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- PDB-7c9z: Coxsackievirus B1 F-particle -

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Basic information

Entry
Database: PDB / ID: 7c9z
TitleCoxsackievirus B1 F-particle
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Echovirus B / mature
Function / homology
Function and homology information


: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein / VP4
Similarity search - Component
Biological speciesCoxsackievirus B1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFeng, R. / Wang, K. / Rao, Z. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesKJZD-SW-L05 China
CitationJournal: Nat Commun / Year: 2020
Title: Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage.
Authors: Kang Wang / Ling Zhu / Yao Sun / Minhao Li / Xin Zhao / Lunbiao Cui / Li Zhang / George F Gao / Weiwei Zhai / Fengcai Zhu / Zihe Rao / Xiangxi Wang /
Abstract: Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor ...Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor usage, among which echovirus 30 (E30), a leading causative agent for human aseptic meningitis, utilizes FcRn as an uncoating receptor. However, receptors for many EVs remain unknown. Here we analyzed the atomic structures of E30 mature virion, empty- and A-particles, which reveals serotype-specific epitopes and striking conformational differences between the subgroups within EV-Bs. Of these, the VP1 BC loop markedly distinguishes E30 from other EV-Bs, indicative of a role as a structural marker for EV-B. By obtaining cryo-electron microscopy structures of E30 in complex with its receptor FcRn and CD55 and comparing its homologs, we deciphered the underlying molecular basis for receptor recognition. Together with experimentally derived viral receptor identifications, we developed a structure-based in silico algorithm to inform a rational prediction for EV receptor usage.
History
DepositionJun 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7336
Polymers94,2484
Non-polymers4852
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,683,957360
Polymers5,654,869240
Non-polymers29,088120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)473,66330
Polymers471,23920
Non-polymers2,42410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 568 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)568,39636
Polymers565,48724
Non-polymers2,90912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 5.68 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)5,683,957360
Polymers5,654,869240
Non-polymers29,088120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.80901699, 0.309017, -0.5), (0.309017, 0.5, 0.80901699), (0.5, -0.80901699, 0.309017)82.19908, -133.00091, 215.19999
3generate(0.5, 0.809017, -0.30901699), (0.809017, -0.309017, 0.5), (0.309017, -0.5, -0.80901699)430.39999
4generate(0.5, 0.80901699, 0.309017), (0.809017, -0.30901699, -0.5), (-0.309017, 0.5, -0.809017)-133.00091, 215.19999, 348.20091
5generate(0.809017, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699), (-0.5, 0.809017, 0.30901699)-133.00091, 215.2, 82.19909
6generate(0.30901699, 0.49999999, 0.809017), (0.50000001, -0.80901699, 0.309017), (0.80901699, 0.30901699, -0.5)-133.00091, 215.19999, 82.19908
7generate(0.80901699, -0.309017, 0.5), (0.309017, -0.5, -0.80901699), (0.5, 0.80901699, -0.309017)430.39999
8generate(0.80901699, -0.309017, -0.5), (-0.30901699, 0.5, -0.809017), (0.5, 0.80901699, 0.30901699)215.2, 348.20091, -133.00091
9generate(0.30901699, 0.5, -0.809017), (-0.5, 0.809017, 0.30901699), (0.80901699, 0.30901699, 0.5)215.2, 82.19909, -133.00091
10generate(1), (1), (1)
11generate(-0.80901699, 0.309017, -0.50000001), (0.30901699, -0.5, -0.80901699), (-0.49999999, -0.809017, 0.30901699)430.4, 430.39999, 430.4
12generate(-0.80901699, 0.309017, 0.5), (-0.309017, 0.5, -0.80901699), (-0.5, -0.80901699, -0.309017)215.2, 348.20091, 563.40091
13generate(-0.30901699, -0.5, 0.809017), (-0.5, 0.80901699, 0.30901699), (-0.809017, -0.30901699, -0.5)215.2, 82.19909, 563.40091
14generate(-1), (1), (-1)430.39999, 430.4
15generate(-0.30901699, -0.5, -0.809017), (0.5, -0.809017, 0.309017), (-0.80901699, -0.309017, 0.5)563.40091, 215.2, 348.20091
16generate(-0.5, -0.80901699, -0.30901699), (-0.809017, 0.30901699, 0.49999999), (-0.309017, 0.50000001, -0.80901699)563.40091, 215.2, 348.20091
17generate(-0.80901699, -0.309017, -0.5), (-0.309017, -0.5, 0.80901699), (-0.5, 0.80901699, 0.309017)563.40091, 215.2, 82.19909
18generate(-1), (-1), (1)430.4, 430.39999
19generate(-0.80901699, -0.30901699, 0.5), (-0.309017, -0.5, -0.80901699), (0.5, -0.809017, 0.30901699)348.20091, 563.40091, 215.2
20generate(-0.5, -0.80901699, 0.309017), (-0.809017, 0.30901699, -0.5), (0.30901699, -0.5, -0.80901699)430.4, 430.4, 430.39999
21generate(-0.309017, 0.50000001, -0.80901699), (0.5, 0.80901699, 0.30901699), (0.809017, -0.30901699, -0.49999999)348.20091, -133.00091, 215.19999
22generate(-0.5, 0.80901699, 0.309017), (0.80901699, 0.309017, 0.5), (0.309017, 0.5, -0.80901699)82.19909, -133.00091, 215.2
23generate(1), (1), (1)
24generate(0.5, -0.809017, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.309017, 0.5, 0.80901699)215.2, 82.19908, -133.00091
25generate(0.30901699, -0.5, -0.80901699), (0.5, 0.80901699, -0.309017), (0.809017, -0.30901699, 0.5)430.4
26generate(-0.49999999, -0.809017, 0.30901699), (0.80901699, -0.309017, 0.50000001), (-0.30901699, 0.5, 0.80901699)430.4
27generate(-0.5, -0.80901699, -0.309017), (0.80901699, -0.309017, -0.5), (0.309017, -0.5, 0.80901699)563.40091, 215.2, 82.19908
28generate(-0.809017, -0.30901699, -0.5), (0.30901699, 0.5, -0.809017), (0.5, -0.80901699, -0.30901699)563.40091, 215.2, 348.20091
29generate(-1), (1), (-1)430.4, 430.39999
30generate(-0.80901699, -0.309017, 0.5), (0.30901699, 0.5, 0.809017), (-0.5, 0.809017, -0.309017)348.20091, -133.00091, 215.2
31generate(0.80901699, 0.30901699, -0.5), (-0.30901699, -0.49999999, -0.809017), (-0.50000001, 0.80901699, -0.309017)82.19909, 563.40091, 215.2
32generate(0.5, 0.80901699, -0.309017), (-0.80901699, 0.309017, -0.5), (-0.309017, 0.5, 0.80901699)430.4
33generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.309017, 0.5), (0.30901699, -0.5, 0.809017)-133.00091, 215.2, 82.19908
34generate(0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.809017), (0.5, -0.809017, -0.30901699)-133.00091, 215.2, 348.20091
35generate(1), (-1), (-1)430.39999, 430.4
36generate(1), (-1), (-1)430.4, 430.4
37generate(0.5, -0.80901699, 0.309017), (-0.80901699, -0.309017, 0.5), (-0.309017, -0.5, -0.80901699)215.2, 348.20091, 563.40091
38generate(0.309017, -0.5, -0.80901699), (-0.5, -0.809017, 0.30901699), (-0.809017, 0.309017, -0.5)430.39999, 430.4, 430.4
39generate(-0.309017, 0.5, -0.809017), (-0.5, -0.80901699, -0.309017), (-0.809017, 0.30901699, 0.5)348.20091, 563.40091, 215.2
40generate(-0.5, 0.809017, 0.30901699), (-0.809017, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699)82.19909, 563.40091, 215.2
41generate(-0.30901699, 0.5, 0.80901699), (0.49999999, 0.809017, -0.30901699), (-0.80901699, 0.309017, -0.50000001)430.4
42generate(0.309017, -0.5, 0.80901699), (0.5, 0.80901699, 0.309017), (-0.80901699, 0.309017, 0.5)82.19908, -133.00091, 215.2
43generate(0.5, -0.80901699, -0.30901699), (0.809017, 0.30901699, 0.5), (-0.30901699, -0.5, 0.809017)348.20091, -133.00091, 215.2
44generate(-1), (1), (-1)430.4, 430.39999
45generate(-0.5, 0.809017, -0.309017), (0.80901699, 0.309017, -0.5), (-0.30901699, -0.5, -0.809017)215.2, 82.19908, 563.40091
46generate(0.809017, -0.30901699, -0.49999999), (0.309017, -0.50000001, 0.80901699), (-0.5, -0.80901699, -0.30901699)215.2, 82.19908, 563.40091
47generate(0.309017, 0.5, -0.80901699), (0.5, -0.80901699, -0.309017), (-0.80901699, -0.309017, -0.5)215.2, 348.20091, 563.40091
48generate(1), (-1), (-1)430.39999, 430.4
49generate(0.309017, 0.5, 0.80901699), (-0.5, 0.809017, -0.30901699), (-0.80901699, -0.30901699, 0.5)-133.00091, 215.2, 348.20091
50generate(0.809017, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.309017)430.4
51generate(-1), (-1), (1)430.4, 430.4
52generate(-0.309017, -0.5, -0.80901699), (-0.5, 0.80901699, -0.309017), (0.80901699, 0.309017, -0.5)563.40091, 215.2, 82.19908
53generate(-0.809017, 0.309017, -0.5), (-0.309017, 0.5, 0.80901699), (0.5, 0.809017, -0.30901699)430.4
54generate(-0.809017, 0.30901699, 0.5), (0.309017, -0.5, 0.809017), (0.5, 0.80901699, 0.309017)215.2, 82.19908, -133.00091
55generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.809017, -0.30901699), (0.809017, 0.30901699, 0.5)215.2, 348.20091, -133.00091
56generate(-0.50000001, 0.80901699, -0.309017), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.49999999, 0.809017)215.2, 348.20091, -133.00091
57generate(-0.309017, 0.5, 0.80901699), (-0.5, -0.80901699, 0.309017), (0.80901699, -0.309017, 0.5)430.39999
58generate(0.30901699, -0.5, 0.809017), (-0.5, -0.80901699, -0.30901699), (0.80901699, -0.309017, -0.5)82.19909, 563.40091, 215.2
59generate(0.5, -0.809017, -0.30901699), (-0.80901699, -0.30901699, -0.5), (0.30901699, 0.5, -0.809017)348.20091, 563.40091, 215.2
60generate(-1), (-1), (1)430.4, 430.4

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 31247.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: P08291
#2: Protein VP2


Mass: 29125.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: P08291
#3: Protein VP3


Mass: 26507.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: P08291
#4: Protein VP4


Mass: 7367.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: Q8QWF8, UniProt: P08291*PLUS

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Coxsackievirus B1 / Type: VIRUS
Details: Particles purified from the cell cultures innoculated with the live CB1.
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Coxsackievirus B1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 30 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 25

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2RELION3image acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5568 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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