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- PDB-3vbf: Crystal structure of formaldehyde treated human Enterovirus 71 (s... -

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Basic information

Entry
Database: PDB / ID: 3vbf
TitleCrystal structure of formaldehyde treated human Enterovirus 71 (space group I23)
Components(Genome Polyprotein, capsid protein ...) x 4
KeywordsVIRUS / hand-foot-and-mouth disease / enterovirus uncoating / pocket factor / adaptor-sensor / icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein / 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 ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Few Secondary Structures / Irregular / 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. / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / SPHINGOSINE / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. ...Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D. ...Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Apr 25, 2012Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,23510
Polymers92,4514
Non-polymers7836
Water5,080282
1
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,594,080600
Polymers5,547,079240
Non-polymers47,001360
Water4,324240
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: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 466 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)466,17350
Polymers462,25720
Non-polymers3,91730
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 559 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)559,40860
Polymers554,70824
Non-polymers4,70036
Water43224
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: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.86 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,864,693200
Polymers1,849,02680
Non-polymers15,667120
Water1,44180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)600.100, 600.100, 600.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.4676, 0.5853, 0.6624), (-0.1951, 0.6626, -0.7231), (-0.8621, -0.4674, -0.1956)32.08, 184, 369.9
3generate(0.3244, 0.8959, 0.3037), (-0.8074, 0.4295, -0.4046), (-0.4929, -0.114, 0.8626)-76.91, 261.2, 108.8
4generate(0.3099, 0.7339, -0.6045), (-0.7574, 0.5749, 0.3097), (0.5748, 0.3618, 0.7339)82.21, 127.8, -98.25
5generate(-0.4918, 0.3235, -0.8084), (-0.1165, 0.8956, 0.4293), (0.8629, 0.3052, -0.4028)289.7, -30.66, 34.41
6generate(-0.9725, 0.2317, -0.02495), (0.2317, 0.9501, -0.2088), (-0.02466, -0.2088, -0.9776)258.7, 3.922, 324.1
7generate(0.4305, -0.4044, -0.8069), (-0.1155, 0.862, -0.4937), (0.8952, 0.3057, 0.3243)261.1, 109.5, -77
8generate(-0.4914, -0.7681, -0.4105), (-0.5901, 0.6403, -0.4917), (0.6406, 0.000626, -0.7679)391.3, 211.2, 165.2
9generate(-0.4916, -0.5888, 0.6416), (-0.7671, 0.6416, 0.001118), (-0.4123, -0.4916, -0.767)210.6, 164.6, 391.4
10generate(0.4301, -0.1137, 0.8956), (-0.4018, 0.8643, 0.3027), (-0.8084, -0.49, 0.326)-31.29, 34.14, 288.8
11generate(0.8628, -0.4924, -0.1146), (0.3048, 0.3257, 0.895), (-0.4034, -0.8071, 0.4311)109.1, -77.13, 260.6
12generate(-0.2073, -0.978, -0.02248), (0.2328, -0.02698, -0.9722), (0.9502, -0.2067, 0.2333)323.6, 259.1, 3.378
13generate(-0.2075, 0.2346, 0.9497), (-0.9779, -0.02574, -0.2073), (-0.02418, -0.9718, 0.2348)3.075, 324, 258.1
14generate(0.7347, 0.5742, 0.3612), (-0.6039, 0.311, 0.7339), (0.3091, -0.7573, 0.5753)-98.26, 81.69, 127.8
15generate(0.5739, 0.3084, -0.7586), (0.3628, 0.7347, 0.5732), (0.7342, -0.6042, 0.3098)128.5, -98.28, 82.12
16generate(-0.4675, -0.1975, -0.8616), (0.5847, 0.6619, -0.469), (0.663, -0.7231, -0.1939)370.4, 32.67, 183.9
17generate(-0.9504, -0.2429, 0.1944), (-0.2434, 0.1913, -0.9509), (0.1938, -0.951, -0.2409)292.8, 293.7, 292.9
18generate(0.3247, -0.8085, -0.4908), (0.8955, 0.4298, -0.1155), (0.3044, -0.402, 0.8636)289.4, -30.64, 34.17
19generate(0.001717, -0.7666, 0.6421), (-0.7673, -0.4128, -0.4908), (0.6413, -0.4918, -0.5889)164.4, 391.5, 211
20generate(0.6629, -0.4664, 0.5857), (-0.7227, -0.1943, 0.6633), (-0.1956, -0.863, -0.4659)31.83, 183.5, 370

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Components

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Genome Polyprotein, capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Genome Polyprotein, capsid protein VP1


Mass: 32727.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / References: UniProt: B2ZUN0
#2: Protein Genome Polyprotein, capsid protein VP2


Mass: 26874.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / References: UniProt: B2ZUN0
#3: Protein Genome Polyprotein, capsid protein VP3


Mass: 26468.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / References: UniProt: B2ZUN0
#4: Protein Genome Polyprotein, capsid protein VP4


Mass: 6380.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / References: UniProt: B2ZUN0

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Non-polymers , 6 types, 288 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS INDICATE THAT BASED ON ELECTRON DENSITY MAPS, A225 IS MET.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 76

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG400, 0.2 M tri-Sodium Citrate, 0.1 M Tris.HCl pH 8.5, mixed with virus and equilibrated against salt reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 918888 / % possible obs: 84.8 % / Observed criterion σ(I): -1.5 / Redundancy: 2.9 % / Rmerge(I) obs: 0.576 / Net I/σ(I): 1.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.3 / Num. unique all: 40599 / % possible all: 37.6

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BEV

1bev


Resolution: 2.6→49.67 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 42557276.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED STRICT NCS CONSTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 8932 1 %RANDOM
Rwork0.236 ---
obs0.236 877371 80.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.9972 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 48 282 6838
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.268
X-RAY DIFFRACTIONc_mcangle_it8.6816
X-RAY DIFFRACTIONc_scbond_it12.2712
X-RAY DIFFRACTIONc_scangle_it13.5820
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 803 1 %
Rwork0.359 78058 -
obs--43.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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