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- EMDB-24881: Structure of a cell-entry defective human adenovirus provides ins... -

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Basic information

Entry
Database: EMDB / ID: EMD-24881
TitleStructure of a cell-entry defective human adenovirus provides insights into precursor proteins and capsid maturation
Map dataCropped map file from the original 928x928x928 pixel size map
Sample
  • Virus: Human adenovirus C serotype 5
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Unknown-1
    • Protein or peptide: Unknown-2
Function / homology
Function and homology information


hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid ...hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI / Minor capsid protein VI ...Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Hexon-interlacing protein / Hexon protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-hexon-linking protein VIII / Pre-protein VI
Similarity search - Component
Biological speciesHAdV-5 (virus) / HAdV-5, Human adenovirus 5 / Human adenovirus C serotype 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsReddy VS / Yu X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146644 United States
CitationJournal: J Mol Biol / Year: 2022
Title: Structure of a Cell Entry Defective Human Adenovirus Provides Insights into Precursor Proteins and Capsid Maturation.
Authors: Xiaodi Yu / Tina-Marie Mullen / Vahid Abrishami / Juha T Huiskonen / Glen R Nemerow / Vijay S Reddy /
Abstract: Maturation of adenoviruses is distinguished by proteolytic processing of several interior minor capsid proteins and core proteins by the adenoviral protease and subsequent reorganization of ...Maturation of adenoviruses is distinguished by proteolytic processing of several interior minor capsid proteins and core proteins by the adenoviral protease and subsequent reorganization of adenovirus core. We report the results derived from the icosahedrally averaged cryo-EM structure of a cell entry defective form of adenovirus, designated ts1, at a resolution of 3.7 Å as well as of the localized reconstructions of unique hexons and penton base. The virion structure revealed the structures and organization of precursors of minor capsid proteins, pIIIa, pVI and pVIII, which are closely associated with the hexons on the capsid interior. In addition to a well-ordered helical domain (a.a. 310-397) of pIIIa, highlights of the structure include the precursors of VIII display significantly different structures near the cleavage sites. Moreover, we traced residues 4-96 of the membrane lytic protein (pVI) that includes an amphipathic helix occluded deep in the hexon cavity suggesting the possibility of co-assembly of hexons with the precursors of VI. In addition, we observe a second copy of pVI ordered up to residue L40 in the peripentonal hexons and a few fragments of density corresponding to 2nd and 3rd copies of pVI in other hexons. However, we see no evidence of precursors of VII binding in the hexon cavity. These findings suggest the possibility that differently bound pVI molecules undergo processing at the N-terminal cleavage sites at varying efficiencies, subsequently creating competition between the cleaved and uncleaved forms of VI, followed by reorganization, processing, and release of VI molecules from the hexon cavities.
History
DepositionSep 15, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7s78
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7s78
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24881.png

Downloads & links

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Map

FileDownload / File: emd_24881.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCropped map file from the original 928x928x928 pixel size map
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 3.15 / Movie #1: 3.15
Minimum - Maximum-27.572844 - 36.862076
Average (Standard dev.)-0.024104483 (±3.1642137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin484848
Dimensions832832832
Spacing832832832
CellA=B=C: 1089.9199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z832832832
origin x/y/z0.0000.0000.000
length x/y/z1089.9201089.9201089.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS-416-416-416
NC/NR/NS832832832
D min/max/mean-27.57336.862-0.024

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Supplemental data

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Sample components

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Entire : Human adenovirus C serotype 5

EntireName: Human adenovirus C serotype 5
Components
  • Virus: Human adenovirus C serotype 5
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Unknown-1
    • Protein or peptide: Unknown-2

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Supramolecule #1: Human adenovirus C serotype 5

SupramoleculeName: Human adenovirus C serotype 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 28285 / Sci species name: Human adenovirus C serotype 5 / Sci species strain: Ad2-ts1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / Strain: ts1 mutant
Molecular weightTheoretical: 150 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1000.0 Å / T number (triangulation number): 25

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Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus) / Strain: Ad2-ts1
Molecular weightTheoretical: 108.107617 KDa
SequenceString: MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV ...String:
MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV FGQAPYSGIN ITKEGIQIGV EGQTPKYADK TFQPEPQIGE SQWYETEINH AAGRVLKKTT PMKPCYGSYA KP TNENGGQ GILVKQQNGK LESQVEMQFF STTEATAGNG DNLTPKVVLY SEDVDIETPD THISYMPTIK EGNSRELMGQ QSM PNRPNY IAFRDNFIGL MYYNSTGNMG VLAGQASQLN AVVDLQDRNT ELSYQLLLDS IGDRTRYFSM WNQAVDSYDP DVRI IENHG TEDELPNYCF PLGGVINTET LTKVKPKTGQ ENGWEKDATE FSDKNEIRVG NNFAMEINLN ANLWRNFLYS NIALY LPDK LKYSPSNVKI SDNPNTYDYM NKRVVAPGLV DCYINLGARW SLDYMDNVNP FNHHRNAGLR YRSMLLGNGR YVPFHI QVP QKFFAIKNLL LLPGSYTYEW NFRKDVNMVL QSSLGNDLRV DGASIKFDSI CLYATFFPMA HNTASTLEAM LRNDTND QS FNDYLSAANM LYPIPANATN VPISIPSRNW AAFRGWAFTR LKTKETPSLG SGYDPYYTYS GSIPYLDGTF YLNHTFKK V AITFDSSVSW PGNDRLLTPN EFEIKRSVDG EGYNVAQCNM TKDWFLVQML ANYNIGYQGF YIPESYKDRM YSFFRNFQP MSRQVVDDTK YKDYQQVGIL HQHNNSGFVG YLAPTMREGQ AYPANFPYPL IGKTAVDSIT QKKFLCDRTL WRIPFSSNFM SMGALTDLG QNLLYANSAH ALDMTFEVDP MDEPTLLYVL FEVFDVVRVH RPHRGVIETV YLRTPFSAGN ATT

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Macromolecule #2: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus) / Strain: Ad2-ts1
Molecular weightTheoretical: 63.356602 KDa
SequenceString: MRRAAMYEEG PPPSYESVVS AAPVAAALGS PFDAPLDPPF VPPRYLRPTG GRNSIRYSEL APLFDTTRVY LVDNKSTDVA SLNYQNDHS NFLTTVIQNN DYSPGEASTQ TINLDDRSHW GGDLKTILHT NMPNVNEFMF TNKFKARVMV SRLPTKDNQV E LKYEWVEF ...String:
MRRAAMYEEG PPPSYESVVS AAPVAAALGS PFDAPLDPPF VPPRYLRPTG GRNSIRYSEL APLFDTTRVY LVDNKSTDVA SLNYQNDHS NFLTTVIQNN DYSPGEASTQ TINLDDRSHW GGDLKTILHT NMPNVNEFMF TNKFKARVMV SRLPTKDNQV E LKYEWVEF TLPEGNYSET MTIDLMNNAI VEHYLKVGRQ NGVLESDIGV KFDTRNFRLG FDPVTGLVMP GVYTNEAFHP DI ILLPGCG VDFTHSRLSN LLGIRKRQPF QEGFRITYDD LEGGNIPALL DVDAYQASLK DDTEQGGGGA GGSNSSGSGA EEN SNAAAA AMQPVEDMND HAIRGDTFAT RAEEKRAEAE AAAEAAAPAA QPEVEKPQKK PVIKPLTEDS KKRSYNLISN DSTF TQYRS WYLAYNYGDP QTGIRSWTLL CTPDVTCGSE QVYWSLPDMM QDPVTFRSTR QISNFPVVGA ELLPVHSKSF YNDQA VYSQ LIRQFTSLTH VFNRFPENQI LARPPAPTIT TVSENVPALT DHGTLPLRNS IGGVQRVTIT DARRRTCPYV YKALGI VSP RVLSSRTF

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Macromolecule #3: Pre-hexon-linking protein IIIa

MacromoleculeName: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus) / Strain: Ad2-ts1
Molecular weightTheoretical: 65.322805 KDa
SequenceString: MMQDATDPAV RAALQSQPSG LNSTDDWRQV MDRIMSLTAR NPDAFRQQPQ ANRLSAILEA VVPARANPTH EKVLAIVNAL AENRAIRPD EAGLVYDALL QRVARYNSGN VQTNLDRLVG DVREAVAQRE RAQQQGNLGS MVALNAFLST QPANVPRGQE D YTNFVSAL ...String:
MMQDATDPAV RAALQSQPSG LNSTDDWRQV MDRIMSLTAR NPDAFRQQPQ ANRLSAILEA VVPARANPTH EKVLAIVNAL AENRAIRPD EAGLVYDALL QRVARYNSGN VQTNLDRLVG DVREAVAQRE RAQQQGNLGS MVALNAFLST QPANVPRGQE D YTNFVSAL RLMVTETPQS EVYQSGPDYF FQTSRQGLQT VNLSQAFKNL QGLWGVRAPT GDRATVSSLL TPNSRLLLLL IA PFTDSGS VSRDTYLGHL LTLYREAIGQ AHVDEHTFQE ITSVSRALGQ EDTGSLEATL NYLLTNRRQK IPSLHSLNSE EER ILRYVQ QSVSLNLMRD GVTPSVALDM TARNMEPGMY ASNRPFINRL MDYLHRAAAV NPEYFTNAIL NPHWLPPPGF YTGG FEVPE GNDGFLWDDI DDSVFSPQPQ TLLELQQREQ AEAALRKESF RRPSSLSDLG AAAPRSDASS PFPSLIGSLT STRTT RPRL LGEEEYLNNS LLQPQREKNL PPAFPNNGIE SLVDKMSRWK TYAQEHRDVP GPRPPTRRQR HDRQRGLVWE DDDSAD DSS VLDLGGSGNP FAHLRPRLGR MF

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Macromolecule #4: Hexon-interlacing protein

MacromoleculeName: Hexon-interlacing protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus) / Strain: Ad2-ts1
Molecular weightTheoretical: 14.468134 KDa
SequenceString:
MSTNSFDGSI VSSYLTTRMP PWAGVRQNVM GSSIDGRPVL PANSTTLTYE TVSGTPLETA ASAAASAAAA TARGIVTDFA FLSPLASSA ASRSSARDDK LTALLAQLDS LTRELNVVSQ QLLDLRQQVS ALKASSPPNA V

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Macromolecule #5: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus) / Strain: Ad2-ts1
Molecular weightTheoretical: 24.71059 KDa
SequenceString: MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR INYMSAGPHM ISRVNGIRAH RNRILLEQAA ITTTPRNNLN PRSWPAALVY QESPAPTTV VLPRDAQAEV QMTNSGAQLA GGFRHRVRSP GQGITHLTIR GRGIQLNDES VSSSLGLRPD GTFQIGGAGR P SFTPRQAI ...String:
MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR INYMSAGPHM ISRVNGIRAH RNRILLEQAA ITTTPRNNLN PRSWPAALVY QESPAPTTV VLPRDAQAEV QMTNSGAQLA GGFRHRVRSP GQGITHLTIR GRGIQLNDES VSSSLGLRPD GTFQIGGAGR P SFTPRQAI LTLQTSSSEP RSGGIGTLQF IEEFVPSVYF NPFSGPPGHY PDQFIPNFDA VKDSADGYD

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Macromolecule #6: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 6 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5, Human adenovirus 5 / Strain: Ad2-ts1
Molecular weightTheoretical: 27.02751 KDa
SequenceString: MEDINFASLA PRHGSRPFMG NWQDIGTSNM SGGAFSWGSL WSGIKNFGST VKNYGSKAWN SSTGQMLRDK LKEQNFQQKV VDGLASGIS GVVDLANQAV QNKINSKLDP RPPVEEPPPA VETVSPEGRG EKRPRPDREE TLVTQIDEPP SYEEALKQGL P TTRPIAPM ...String:
MEDINFASLA PRHGSRPFMG NWQDIGTSNM SGGAFSWGSL WSGIKNFGST VKNYGSKAWN SSTGQMLRDK LKEQNFQQKV VDGLASGIS GVVDLANQAV QNKINSKLDP RPPVEEPPPA VETVSPEGRG EKRPRPDREE TLVTQIDEPP SYEEALKQGL P TTRPIAPM ATGVLGQHTP VTLDLPPPAD TQQKPVLPGP TAVVVTRPSR ASLRRAASGP RSLRPVASGN WQSTLNSIVG LG VQSLKRR RCF

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Macromolecule #7: Unknown-1

MacromoleculeName: Unknown-1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus) / Strain: Ad2-ts1
Molecular weightTheoretical: 1.379692 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #8: Unknown-2

MacromoleculeName: Unknown-2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus) / Strain: Ad2-ts1
Molecular weightTheoretical: 869.063 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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: 8.1 / Component - Concentration: 40.0 mM / Component - Name: Tris / Details: 40 mM Tris, pH 8.1
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Details: 20mA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 1510 / Average electron dose: 12.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 21320
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3iyn
PDB Unreleased entry


Details: Human adenovirus 5
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 18 / Avg.num./class: 625 / Software - Name: cisTEM
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 18 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 11277
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3iyn
PDB Unreleased entry

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7s78:
Structure of a cell-entry defective human adenovirus provides insights into precursor proteins and capsid maturation

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