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- EMDB-33763: BAM-EspP complex structure with BamA-G431C and G781C/EspP-N1293C ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33763
TitleBAM-EspP complex structure with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc
Map dataBAM-EspP pair1 3 nanodisc
Sample
  • Complex: BAM-EspP complex with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc
    • Complex: BAM
      • Protein or peptide: Outer membrane protein assembly factor BamA
      • Protein or peptide: Outer membrane protein assembly factor BamB
      • Protein or peptide: Outer membrane protein assembly factor BamC
      • Protein or peptide: Outer membrane protein assembly factor BamD
      • Protein or peptide: Outer membrane protein assembly factor BamE
    • Complex: EspP
      • Protein or peptide: Serine protease EspP
KeywordsBAM / BamABCDE / EspP / Gram-negative bacteria / outer membrane protein / outer membrane barrel / BamA / BamB / BamC / BamD / BamE / MEMBRANE PROTEIN
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / protein-macromolecule adaptor activity / periplasmic space / cell adhesion / serine-type endopeptidase activity / response to antibiotic ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / protein-macromolecule adaptor activity / periplasmic space / cell adhesion / serine-type endopeptidase activity / response to antibiotic / cell surface / proteolysis / extracellular region / identical protein binding / membrane
Similarity search - Function
Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily ...Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Pyrrolo-quinoline quinone beta-propeller repeat / Omp85 superfamily domain / beta-propeller repeat / Pectin lyase fold/virulence factor / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB / Serine protease EspP
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli O157:H7 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShen C / Chang S / Luo Q / Zhang Z / Luo B / Lu G / Zhu X / Wei X / Dong C / Zhang X ...Shen C / Chang S / Luo Q / Zhang Z / Luo B / Lu G / Zhu X / Wei X / Dong C / Zhang X / Tang X / Dong H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900039;32000844;81971974 China
CitationJournal: Nature / Year: 2023
Title: Structural basis of BAM-mediated outer membrane β-barrel protein assembly.
Authors: Chongrong Shen / Shenghai Chang / Qinghua Luo / Kevin Chun Chan / Zhibo Zhang / Bingnan Luo / Teng Xie / Guangwen Lu / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Ruhong Zhou / Xing Zhang ...Authors: Chongrong Shen / Shenghai Chang / Qinghua Luo / Kevin Chun Chan / Zhibo Zhang / Bingnan Luo / Teng Xie / Guangwen Lu / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Ruhong Zhou / Xing Zhang / Xiaodi Tang / Haohao Dong /
Abstract: The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of ...The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane β-barrel proteins (OMPs) that are essential interchange portals of materials. All known OMPs share the antiparallel β-strand topology, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial β-barrel assembly machinery (BAM) to initiate OMP folding; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly.
History
DepositionJul 5, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33763.png

Downloads & links

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Map

FileDownload / File: emd_33763.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBAM-EspP pair1 3 nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.104434334 - 0.15713747
Average (Standard dev.)0.00020261365 (±0.0035130237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: BAM-EspP pair 1-3 nanodisc half map1

Fileemd_33763_half_map_1.map
AnnotationBAM-EspP pair 1-3 nanodisc half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BAM-EspP pair 1-3 nanodisc half map2

Fileemd_33763_half_map_2.map
AnnotationBAM-EspP pair 1-3 nanodisc half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BAM-EspP complex with BamA-G431C and G781C/EspP-N1293C and A1043C...

EntireName: BAM-EspP complex with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc
Components
  • Complex: BAM-EspP complex with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc
    • Complex: BAM
      • Protein or peptide: Outer membrane protein assembly factor BamA
      • Protein or peptide: Outer membrane protein assembly factor BamB
      • Protein or peptide: Outer membrane protein assembly factor BamC
      • Protein or peptide: Outer membrane protein assembly factor BamD
      • Protein or peptide: Outer membrane protein assembly factor BamE
    • Complex: EspP
      • Protein or peptide: Serine protease EspP

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Supramolecule #1: BAM-EspP complex with BamA-G431C and G781C/EspP-N1293C and A1043C...

SupramoleculeName: BAM-EspP complex with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: BAM

SupramoleculeName: BAM / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #3: EspP

SupramoleculeName: EspP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Escherichia coli O157:H7 (bacteria)

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Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 90.735562 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV ...String:
MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVK ERPTIASITF SGNKSVKDDM LKQNLEASGV RVGESLDRTT IADIEKGLED FYYSVGKYSA SVKAVVTPLP R NRVDLKLV FQEGVSAEIQ QINIVGNHAF TTDELISHFQ LRDEVPWWNV VGDRKYQKQK LAGDLETLRS YYLDRGYARF NI DSTQVSL TPDKKGIYVT VNITEGDQYK LSGVEVSGNL AGHSAEIEQL TKIEPGELYN GTKVTKMEDD IKKLLGRYGY AYP RVQSMP EINDADKTVK LRVNVDAGNR FYVRKIRFEG NDTSKDAVLR REMRQMEGAW LGSDLVDQGK ERLNRLGFFE TVDT DTQRV PGSPDQVDVV YKVKERNTGS FNFGICYGTE SGVSFQAGVQ QDNWLGTGYA VGINGTKNDY QTYAELSVTN PYFTV DGVS LGGRLFYNDF QADDADLSDY TNKSYGTDVT LGFPINEYNS LRAGLGYVHN SLSNMQPQVA MWRYLYSMGE HPSTSD QDN SFKTDDFTFN YGWTYNKLDR GYFPTDGSRV NLTGKVTIPG SDNEYYKVTL DTATYVPIDD DHKWVVLGRT RWGYGDG LG GKEMPFYENF YAGGSSTVRG FQSNTIGPKA VYFPHQASNY DPDYDYECAT QDGAKDLCKS DDAVGGNAMA VASLEFIT P TPFISDKYAN SVRTSFFWDM GTVWDTNWDS SQYSGYPDYS DPSNIRMSAG IALQWMSPLC PLVFSYAQPF KKYDGDKAE QFQFNIGKTW

UniProtKB: Outer membrane protein assembly factor BamA

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Macromolecule #2: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 41.918945 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN ...String:
MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDG KEIWSVSLAE KDGWFSKEPA LLSGGVTVSG GHVYIGSEKA QVYALNTSDG TVAWQTKVAG EALSRPVVSD G LVLIHTSN GQLQALNEAD GAVKWTVNLD MPSLSLRGES APTTAFGAAV VGGDNGRVSA VLMEQGQMIW QQRISQATGS TE IDRLSDV DTTPVVVNGV VFALAYNGNL TALDLRSGQI MWKRELGSVN DFIVDGNRIY LVDQNDRVMA LTIDGGVTLW TQS DLLHRL LTSPVLYNGN LVVGDSEGYL HWINVEDGRF VAQQKVDSSG FQTEPVAADG KLLIQAKDGT VYSITR

UniProtKB: Outer membrane protein assembly factor BamB

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Macromolecule #3: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 36.875277 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ ...String:
MAYSVQKSRL AKVAGVSLVL LLAACSSDSR YKRQVSGDEA YLEAAPLAEL HAPAGMILPV TSGDYAIPVT NGSGAVGKAL DIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG R YQISVKPQ GYQQAVTVKL LNLEQAGKPV ADAASMQRYS TEMMNVISAG LDKSATDAAN AAQNRASTTM DVQSAADDTG LP MLVVRGP FNVVWQRLPA ALEKVGMKVT DSTRSQGNMA VTYKPLSDSD WQELGASDPG LASGDYKLQV GDLDNRSSLQ FID PKGHTL TQSQNDALVA VFQAAFSK

UniProtKB: Outer membrane protein assembly factor BamC

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Macromolecule #4: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 27.85835 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV ...String:
MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQ AAIDRFIRLN PTHPNIDYVM YMRGLTNMAL DDSALQGFFG VDRSDRDPQH ARAAFSDFSK LVRGYPNSQY T TDATKRLV FLKDRLAKYE YSVAEYYTER GAWVAVVNRV EGMLRDYPDT QATRDALPLM ENAYRQMQMN AQAEKVAKII AA NSSNT

UniProtKB: Outer membrane protein assembly factor BamD

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Macromolecule #5: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 13.530256 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MRCKTLTAAA AVLLMLTAGC STLERVVYRP DINQGNYLTA NDVSKIRVGM TQQQVAYALG TPLMSDPFGT NTWFYVFRQQ PGHEGVTQQ TLTLTFNSSG VLTNIDNKPA LSGNGGHHHH HHHH

UniProtKB: Outer membrane protein assembly factor BamE

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Macromolecule #6: Serine protease EspP

MacromoleculeName: Serine protease EspP / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Escherichia coli O157:H7 (bacteria)
Molecular weightTheoretical: 38.759879 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: NIELVSAPKD TNENVFKASK QTIGFSDVTP VITTRETDDK ITWSLTGYNT VANKEATRNA AALFSVDYKA FLNEVNNLNK RMGDLRDIN GEAGAWCRIM SGTGSASGGF SDNYTHVQVG VDKKHELDGL DLFTGFTVTH TDSSASADVF SGKTKSVGAG L YASAMFDS ...String:
NIELVSAPKD TNENVFKASK QTIGFSDVTP VITTRETDDK ITWSLTGYNT VANKEATRNA AALFSVDYKA FLNEVNNLNK RMGDLRDIN GEAGAWCRIM SGTGSASGGF SDNYTHVQVG VDKKHELDGL DLFTGFTVTH TDSSASADVF SGKTKSVGAG L YASAMFDS GAYIDLIGKY VHHDNEYTAT FAGLGTRDYS THSWYAGAEA GYRYHVTEDA WIEPQAELVY GSVSGKQFAW KD QGMHLSM KDKDYNPLIG RTGVDVGKSF SGKDWKVTAR AGLGYQFDLL ANGETVLRDA SGEKRIKGEK DSRMLMSVGL NAE IRDNVR FGLEFEKSAF GKYNVDNAVC ANFRYSF

UniProtKB: Serine protease EspP

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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: 7.8 / Details: 20 mM Tris-HCl, pH 7.8, 150 mM NaCl
VitrificationCryogen name: ETHANE
DetailsBAM-EspP complex structure with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 7.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2315966
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7yd5
PDB Unreleased entry

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142423
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelPDB ID:

7yd5
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 100 / Target criteria: 0.3
Output model

PDB-7ye4:
BAM-EspP complex structure with BamA-G431C and G781C/EspP-N1293C and A1043C mutations in nanodisc

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