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- PDB-8ozk: In situ cryoEM structure of the Prototype Foamy Virus capsid, ico... -

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Basic information

Entry
Database: PDB / ID: 8ozk
TitleIn situ cryoEM structure of the Prototype Foamy Virus capsid, icosahedral map
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / capsid / Gag / foamy virus
Function / homology
Function and homology information


host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / DNA binding / RNA binding / cytoplasm
Similarity search - Function
Gag polyprotein / : / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal
Similarity search - Domain/homology
Biological speciesEastern chimpanzee simian foamy virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsCalcraft, T. / Nans, A. / Rosenthal, P.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell / Year: 2024
Title: Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry.
Authors: Thomas Calcraft / Nicole Stanke-Scheffler / Andrea Nans / Dirk Lindemann / Ian A Taylor / Peter B Rosenthal /
Abstract: Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates ...Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Jul 24, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein
F: Gag polyprotein
G: Gag polyprotein
H: Gag polyprotein
I: Gag polyprotein
J: Gag polyprotein
K: Gag polyprotein
L: Gag polyprotein
M: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)919,01413
Polymers919,01413
Non-polymers00
Water00
1
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein
F: Gag polyprotein
G: Gag polyprotein
H: Gag polyprotein
I: Gag polyprotein
J: Gag polyprotein
K: Gag polyprotein
L: Gag polyprotein
M: Gag polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)55,140,863780
Polymers55,140,863780
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.67082, -0.16246, 0.723608), (0.688191, 0.500001, -0.52573), (-0.276394, 0.85065, 0.447214)-100.20985, 145.81638, -9.27508
3generate(0.138194, 0.425325, 0.894427), (0.951057, -0.309015, 2.0E-6), (0.276392, 0.850651, -0.447213)-197.83314, 154.63727, 138.31316
4generate(0.138194, 0.951057, 0.276392), (0.425325, -0.309015, 0.850651), (0.894427, 2.0E-6, -0.447213)-157.9581, 14.27269, 238.80268
5generate(0.67082, 0.688191, -0.276394), (-0.16246, 0.500001, 0.85065), (0.723608, -0.52573, 0.447214)-35.6905, -81.2985, 153.32045
6generate(0.361803, -0.262871, -0.894426), (0.587788, 0.809015, -3.0E-6), (0.723604, -0.525732, 0.447216)775.65332, -171.41769, 153.32182
7generate(-0.670821, 0.162455, -0.723607), (0.688191, 0.499994, -0.525737), (0.276391, -0.850655, -0.447206)964.21258, 145.82245, 873.27552
8generate(-0.670821, 0.688191, 0.276391), (0.162455, 0.499994, -0.850655), (-0.723607, -0.525737, -0.447206)305.09551, 513.30529, 1164.90981
9generate(0.361803, 0.587788, 0.723604), (-0.262871, 0.809015, -0.525732), (-0.894426, -3.0E-6, 0.447216)-290.82054, 423.18212, 625.19585
10generate(0.67082, -0.688196, -0.276382), (0.162472, 0.499995, -0.850652), (0.723604, 0.52573, 0.447219)558.90346, 513.2959, -300.91098
11generate(0.138196, -0.951052, 0.276408), (-0.425311, -0.30903, -0.850653), (0.894434, -3.0E-6, -0.4472)663.74556, 1116.7176, 238.79595
12generate(0.138196, -0.425311, 0.894434), (-0.951052, -0.30903, -3.0E-6), (0.276408, -0.850653, -0.4472)169.63815, 976.35687, 873.26408
13generate(0.67082, 0.162472, 0.723604), (-0.688196, 0.499995, 0.52573), (-0.276382, -0.850652, 0.447219)-240.57917, 286.18744, 725.68009
14generate(0.309017, -0.951057, 3.0E-6), (0.951057, 0.309017, 4.0E-6), (-4.0E-6, 2.0E-6, 1)709.35998, -112.35344, 0.00114
15generate(-0.809017, -0.587785), (0.587785, -0.809017, 7.0E-6), (-4.0E-6, 6.0E-6, 1)1035.41855, 527.56898, -0.00081
16generate(-0.809017, 0.587785, -4.0E-6), (-0.587785, -0.809017, 6.0E-6), (7.0E-6, 1)527.57401, 1035.41595, -0.00322
17generate(0.309017, 0.951057, -4.0E-6), (-0.951057, 0.309017, 2.0E-6), (3.0E-6, 4.0E-6, 1)-112.34996, 709.36045, -0.00286
18generate(-0.361792, -0.587809, -0.723593), (-0.26287, 0.808999, -0.525756), (0.89443, -4.0E-6, -0.447207)1154.82001, 423.19873, 238.80124
19generate(-0.361792, -0.26287, 0.89443), (-0.587809, 0.808999, -4.0E-6), (-0.723593, -0.525756, -0.447207)315.46015, 336.44761, 1164.91221
20generate(-0.138199, -0.425331, -0.894424), (0.951055, -0.30902, 1.0E-6), (-0.276396, -0.850647, 0.447219)1061.83613, 154.64038, 725.6839
21generate(-0.138199, 0.951055, -0.276396), (-0.425331, -0.30902, -0.850647), (-0.894424, 1.0E-6, 0.447219)200.24904, 1116.71918, 625.1922
22generate(-1, -4.0E-6), (-4.0E-6, 1, -9.0E-6), (-9.0E-6, -1)864.00181, 0.00559, 864.00385
23generate(-0.052791, 0.688189, -0.723608), (0.688189, -0.500001, -0.525733), (-0.723608, -0.525733, -0.447209)470.10669, 577.81935, 1164.90973
24generate(-0.361798, 0.262879, 0.894425), (0.587787, 0.809016, -1.4E-5), (-0.723608, 0.525726, -0.447217)88.34153, -171.41262, 710.68296
25generate(-0.361798, 0.587787, -0.723608), (0.262879, 0.809016, 0.525726), (0.894425, -1.4E-5, -0.447217)646.97174, -258.17225, 238.81239
26generate(0.447206, 0.525737, -0.723607), (0.850652, 9.0E-6, 0.525729), (0.276401, -0.850647, -0.447215)324.28708, -162.60046, 873.27126
27generate(0.447206, 0.850652, 0.276401), (0.525737, 9.0E-6, -0.850647), (-0.723607, 0.525729, -0.447215)-248.08011, 572.35766, 710.68031
28generate(0.947209, -0.162451, 0.276415), (0.162484, -0.5, -0.850646), (0.276396, 0.850652, -0.447209)-26.42666, 945.2862, 138.30927
29generate(0.947209, 0.162484, 0.276396), (-0.162451, -0.5, 0.850652), (0.276415, -0.850646, -0.447209)-166.79029, 350.69707, 873.26203
30generate(-0.447216, -0.525734, 0.723604), (0.850648, 3.0E-6, 0.525736), (-0.2764, 0.850649, 0.447213)539.71754, -162.59924, -9.27164
31generate(-0.447216, 0.850648, -0.2764), (-0.525734, 3.0E-6, 0.850649), (0.723604, 0.525736, 0.447213)377.12218, 291.63522, -300.91079
32generate(0.447185, -0.850663, 0.276401), (-0.525732, 2.5E-5, 0.85065), (-0.723624, -0.525711, -0.44721)486.89727, 291.62471, 1164.90737
33generate(0.447185, -0.525732, -0.723624), (-0.850663, 2.5E-5, -0.525711), (0.276401, 0.85065, -0.44721)778.53781, 1026.58304, 138.30857
34generate(-0.138194, -0.951056, -0.276395), (0.425324, -0.309017, 0.850652), (-0.894428, -2.0E-6, 0.447211)1021.95872, 14.27399, 625.19882
35generate(-0.138194, 0.425324, -0.894428), (-0.951056, -0.309017, -2.0E-6), (-0.276395, 0.850652, 0.447211)694.35304, 976.35274, -9.27423
36generate(0.361802, -0.587782, 0.723611), (0.262866, 0.80902, 0.525727), (-0.894428, 4.0E-6, 0.447213)217.02356, -258.16866, 625.19535
37generate(-0.670825, -0.688185, 0.276399), (-0.162456, 0.500007, 0.850648), (-0.723604, 0.525733, -0.447216)899.68787, -81.30194, 710.67773
38generate(-0.670825, -0.162456, -0.723604), (-0.688185, 0.500007, 0.525733), (0.276399, 0.850648, -0.447216)1104.57409, 286.17628, 138.31332
39generate(0.361802, 0.262866, -0.894428), (-0.587782, 0.80902, 4.0E-6), (0.723611, 0.525727, 0.447213)548.53633, 336.42362, -300.9097
40generate(0.861803, -0.425324, -0.276397), (0.425329, 0.309017, 0.850649), (-0.27639, -0.850652, 0.447214)362.84467, -252.71779, 725.68555
41generate(0.638195, -0.26286, -0.72361), (0.262872, -0.809017, 0.525728), (-0.723606, -0.525734, -0.447212)582.45477, 440.82021, 1164.91044
42generate(0.638195, 0.262872, -0.723606), (-0.26286, -0.809017, -0.525734), (-0.72361, 0.525728, -0.447212)355.33665, 1122.16801, 710.68079
43generate(0.861803, 0.425329, -0.27639), (-0.425324, 0.309017, -0.850652), (-0.276397, 0.850649, 0.447214)-4.64034, 849.72618, -9.27337
44generate(-0.861802, 0.425327, 0.276393), (0.425327, 0.309019, 0.850649), (0.276393, 0.850649, -0.447217)501.1554, -252.71805, 138.31546
45generate(0.809018, 0.587783, 1.2E-5), (0.587783, -0.809018, 4.0E-6), (1.2E-5, 4.0E-6, -1)-171.42353, 527.57183, 863.99314
46generate(0.052781, -0.688185, 0.723613), (0.688201, -0.5, -0.525718), (0.723598, 0.525739, 0.447219)393.89414, 577.80745, -300.91216
47generate(0.052781, 0.688201, 0.723598), (-0.688185, -0.5, 0.525739), (0.723613, -0.525718, 0.447219)-200.69831, 718.17699, 153.31076
48generate(0.80902, -0.587781, 3.9E-5), (-0.587781, -0.80902, -1.3E-5), (3.9E-5, -1.3E-5, -1)336.408, 1035.42371, 863.98869
49generate(-0.638197, -0.262856, 0.72361), (-0.262856, -0.80903, -0.525716), (0.72361, -0.525716, 0.447227)508.65561, 1122.16417, 153.3077
50generate(-0.447212, -0.850655, -0.276382), (0.525736, -1.4E-5, -0.850648), (0.723604, -0.525724, 0.447226)1112.07571, 572.36812, 153.31409
51generate(-0.447212, 0.525736, 0.723604), (-0.850655, -1.4E-5, -0.525724), (-0.276382, -0.850648, 0.447226)85.48074, 1026.60183, 725.67535
52generate(-0.947213, -0.162462, -0.276394), (-0.162462, -0.499995, 0.850654), (-0.276394, 0.850654, 0.447207)1030.78192, 350.69885, -9.27365
53generate(-0.309004, 0.951061, -4.0E-6), (0.951061, 0.309004, -5.0E-6), (-4.0E-6, -5.0E-6, -1)154.63322, -112.34595, 864.00377
54generate(0.447209, 3.0E-5, 0.894429), (3.0E-5, -1, 1.9E-5), (0.894429, 1.9E-5, -0.447209)-147.60082, 863.97895, 238.79276
55generate(-0.638202, 0.262864, 0.723603), (0.262864, -0.809016, 0.525733), (0.723603, 0.525733, 0.447218)281.5495, 440.82087, -300.91125
56generate(-0.309008, -0.95106, 1.1E-5), (-0.95106, 0.309008, -1.6E-5), (1.1E-5, -1.6E-5, -1)976.34429, 709.37328, 864.00201
57generate(-0.447212, -2.0E-6, -0.894428), (-2.0E-6, -1, 3.0E-6), (-0.894428, 3.0E-6, 0.447212)1011.58945, 863.99952, 625.19574
58generate(-0.861802, -0.425323, 0.276401), (-0.425323, 0.308988, -0.850662), (0.276401, -0.850662, -0.447186)868.63263, 849.74279, 873.26529
59generate(-0.947215, 0.162457, -0.276391), (0.162457, -0.500007, -0.850647), (-0.276391, -0.850647, 0.447222)890.41638, 945.30124, 725.68084
60generate(-0.052773, -0.688186, -0.723612), (-0.688186, -0.500014, 0.525724), (-0.723612, 0.525724, -0.447213)1064.69477, 718.18992, 710.68394

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Components

#1: Protein
Gag polyprotein


Mass: 70693.414 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern chimpanzee simian foamy virus / Gene: gag / Production host: Homo sapiens (human) / References: UniProt: A0A1Q1N9V7

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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: Eastern chimpanzee simian foamy virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Eastern chimpanzee simian foamy virus
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Virus shellTriangulation number (T number): 13
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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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: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710

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Processing

SoftwareName: REFMAC / Version: 5.8.0352 / Classification: refinement
EM software
IDNameCategory
1crYOLOparticle selection
2EPUimage acquisition
4GctfCTF correction
9REFMACmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 52141
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8156 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
RefinementResolution: 3.89→686.88 Å / Cor.coef. Fo:Fc: 0.948 / SU B: 25.173 / SU ML: 0.335 / ESU R: 0.052
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS /
Rfactor% reflection
Rwork0.32044 -
obs0.32044 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 145.507 Å2
Refinement stepCycle: 1 / Total: 17417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0150.01117755
ELECTRON MICROSCOPYr_bond_other_d00.01616469
ELECTRON MICROSCOPYr_angle_refined_deg1.8331.63824220
ELECTRON MICROSCOPYr_angle_other_deg0.91.5438312
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.02552259
ELECTRON MICROSCOPYr_dihedral_angle_2_deg1.25710154
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.119102866
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0670.22843
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0220462
ELECTRON MICROSCOPYr_gen_planes_other0.0060.023306
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it24.87113.5599075
ELECTRON MICROSCOPYr_mcbond_other24.86713.569075
ELECTRON MICROSCOPYr_mcangle_it37.14720.17911321
ELECTRON MICROSCOPYr_mcangle_other37.14620.18311322
ELECTRON MICROSCOPYr_scbond_it29.26616.4218680
ELECTRON MICROSCOPYr_scbond_other29.26416.4268681
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other44.59523.62812900
ELECTRON MICROSCOPYr_long_range_B_refined51.79318991
ELECTRON MICROSCOPYr_long_range_B_other51.79218992
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.89→3.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.537 744714 -
obs--100 %

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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