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- PDB-5cfd: Crystal Structure of DTT treated Human Cardiovirus SAFV-3 -

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Basic information

Entry
Database: PDB / ID: 5cfd
TitleCrystal Structure of DTT treated Human Cardiovirus SAFV-3
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Virion / capsid / DTT / saffold virus / pathogen
Function / homology
Function and homology information


RNA-protein covalent cross-linking / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity ...RNA-protein covalent cross-linking / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / 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 / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesSaffold virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMullapudi, E. / Plevka, P.
CitationJournal: J Virol / Year: 2016
Title: Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3.
Authors: Edukondalu Mullapudi / Jiří Nováček / Lenka Pálková / Pavel Kulich / A Michael Lindberg / Frank J M van Kuppeveld / Pavel Plevka /
Abstract: In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not ...In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an "altered" particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection.
IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from ...IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release of Human Saffold virus 3 Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Feb 14, 2018Group: Refinement description / Category: refine / Item: _refine.ls_R_factor_obs
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,3044
Polymers85,3044
Non-polymers00
Water6,089338
1
A: VP1
B: VP3
C: VP2
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,118,218240
Polymers5,118,218240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
B: VP3
C: VP2
D: VP4
x 5


  • icosahedral pentamer
  • 427 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)426,51820
Polymers426,51820
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP3
C: VP2
D: VP4
x 6


  • icosahedral 23 hexamer
  • 512 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)511,82224
Polymers511,82224
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)299.946, 299.946, 723.471
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.309, -0.940019, -0.14438), (0.940019, 0.324954, -0.103685), (0.14438, -0.103685, 0.984046)89.7569, -85.9178, -13.1929
3generate(0.309, -0.291235, -0.905353), (0.291235, 0.935175, -0.201426), (0.905353, -0.201426, 0.373825)181.5138, -6.2046, -19.2871
4generate(0.809, -0.580961, -0.089252), (0.180012, 0.389396, -0.903298), (0.559533, 0.714702, 0.419604)30.7595, 90.0711, 11.4002
5generate(0.809, -0.180012, -0.559533), (0.580961, 0.389396, 0.714702), (0.089252, -0.903298, 0.419604)87.4653, -147.0043, 60.6386
6generate(0.5, -0.289726, 0.816101), (0.760007, 0.598539, -0.253146), (-0.415152, 0.746853, 0.51946)-46.0542, -49.0487, 101.4092
7generate(0.5, -0.760007, 0.415152), (0.289726, 0.598539, 0.746853), (-0.816101, -0.253146, 0.51946)2.2916, -120.3888, 143.3885
8generate(0.5, 0.760007, -0.415152), (-0.289726, 0.598539, 0.746853), (0.816101, -0.253146, 0.51946)102.4084, -59.7202, -27.503
9generate(0.5, 0.289726, -0.816101), (-0.760007, 0.598539, -0.253146), (0.415152, 0.746853, 0.51946)150.7542, 110.0968, 14.4763
10generate(0.809, 0.580961, 0.089252), (-0.180012, 0.389396, -0.903298), (-0.559533, 0.714702, 0.419604)9.2359, 127.7656, 128.5663
11generate(0.809, 0.180012, 0.559533), (-0.580961, 0.389396, 0.714702), (-0.089252, -0.903298, 0.419604)-47.4699, -25.3511, 79.3279
12generate(0.309, 0.291235, 0.905353), (-0.291235, 0.935175, -0.201426), (-0.905353, -0.201426, 0.373825)-36.8184, 54.7799, 170.2937
13generate(0.309, 0.940019, 0.14438), (-0.940019, 0.324954, -0.103685), (-0.14438, -0.103685, 0.984046)54.9385, 110.9221, 17.0403
14generate(-0.309, -0.940019, -0.14438), (0.291235, 0.050986, -0.955262), (0.905353, -0.337262, 0.258015)154.4615, 84.6918, -5.3229
15generate(-0.309, -0.291235, -0.905353), (0.940019, 0.050986, -0.337262), (0.14438, -0.955262, 0.258015)246.2184, -57.7534, 74.3509
16generate(-0.648784, 0.760972), (0.760972, -0.493707, -0.420921), (0.648784, 0.579079, 0.493707)12.9431, -28.9198, -6.8796
17generate(-0.760972, -0.648784), (0.648784, -0.493707, 0.579079), (-0.760972, -0.420921, 0.493707)182.9294, -137.7522, 140.7219
18generate(0.648784, -0.760972), (0.760972, 0.493707, 0.420921), (0.648784, -0.579079, -0.493707)196.4569, -130.4278, 112.1812
19generate(-0.760972, -0.648784), (-0.648784, 0.493707, -0.579079), (0.760972, 0.420921, -0.493707)182.9294, 137.7522, 100.4351
20generate(-0.5, -0.760007, 0.415152), (0.760007, -0.155297, 0.631043), (-0.415152, 0.631043, 0.655297)106.9915, -155.663, 85.0303
21generate(-0.5, 0.289726, -0.816101), (-0.289726, 0.832117, 0.472885), (0.816101, 0.472885, -0.332117)255.4542, -26.6855, 75.1789
22generate(0.809, 0.180012, 0.559533), (0.580961, -0.389396, -0.714702), (0.089252, 0.903298, -0.419604)-47.4699, 25.3511, 161.8291
23generate(0.809, -0.580961, -0.089252), (-0.180012, -0.389396, 0.903298), (-0.559533, -0.714702, -0.419604)30.7595, -90.0711, 229.7568
24generate(0.809, 0.580961, 0.089252), (0.180012, -0.389396, 0.903298), (0.559533, -0.714702, -0.419604)9.2359, -127.7656, 112.5907
25generate(0.809, -0.180012, -0.559533), (-0.580961, -0.389396, -0.714702), (-0.089252, 0.903298, -0.419604)87.4653, 147.0043, 180.5184
26generate(-0.5, -0.289726, 0.816101), (0.289726, 0.832117, 0.472885), (-0.816101, 0.472885, -0.332117)58.6458, -87.3541, 246.0705
27generate(-0.5, 0.760007, -0.415152), (-0.760007, -0.155297, 0.631043), (0.415152, 0.631043, 0.655297)207.1084, 3.4825, -1.9026
28generate(0.760972, 0.648784), (0.648784, 0.493707, -0.579079), (-0.760972, 0.420921, -0.493707)26.4706, 1.8968, 259.7827
29generate(-0.648784, 0.760972), (-0.760972, 0.493707, 0.420921), (-0.648784, -0.579079, -0.493707)12.9431, 28.9198, 248.0367
30generate(0.760972, 0.648784), (-0.648784, -0.493707, 0.579079), (0.760972, -0.420921, 0.493707)26.4706, -1.8968, -18.6258
31generate(0.648784, -0.760972), (-0.760972, -0.493707, -0.420921), (-0.648784, 0.579079, 0.493707)196.4569, 130.4278, 128.9758
32generate(-0.309, 0.940019, 0.14438), (-0.291235, 0.050986, -0.955262), (-0.905353, -0.337262, 0.258015)119.6432, 145.6764, 184.2579
33generate(-0.309, 0.291235, 0.905353), (-0.940019, 0.050986, -0.337262), (-0.14438, -0.955262, 0.258015)27.8862, 139.0865, 104.5841
34generate(-0.809, -0.580961, -0.089252), (0.580961, -0.767293, -0.271459), (0.089252, -0.271459, 0.958293)200.1641, -28.0944, -4.3156
35generate(-0.809, -0.180012, -0.559533), (0.180012, 0.830343, -0.527359), (0.559533, -0.527359, -0.639343)256.8699, 44.7409, 139.0864
36generate(0.5, -0.760007, 0.415152), (-0.289726, -0.598539, -0.746853), (0.816101, 0.253146, -0.51946)2.2916, 120.3888, 97.7685
37generate(0.5, 0.289726, -0.816101), (0.760007, -0.598539, 0.253146), (-0.415152, -0.746853, -0.51946)150.7542, -110.0968, 226.6807
38generate(-0.309, 0.291235, 0.905353), (0.940019, -0.050986, 0.337262), (0.14438, 0.955262, -0.258015)27.8862, -139.0865, 136.5729
39generate(-0.309, -0.940019, -0.14438), (-0.291235, -0.050986, 0.955262), (-0.905353, 0.337262, -0.258015)154.4615, -84.6918, 246.4799
40generate(-0.309, 0.940019, 0.14438), (0.291235, -0.050986, 0.955262), (0.905353, 0.337262, -0.258015)119.6432, -145.6764, 56.8991
41generate(-0.309, -0.291235, -0.905353), (-0.940019, -0.050986, 0.337262), (-0.14438, 0.955262, -0.258015)246.2184, 57.7534, 166.8061
42generate(0.5, 0.760007, -0.415152), (0.289726, -0.598539, -0.746853), (-0.816101, 0.253146, -0.51946)102.4084, 59.7202, 268.66
43generate(0.5, -0.289726, 0.816101), (-0.760007, -0.598539, 0.253146), (0.415152, -0.746853, -0.51946)-46.0542, 49.0487, 139.7478
44generate(-0.809, 0.180012, 0.559533), (-0.180012, 0.830343, -0.527359), (-0.559533, -0.527359, -0.639343)121.9347, 82.4354, 256.2526
45generate(-0.809, 0.580961, 0.089252), (-0.580961, -0.767293, -0.271459), (-0.089252, -0.271459, 0.958293)178.6405, 93.5587, 14.3736
46generate(-1), (-0.158158, -0.987414), (-0.987414, 0.158158)209.4, 119.0609, 101.508
47generate(-0.5, -0.289726, 0.816101), (-0.289726, -0.832117, -0.472885), (0.816101, -0.472885, 0.332117)58.6458, 87.3541, -4.9135
48generate(-0.5, 0.289726, -0.816101), (0.289726, -0.832117, -0.472885), (-0.816101, -0.472885, 0.332117)255.4542, 26.6855, 165.9781
49generate(-0.5, 0.760007, -0.415152), (0.760007, 0.155297, -0.631043), (-0.415152, -0.631043, -0.655297)207.1084, -3.4825, 243.0596
50generate(-0.5, -0.760007, 0.415152), (-0.760007, 0.155297, -0.631043), (0.415152, -0.631043, -0.655297)106.9915, 155.663, 156.1267
51generate(-0.809, 0.180012, 0.559533), (0.180012, -0.830343, 0.527359), (0.559533, 0.527359, 0.639343)121.9347, -82.4354, -15.0956
52generate(-0.809, -0.180012, -0.559533), (-0.180012, -0.830343, 0.527359), (-0.559533, 0.527359, 0.639343)256.8699, -44.7409, 102.0706
53generate(-0.809, 0.580961, 0.089252), (0.580961, 0.767293, 0.271459), (0.089252, 0.271459, -0.958293)178.6405, -93.5587, 226.7834
54generate(-0.809, -0.580961, -0.089252), (-0.580961, 0.767293, 0.271459), (-0.089252, 0.271459, -0.958293)200.1641, 28.0944, 245.4726
55generate(0.309, 0.291235, 0.905353), (0.291235, -0.935175, 0.201426), (0.905353, 0.201426, -0.373825)-36.8184, -54.7799, 70.8633
56generate(0.309, -0.291235, -0.905353), (-0.291235, -0.935175, 0.201426), (-0.905353, 0.201426, -0.373825)181.5138, 6.2046, 260.4441
57generate(0.309, 0.940019, 0.14438), (0.940019, -0.324954, 0.103685), (0.14438, 0.103685, -0.984046)54.9385, -110.9221, 224.1167
58generate(0.309, -0.940019, -0.14438), (-0.940019, -0.324954, 0.103685), (-0.14438, 0.103685, -0.984046)89.7569, 85.9178, 254.3499
59generate(1), (-1), (-1)241.157
60generate(-1), (0.158158, 0.987414), (0.987414, -0.158158)209.4, -119.0609, 139.649

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Components

#1: Protein VP1


Mass: 28302.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saffold virus / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: C0MHL9
#2: Protein VP3


Mass: 25611.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saffold virus / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: C0MHL9
#3: Protein VP2


Mass: 28698.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saffold virus / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: C0MHL9
#4: Protein/peptide VP4


Mass: 2690.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saffold virus / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: C0MHL9, UniProt: C3U5A3*PLUS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 2.8 M Na acetate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→70 Å / Num. obs: 864367 / % possible obs: 67.51 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 5.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
CNSrefinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→70 Å / Cross valid method: NONE / σ(F): 0
RfactorNum. reflection% reflection
obs0.2155 864367 67.4 %
Rfree-0 0 %
Rwork-864367 -
Solvent computationBsol: 16.3551 Å2
Displacement parametersBiso max: 230.93 Å2 / Biso mean: 27.5552 Å2 / Biso min: 6 Å2
Baniso -1Baniso -2Baniso -3
1-0.792 Å2-0 Å2-0 Å2
2--0.792 Å20 Å2
3----1.584 Å2
Refinement stepCycle: final / Resolution: 2.5→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 0 338 6350
Biso mean---35.38 -
Num. residues----766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1351.5
X-RAY DIFFRACTIONc_scbond_it1.9032
X-RAY DIFFRACTIONc_mcangle_it1.9312
X-RAY DIFFRACTIONc_scangle_it2.8592.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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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

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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

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