[English] 日本語
Yorodumi
- EMDB-4660: Influenza B virus (B/Panama/45) polymerase Hetermotrimer in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4660
TitleInfluenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
Map dataNone
Sample
  • Complex: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
    • Complex: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
      • Protein or peptide: Polymerase acidic protein
      • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
      • Protein or peptide: Polymerase basic protein 2
    • Complex: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
      • RNA: 3' cRNA
      • RNA: 5' cRNA
KeywordsInfluenza A / RNA polymerase / Influenza polymerase / Influenza dimer / RDRP / RNA BINDING PROTEIN
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral translational frameshifting ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 2 / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus (B/Panama/45/1990) / Influenza A virus / Influenza B virus (strain B/Panama/45/1990)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsKeown JR / Carrique L
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)MR/R009945/1 United Kingdom
Medical Research Council (United Kingdom)MR/K000241/1 United Kingdom
CitationJournal: Nature / Year: 2019
Title: Structures of influenza A virus RNA polymerase offer insight into viral genome replication.
Authors: Haitian Fan / Alexander P Walker / Loïc Carrique / Jeremy R Keown / Itziar Serna Martin / Dimple Karia / Jane Sharps / Narin Hengrung / Els Pardon / Jan Steyaert / Jonathan M Grimes / Ervin Fodor /
Abstract: Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans. Influenza A viruses contain a segmented ...Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans. Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPol) composed of PB1, PB2 and PA subunits. Although the high-resolution crystal structure of FluPol of bat influenza A virus has previously been reported, there are no complete structures available for human and avian FluPol. Furthermore, the molecular mechanisms of genomic viral RNA (vRNA) replication-which proceeds through a complementary RNA (cRNA) replicative intermediate, and requires oligomerization of the polymerase-remain largely unknown. Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPol from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0-4.3 Å, in the presence or absence of a cRNA or vRNA template. In solution, FluPol forms dimers of heterotrimers through the C-terminal domain of the PA subunit, the thumb subdomain of PB1 and the N1 subdomain of PB2. The cryo-electron microscopy structure of monomeric FluPol bound to the cRNA template reveals a binding site for the 3' cRNA at the dimer interface. We use a combination of cell-based and in vitro assays to show that the interface of the FluPol dimer is required for vRNA synthesis during replication of the viral genome. We also show that a nanobody (a single-domain antibody) that interferes with FluPol dimerization inhibits the synthesis of vRNA and, consequently, inhibits virus replication in infected cells. Our study provides high-resolution structures of medically relevant FluPol, as well as insights into the replication mechanisms of the viral RNA genome. In addition, our work identifies sites in FluPol that could be targeted in the development of antiviral drugs.
History
DepositionMar 5, 2019-
Header (metadata) releaseMar 13, 2019-
Map releaseSep 4, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qwl
  • Surface level: 5.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4660.png

Downloads & links

-
Map

FileDownload / File: emd_4660.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.6 / Movie #1: 5.6
Minimum - Maximum-25.019183999999999 - 38.010629999999999
Average (Standard dev.)-0.000000000005538 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-39-149-104
NX/NY/NZ201201211
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-25.01938.011-0.000

-
Supplemental data

-
Sample components

-
Entire : Influenza B (Panama/45) polymerase Hetermotrimer in complex with ...

EntireName: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
Components
  • Complex: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
    • Complex: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
      • Protein or peptide: Polymerase acidic protein
      • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
      • Protein or peptide: Polymerase basic protein 2
    • Complex: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
      • RNA: 3' cRNA
      • RNA: 5' cRNA

-
Supramolecule #1: Influenza B (Panama/45) polymerase Hetermotrimer in complex with ...

SupramoleculeName: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Sample was treated with 0.001% glutaraldehyde for 20 min on ice prior quenching with 100 mM Tris-HCl pH 7.5 and gel filtration.
Molecular weightTheoretical: 250 KDa

-
Supramolecule #2: Influenza B (Panama/45) polymerase Hetermotrimer in complex with ...

SupramoleculeName: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Details: Sample was treated with 0.001% glutaraldehyde for 20 min on ice prior quenching with 100 mM Tris-HCl pH 7.5 and gel filtration.
Source (natural)Organism: Influenza B virus (B/Panama/45/1990)

-
Supramolecule #3: Influenza B (Panama/45) polymerase Hetermotrimer in complex with ...

SupramoleculeName: Influenza B (Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Details: Sample was treated with 0.001% glutaraldehyde for 20 min on ice prior quenching with 100 mM Tris-HCl pH 7.5 and gel filtration.
Source (natural)Organism: Influenza A virus

-
Macromolecule #1: Polymerase acidic protein

MacromoleculeName: Polymerase acidic protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Influenza B virus (strain B/Panama/45/1990)
Molecular weightTheoretical: 83.161055 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDTFITRNFQ TTIIQKAKNT MAEFSEDPEL QPAMLFNICV HLEVCYVISD MNFLDEEGKS YTALEGQGKE QNLRPQYEVI EGMPRTIAW MVQRSLAQEH GIETPKYLAD LFDYKTKRFI EVGITKGLAD DYFWKKKEKL GNSMELMIFS YNQDYSLSNE S SLDEEGKG ...String:
MDTFITRNFQ TTIIQKAKNT MAEFSEDPEL QPAMLFNICV HLEVCYVISD MNFLDEEGKS YTALEGQGKE QNLRPQYEVI EGMPRTIAW MVQRSLAQEH GIETPKYLAD LFDYKTKRFI EVGITKGLAD DYFWKKKEKL GNSMELMIFS YNQDYSLSNE S SLDEEGKG RVLSRLTELQ AELSLKNLWQ VLIGEEDVEK GIDFKLGQTI SRLRDISVPA GFSNFEGMRS YIDNIDPKGA IE RNLARMS PLVSATPKKL KWEDLRPIGP HIYNHELPEV PYNAFLLMSD ELGLANMTEG KSKKPKTLAK ECLEKYSTLR DQT DPILIM KSEKANENFL WKLWRDCVNT ISNEEMSNEL QKTNYAKWAT GDGLTYQKIM KEVAIDDETM CQEEPKIPNK CRVA AWVQT EMNLLSTLTS KRALDLPEIG PDVAPVEHVG SERRKYFVNE INYCKASTVM MKYVLFHTSL LNESNASMGK YKVIP ITNR VVNEKGESFD MLYGLAVKGQ SHLRGDTDVV TVVTFEFSST DPRVDSGKWP KYTVFRIGSL FVSGREKSVY LYCRVN GTN KIQMKWGMEA RRCLLQSMQQ MEAIVEQESS IQGYDMTKAC FKGDRVNSPK TFSIGTQEGK LVKGSFGKAL RVIFTKC LM HYVFGNAQLE GFSAESRRLL LLIQALKDRK GPWVFDLEGM YSGIEECISN NPWVIQSAYW FNEWLGFEKE GSKVLESV D EIMDE

UniProtKB: Polymerase acidic protein

-
Macromolecule #2: RNA-directed RNA polymerase catalytic subunit

MacromoleculeName: RNA-directed RNA polymerase catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Influenza B virus (strain B/Panama/45/1990)
Molecular weightTheoretical: 84.37818 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNINPYFLFI DVPIQAAIST TFPYTGVPPY SHGTGTGHTI DTVIRTHEYS NKGKQYVSDV TGCTMVDPTN GPLPEDNEPS AYAQLDCVL EALDRMDEEH PGLFQAASQN AMEALMVTTV DKLTQGRQTF DWTVCRNQPA ATALNTTITS FRLNDLNGAD K GGLVPFCQ ...String:
MNINPYFLFI DVPIQAAIST TFPYTGVPPY SHGTGTGHTI DTVIRTHEYS NKGKQYVSDV TGCTMVDPTN GPLPEDNEPS AYAQLDCVL EALDRMDEEH PGLFQAASQN AMEALMVTTV DKLTQGRQTF DWTVCRNQPA ATALNTTITS FRLNDLNGAD K GGLVPFCQ DIIDSLDKPE MTFFSVKNIK KKLPAKNRKG FLIKRIPMKV KDRITRVEYI KRALSLNTMT KDAERGKLKR RA IATAGIQ IRGFVLVVEN LAKNICENLE QSGLPVGGNE KKAKLSNAVA KMLSNCPPGG ISMTVTGDNT KWNECLNPRI FLA MTERIT RDSPIWFRDF CSIAPVLFSN KIARLGKGFM ITSKTKRLKA QIPCPDLFSI PLERYNEETR AKLKKLKPFF NEEG TASLS PGMMMGMFNM LSTVLGVAAL GIKNIGNKEY LWDGLQSSDD FALFVNAKDE ETCMEGINDF YRTCKLLGIN MSKKK SYCN ETGMFEFTSM FYRDGFVSNF AMEIPSFGVA GVNESADMAI GMTIIKNNMI NNGMGPATAQ TAIQLFIADY RYTYKC HRG DSKVEGKRMK IIKELWENTK GRDGLLVADG GPNIYNLRNL HIPEIVLKYN LMDPEYKGRL LHPQNPFVGH LSIEGIK EA DITPAHGPVK KMDYDAVSGT HSWRTKRNRS ILNTDQRNMI LEEQCYAKCC NLFEACFNSA SYRKPVGQHS MLEAMAHR L RMDARLDYES GRMSKDDFEK AMAHLGEIGY I

UniProtKB: RNA-directed RNA polymerase catalytic subunit

-
Macromolecule #3: Polymerase basic protein 2

MacromoleculeName: Polymerase basic protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus (strain B/Panama/45/1990)
Molecular weightTheoretical: 89.097453 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTLAKIELLK QLLRDNEAKT VLKQTTVDQY NIIRKFNTSR IEKNPSLRMK WAMCSNFPLA LTKGDMANRI PLEYKGIQLK TNAEDIGTK GQMCSIAAVT WWNTYGPIGD TEGFEKVYES FFLRKMRLDN ATWGRITFGP VERVRKRVLL NPLTKEMPPD E ASNVIMEI ...String:
MTLAKIELLK QLLRDNEAKT VLKQTTVDQY NIIRKFNTSR IEKNPSLRMK WAMCSNFPLA LTKGDMANRI PLEYKGIQLK TNAEDIGTK GQMCSIAAVT WWNTYGPIGD TEGFEKVYES FFLRKMRLDN ATWGRITFGP VERVRKRVLL NPLTKEMPPD E ASNVIMEI LFPKEAGIPR ESTWIHRELI KEKREKLKGT MITPIVLAYM LERELVARRR FLPVAGATSA EFIEMLHCLQ GE NWRQIYH PGGNKLTESR SQSMIVACRK IIRRSIVASN PLELAVEIAN KTVIDTEPLK SCLTAIDGGD VACDIIRAAL GLK IRQRQR FGRLELKRIS GRGFKNDEEI LIGNGTIQKI GIWDGEEEFH VRCGECRGIL KKSKMRMEKL LINSAKKEDM KDLI ILCMV FSQDTRMFQG VRGEINFLNR AGQLLSPMYQ LQRYFLNRSN DLFDQWGYEE SPKASELHGI NELMNASDYT LKGVV VTKN VIDDFSSTET EKVSITKNLS LIKRTGEVIM GANDVSELES QAQLMITYDT PKMWEMGTTK ELVQNTYQWV LKNLVT LKA QFLLGKEDMF QWDAFEAFES IIPQKMAGQY SGFARAVLKQ MRDQEVMKTD QFIKLLPFCF SPPKLRSNGE PYQFLRL VL KGGGENFIEV RKGSPLFSYN PQTEVLTICG RMMSLKGKIE DEERNRSMGN AVLAGFLVSG KYDPDLGDFK TIEELEKL K PGEKANILLY QGKPVKVVKR KRYSALSNDI SQGIKRQRMT VESMGWALSA RENLYFQ

UniProtKB: Polymerase basic protein 2

-
Macromolecule #4: 3' cRNA

MacromoleculeName: 3' cRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 4.683753 KDa
SequenceString:
GGCCUUGUUU CUACU

-
Macromolecule #5: 5' cRNA

MacromoleculeName: 5' cRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 4.531827 KDa
SequenceString:
AGCAAAAGCA GGCC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.5 / Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMNaCl

Details: Sample was purified in 20 mM HEPES, pH 7.5, 150 mM NaCl with Tween 20 added to a final concentration 0f 0.05% prior to plunging grids.
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3.5 sec before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-28 / Number grids imaged: 1 / Number real images: 4711 / Average exposure time: 4.38 sec. / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1012085 / Details: template picking in cryosparc v2.5
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model was generated by cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 1012085
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.5) / Details: Cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5epi


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 57
Output model

PDB-6qwl:
Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter

+
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