYVAS QTFTAAFAPL HGLDRWMSYL VWVTVFAAKY SESYYFL VL SLRDPIRILS TTAMRCTGEY WWGAVLCKVQ PKIVLGLVIA TDFILFFLDT YLWYIIVNTI FSVGKSFYLG ISILTPWR N IFTRLPKRIY SKILATTDME IKYKPKVLIS QVWNAIIISM YREHLLAIDH VQKLLYHQVP SEIEGKRTLR APTFFVSQD DNNFETEFFP RDSEAERRIS FFAQSLSTPI PEPLPVDNMP TFTVLTPHYA ERILLSLREI IREDDQFSRV TLLEYLKQLH PVEWECFVK DTKILAEETA AYEGNENEAE KEDALKSQID DLPFYCIGFK SAAPEYTLRT RIWASLRSQT LYRTISGFMN Y SRAIKLLY RVENPEIVQM FGGNAEGLER ELEKMARRKF KFLVSMQRLA KFKPHELENA EFLLRAYPDL QIAYLDEEPP LT EGEEPRI YSALIDGHCE ILDNGRRRPK FRVQLSGNPI LGDGKSDNQN HALIFYRGEY IQLIDANQDN YLEECLKIRS VLA EFEELN VEQVNPYAPG LRYEEQTTNH PVAIVGAREY IFSENSGVLG DVAAGKEQTF GTLFARTLSQ IGGKLHYGHP DFIN ATFMT TRGGVSKAQK GLHLNEDIYA GMNAMLRGGR IKHCEYYQCG KGRDLGFGTI LNFTTKIGAG MGEQMLSREY YYLGT QLPV DRFLTFYYAH PGFHLNNLFI QLSLQMFMLT LVNLSSLAHE SIMCIYDRNK PKTDVLVPIG CYNFQPAVDW VRRYTL SIF IVFWIAFVPI VVQELIERGL WKATQRFFCH LLSLSPMFEV FAGQIYSSAL LSDLAIGGAR YISTGRGFAT SRIPFSI LY SRFAGSAIYM GARSMLMLLF GTVAHWQAPL LWFWASLSSL IFAPFVFNPH QFAWEDFFLD YRDYIRWLSR GNNQYHRN S WIGYVRMSRA RITGFKRKLV GDESEKAAGD ASRAHRTNLI MAEIIPCAIY AAGCFIAFTF INAQTGVKTT DDDRVNSVL RIIICTLAPI AVNLGVLFFC MGMSCCSGPL FGMCCKKTGS VMAGIAHGVA VIVHIAFFIV MWVLESFNFV RMLIGVVTCI QCQRLIFHC MTALMLTREF KNDHANTAFW TGKWYGKGMG YMAWTQPSRE LTAKVIELSE FAADFVLGHV ILICQLPLII I PKIDKFHS IMLFWLKPSR QIRPPIYSLK QTRLRKRMVK KYCSLYFLVL AIFAGCIIGP AVASAKIHKH IGDSLDGVVH NL FQPINTT NNDTGSQMST YQSHYYTHTP SLKTWSTIKL EVLFQGPAAA GSAGSAAGSG EFDYKDHDGD YKDHDIDYKD DDD KHHHHH HHHHH

UniProtKB: 1,3-beta-glucan synthase component FKS1

+
Macromolecule #2: GTP-binding protein RHO1

MacromoleculeName: GTP-binding protein RHO1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 26.145652 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MENLYFQSQQ VGNSIRRKLV IVGDGACGKT CLLIVFSKGQ FPEVYVPTVF ENYVADVEVD GRRVELALW DTAGQEDYDR LRPLSYPDSN VVLICFSIDL PDSLENVQEK WIAEVLHFCQ GVPIILVGCK VDLRNDPQTI E QLRQEGQQ ...String:
MGSSHHHHHH SSGLVPRGSH MENLYFQSQQ VGNSIRRKLV IVGDGACGKT CLLIVFSKGQ FPEVYVPTVF ENYVADVEVD GRRVELALW DTAGQEDYDR LRPLSYPDSN VVLICFSIDL PDSLENVQEK WIAEVLHFCQ GVPIILVGCK VDLRNDPQTI E QLRQEGQQ PVTSQEGQSV ADQIGATGYY ECSAKTGYGV REVFEAATRA SLMGKSKTNG KAKKNTTEKK KKKCVLL

UniProtKB: GTP-binding protein RHO1

+
Macromolecule #3: Gsr1p

MacromoleculeName: Gsr1p / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.209684 KDa
SequenceString: MMHFRKKSSI SNTSDHDGAN RASDVKISED DKARLKMRTA SVADPILDAV QEAQPFEQAA DTFHDNMNRQ SYFSNEEGHV LCDVFGQPI TQADISNPTR ARDERPLDTI RSFEYAVSGD PVWAQQLETP TYGFRVRPDF PVFGAAVTYD ANGMPQQVGG A SSQMYGEQ ...String:
MMHFRKKSSI SNTSDHDGAN RASDVKISED DKARLKMRTA SVADPILDAV QEAQPFEQAA DTFHDNMNRQ SYFSNEEGHV LCDVFGQPI TQADISNPTR ARDERPLDTI RSFEYAVSGD PVWAQQLETP TYGFRVRPDF PVFGAAVTYD ANGMPQQVGG A SSQMYGEQ AVYQPQQHVQ TEEKQKKKKK GLFGRMKKK

UniProtKB: Uncharacterized protein YMR295C

+
Macromolecule #4: Caspofungin

MacromoleculeName: Caspofungin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 872.92 Da
SequenceString:
(A1CHS)T(HYP)(A1CHT)(A1CHU)(HY3)

+
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

+
Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 29 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

+
Macromolecule #9: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 9 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

+
Macromolecule #10: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

+
Macromolecule #11: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

MacromoleculeName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: GSP
Molecular weightTheoretical: 539.246 Da
Chemical component information

ChemComp-GSP:
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

+
Macromolecule #12: (10R,12S)-10,12-dimethyltetradecanoic acid

MacromoleculeName: (10R,12S)-10,12-dimethyltetradecanoic acid / type: ligand / ID: 12 / Number of copies: 1 / Formula: A1CHR
Molecular weightTheoretical: 256.424 Da

+
Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: 3D reconstruction from previous preliminary dataset
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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