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- PDB-5do2: Complex structure of MERS-RBD bound with 4C2 antibody -

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Basic information

Entry
Database: PDB / ID: 5do2
TitleComplex structure of MERS-RBD bound with 4C2 antibody
Components
  • 4C2 heavy chain
  • 4C2 light chain
  • S proteinCoronavirus spike protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / receptor-binding domain of MERS-CoV spike / 4C2 antibody / neuralization / receptor-binding blocking. / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...: / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / : / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / : / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome coronavirus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.409 Å
AuthorsLi, Y. / Wan, Y. / Liu, P. / Zhao, J. / Lu, G. / Qi, J. / Wang, Q. / Lu, X. / Wu, Y. / Liu, W. ...Li, Y. / Wan, Y. / Liu, P. / Zhao, J. / Lu, G. / Qi, J. / Wang, Q. / Lu, X. / Wu, Y. / Liu, W. / Yuen, K.Y. / Perlman, S. / Gao, G.F. / Yan, J.
CitationJournal: Cell Res. / Year: 2015
Title: A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein.
Authors: Li, Y. / Wan, Y. / Liu, P. / Zhao, J. / Lu, G. / Qi, J. / Wang, Q. / Lu, X. / Wu, Y. / Liu, W. / Zhang, B. / Yuen, K.Y. / Perlman, S. / Gao, G.F. / Yan, J.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S protein
H: 4C2 heavy chain
L: 4C2 light chain
B: S protein
C: 4C2 heavy chain
D: 4C2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7887
Polymers149,5666
Non-polymers2211
Water2,504139
1
A: S protein
C: 4C2 heavy chain
D: 4C2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0044
Polymers74,7833
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 4C2 heavy chain
L: 4C2 light chain
B: S protein


Theoretical massNumber of molelcules
Total (without water)74,7833
Polymers74,7833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.083, 110.401, 172.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S protein / Coronavirus spike protein


Mass: 27598.953 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 367-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: W5ZZM0, UniProt: K0BRG7*PLUS
#2: Antibody 4C2 heavy chain


Mass: 23477.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 4C2 light chain


Mass: 23707.049 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 30, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 55462 / Num. obs: 55049 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 19.915
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.092 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KR0
Resolution: 2.409→46.531 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2891 2789 5.07 %Random selection
Rwork0.2446 ---
obs0.2468 54975 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.409→46.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9784 0 14 139 9937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410042
X-RAY DIFFRACTIONf_angle_d0.92213655
X-RAY DIFFRACTIONf_dihedral_angle_d14.3983602
X-RAY DIFFRACTIONf_chiral_restr0.0391558
X-RAY DIFFRACTIONf_plane_restr0.0041739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4094-2.4510.3198930.32952159X-RAY DIFFRACTION82
2.451-2.49550.34971380.31582488X-RAY DIFFRACTION97
2.4955-2.54350.32681340.31992598X-RAY DIFFRACTION99
2.5435-2.59550.33751340.31312608X-RAY DIFFRACTION100
2.5955-2.65190.37051590.31012597X-RAY DIFFRACTION100
2.6519-2.71360.37471290.30712608X-RAY DIFFRACTION100
2.7136-2.78140.33241420.30792591X-RAY DIFFRACTION100
2.7814-2.85660.29621330.31082634X-RAY DIFFRACTION100
2.8566-2.94070.34161520.2922593X-RAY DIFFRACTION100
2.9407-3.03560.39351290.30132628X-RAY DIFFRACTION100
3.0356-3.1440.34541430.29872618X-RAY DIFFRACTION100
3.144-3.26990.34671380.28092626X-RAY DIFFRACTION100
3.2699-3.41870.29261410.28762641X-RAY DIFFRACTION100
3.4187-3.59880.29571420.25822633X-RAY DIFFRACTION100
3.5988-3.82420.27121330.25022656X-RAY DIFFRACTION100
3.8242-4.11930.24741440.22272659X-RAY DIFFRACTION100
4.1193-4.53350.23611480.18972647X-RAY DIFFRACTION100
4.5335-5.18880.25711490.18112672X-RAY DIFFRACTION100
5.1888-6.53450.26691610.21532697X-RAY DIFFRACTION100
6.5345-46.53990.25171470.1912833X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.7404-0.7234-0.5172.2675-0.52712.1565-0.2534-0.2173-0.3870.21750.08610.06130.13790.22350.15670.3774-0.0214-0.02990.56590.19160.5361103.3004210.063337.773
21.2995-0.130.48254.9738-1.68250.72760.0481-1.1401-0.02771.0152-0.1253-0.0172-0.25710.19810.07570.4619-0.05840.00360.84280.06850.3494106.2513224.017941.7293
31.82840.7622-0.59552.3569-0.15882.9627-0.1714-0.5741-0.09670.18010.3545-0.10120.30450.0006-0.23350.39530.0404-0.06110.63550.19410.5029108.5974216.848338.077
43.04-4.1342-0.57235.8150.48645.94210.242-0.30860.87130.035-0.2378-0.6225-1.196-0.17140.00420.5561-0.10820.02390.4344-0.00980.5128102.5107241.394734.6491
51.9975-0.4969-0.34393.4277-1.17782.4193-0.1211-0.2408-0.17050.14040.13340.1651-0.0270.0020.00520.2786-0.0481-0.0280.45440.01750.268102.5432226.905733.0226
62.8876-0.9535-1.16621.02810.18873.39920.0694-0.16190.25240.050.0177-0.16120.07170.3779-0.09250.2717-0.066-0.01440.3230.03040.3519119.1458239.211711.7472
71.83370.322-1.17980.4427-0.19564.11640.02570.1376-0.0041-0.0263-0.0409-0.01360.1859-0.09370.01840.2533-0.0254-0.01080.35120.0230.3748117.2989237.6243.272
85.9938-1.17990.79983.3451-0.61822.0165-0.11030.3360.0742-0.19670.06950.2076-0.26120.11470.03540.3526-0.0578-0.02320.30280.03390.2171107.4245247.7447-17.7611
95.2483-2.3155-0.19686.953-0.77570.1345-0.05881.83480.3231-1.12150.03310.1132-0.60520.535-0.01020.5292-0.1241-0.02880.66360.14610.4684110.3115254.675-24.8281
103.193-0.15980.37190.5728-0.08662.78990.0217-0.0243-0.3059-0.160.0123-0.01340.3537-0.2774-0.03130.3179-0.06280.02090.3170.04680.343997.6303229.119110.9888
111.3139-0.09020.73680.0849-0.05572.02440.03310.2063-0.0897-0.10220.0914-0.04830.1394-0.173-0.10310.3744-0.06150.01140.3249-0.0420.3172100.7338234.7359-13.4408
128.11932.3651-4.32212.2791-0.88424.8128-0.37741.09690.2231-0.63290.34990.03810.0282-0.24740.01330.5478-0.1214-0.03870.6575-0.06090.2931103.1653237.0439-33.1451
130.2877-0.4812-0.17130.89970.21960.1272-0.03130.422-0.4037-0.7262-0.0817-0.79790.47550.1893-0.36012.25130.00071.41390.5499-0.49762.123195.9219204.34681.7712
141.56630.7382-0.15811.47250.10941.0203-0.82420.5363-0.9807-1.25030.3964-0.411-0.05040.04040.17912.2393-0.54380.62150.7375-0.20741.020582.9349213.53460.1088
150.2753-0.12430.11590.44360.24620.307-0.68180.3663-1.0907-0.88840.0041-0.66091.2504-0.16360.4371.7162-0.13380.54710.5366-0.05911.140477.7695214.01085.9469
160.01-0.029-0.0080.09170.02810.0091-0.45260.5709-0.06670.11130.54830.8502-0.1931-0.5472-0.12241.81890.44940.59471.674-0.08652.6636112.1752209.65611.324
172.35960.8171-0.64653.3731-0.48330.7308-0.7418-0.4249-0.7743-0.87060.00980.10430.98540.04510.4610.6960.03640.23520.46050.16970.736663.1292211.139526.8862
182.57380.62610.98753.84620.19341.7443-0.2387-0.33961.60560.1692-0.20282.055-0.6045-0.36770.42470.63740.03220.00310.90730.18221.86558.8201228.943953.1601
190.74341.3271-0.03772.477-0.45781.4645-0.2197-0.6634-0.73320.0741-0.5524-0.73980.29131.33940.6750.53560.08850.21251.23770.57480.949587.4958220.754631.5572
201.09330.18441.01571.32570.84721.7456-0.47-0.5291-0.6787-0.6322-0.5373-0.64770.47070.9017-0.32880.56320.11110.32470.69850.4120.674281.4455222.76422.7962
212.8982-0.5016-0.8131.89132.47477.6558-0.2001-0.3838-0.2416-0.2717-0.5054-0.3526-0.68220.8470.41110.3901-0.02470.01331.06240.45650.66280.2241227.555330.8967
221.6091.29690.51411.3383-0.00880.7352-0.4641-0.7864-0.13330.4025-0.37220.82380.27741.07580.55630.69410.14960.39210.85780.29741.010172.8874223.782446.6016
232.86891.03370.15215.8341-0.54334.50950.38650.39930.94591.0435-0.35010.5075-0.53880.7956-0.04570.7183-0.04270.10630.82370.22530.606174.682224.282461.2945
247.46144.6997-2.80036.0871-4.09712.89460.18630.20780.69660.9469-0.24180.7997-1.17790.2701-0.07310.6350.02020.10120.70690.14750.801170.2293225.511256.4135
256.69923.9704-0.4883.2839-1.90332.83440.1562-1.3575-0.5860.9514-0.60090.55430.3599-0.52880.33761.7925-0.04310.61030.97330.13950.829770.27225.129672.0511
261.41711.74621.81438.3497-2.24898.05590.1822-0.93890.57831.6729-0.52711.5339-0.4207-0.42060.3051.249-0.10260.22360.9684-0.17050.725373.9878232.702967.8111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 381 through 439 )
2X-RAY DIFFRACTION2chain 'A' and (resid 440 through 467 )
3X-RAY DIFFRACTION3chain 'A' and (resid 468 through 495 )
4X-RAY DIFFRACTION4chain 'A' and (resid 496 through 515 )
5X-RAY DIFFRACTION5chain 'A' and (resid 516 through 588 )
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 83 )
7X-RAY DIFFRACTION7chain 'H' and (resid 84 through 122 )
8X-RAY DIFFRACTION8chain 'H' and (resid 123 through 205 )
9X-RAY DIFFRACTION9chain 'H' and (resid 206 through 219 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 75 )
11X-RAY DIFFRACTION11chain 'L' and (resid 76 through 174 )
12X-RAY DIFFRACTION12chain 'L' and (resid 175 through 214 )
13X-RAY DIFFRACTION13chain 'B' and (resid 381 through 456 )
14X-RAY DIFFRACTION14chain 'B' and (resid 457 through 528 )
15X-RAY DIFFRACTION15chain 'B' and (resid 529 through 576 )
16X-RAY DIFFRACTION16chain 'B' and (resid 577 through 588 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 122 )
18X-RAY DIFFRACTION18chain 'C' and (resid 123 through 219 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 25 )
20X-RAY DIFFRACTION20chain 'D' and (resid 26 through 75 )
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 90 )
22X-RAY DIFFRACTION22chain 'D' and (resid 91 through 128 )
23X-RAY DIFFRACTION23chain 'D' and (resid 129 through 163 )
24X-RAY DIFFRACTION24chain 'D' and (resid 164 through 186 )
25X-RAY DIFFRACTION25chain 'D' and (resid 187 through 197 )
26X-RAY DIFFRACTION26chain 'D' and (resid 198 through 214 )

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