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- PDB-5u4r: Crystal structure of the broadly neutralizing Influenza A antibod... -

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Basic information

Entry
Database: PDB / ID: 5u4r
TitleCrystal structure of the broadly neutralizing Influenza A antibody VRC 315 53-1A09 Fab.
Components
  • VRC 315 53-1A09 Fab Heavy chain
  • VRC 315 53-1A09 Fab Light chain
KeywordsIMMUNE SYSTEM / antibody / influenza / human vaccine trial
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å
AuthorsJoyce, M.G. / Andrews, S.F. / Mascola, J.R. / McDermott, A.B. / Kwong, P.D.
CitationJournal: Sci Immunol / Year: 2017
Title: Preferential induction of cross-group influenza A hemagglutinin stem-specific memory B cells after H7N9 immunization in humans.
Authors: Andrews, S.F. / Joyce, M.G. / Chambers, M.J. / Gillespie, R.A. / Kanekiyo, M. / Leung, K. / Yang, E.S. / Tsybovsky, Y. / Wheatley, A.K. / Crank, M.C. / Boyington, J.C. / Prabhakaran, M.S. / ...Authors: Andrews, S.F. / Joyce, M.G. / Chambers, M.J. / Gillespie, R.A. / Kanekiyo, M. / Leung, K. / Yang, E.S. / Tsybovsky, Y. / Wheatley, A.K. / Crank, M.C. / Boyington, J.C. / Prabhakaran, M.S. / Narpala, S.R. / Chen, X. / Bailer, R.T. / Chen, G. / Coates, E. / Kwong, P.D. / Koup, R.A. / Mascola, J.R. / Graham, B.S. / Ledgerwood, J.E. / McDermott, A.B.
History
DepositionDec 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VRC 315 53-1A09 Fab Heavy chain
B: VRC 315 53-1A09 Fab Light chain
H: VRC 315 53-1A09 Fab Heavy chain
L: VRC 315 53-1A09 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)97,0744
Polymers97,0744
Non-polymers00
Water21,0781170
1
A: VRC 315 53-1A09 Fab Heavy chain
B: VRC 315 53-1A09 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)48,5372
Polymers48,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-20 kcal/mol
Surface area20270 Å2
MethodPISA
2
H: VRC 315 53-1A09 Fab Heavy chain
L: VRC 315 53-1A09 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)48,5372
Polymers48,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-24 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)77.553, 84.131, 79.273
Angle α, β, γ (deg.)90.000, 111.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and ((resid 1 and (name N or name...
21(chain L and ((resid 1 and (name N or name...
12(chain A and (resseq 1:10 or resseq 12:104 or resseq...
22(chain H and (resseq 1:10 or resseq 12:104 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and ((resid 1 and (name N or name...B1
121(chain B and ((resid 1 and (name N or name...B1 - 212
131(chain B and ((resid 1 and (name N or name...B1 - 212
141(chain B and ((resid 1 and (name N or name...B1 - 212
151(chain B and ((resid 1 and (name N or name...B1 - 212
161(chain B and ((resid 1 and (name N or name...B1 - 212
171(chain B and ((resid 1 and (name N or name...B1 - 212
181(chain B and ((resid 1 and (name N or name...B1 - 212
191(chain B and ((resid 1 and (name N or name...B1 - 212
1101(chain B and ((resid 1 and (name N or name...B1 - 212
1111(chain B and ((resid 1 and (name N or name...B1 - 212
1121(chain B and ((resid 1 and (name N or name...B1 - 212
1131(chain B and ((resid 1 and (name N or name...B1 - 212
211(chain L and ((resid 1 and (name N or name...L1
221(chain L and ((resid 1 and (name N or name...L1 - 214
231(chain L and ((resid 1 and (name N or name...L1 - 214
241(chain L and ((resid 1 and (name N or name...L1 - 214
251(chain L and ((resid 1 and (name N or name...L1 - 214
261(chain L and ((resid 1 and (name N or name...L1 - 214
271(chain L and ((resid 1 and (name N or name...L1 - 214
281(chain L and ((resid 1 and (name N or name...L1 - 214
291(chain L and ((resid 1 and (name N or name...L1 - 214
2101(chain L and ((resid 1 and (name N or name...L1 - 214
2111(chain L and ((resid 1 and (name N or name...L1 - 214
2121(chain L and ((resid 1 and (name N or name...L1 - 214
2131(chain L and ((resid 1 and (name N or name...L1 - 214
112(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 10
122(chain A and (resseq 1:10 or resseq 12:104 or resseq...A12 - 104
132(chain A and (resseq 1:10 or resseq 12:104 or resseq...A106 - 109
142(chain A and (resseq 1:10 or resseq 12:104 or resseq...A110
152(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
162(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
172(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
182(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
192(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
1102(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
1112(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
1122(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
1132(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
1142(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
1152(chain A and (resseq 1:10 or resseq 12:104 or resseq...A1 - 215
212(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 10
222(chain H and (resseq 1:10 or resseq 12:104 or resseq...H12 - 104
232(chain H and (resseq 1:10 or resseq 12:104 or resseq...H106 - 109
242(chain H and (resseq 1:10 or resseq 12:104 or resseq...H110
252(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
262(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
272(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
282(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
292(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
2102(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
2112(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
2122(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
2132(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
2142(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216
2152(chain H and (resseq 1:10 or resseq 12:104 or resseq...H1 - 216

NCS ensembles :
ID
1
2

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Components

#1: Antibody VRC 315 53-1A09 Fab Heavy chain


Mass: 24927.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody VRC 315 53-1A09 Fab Light chain


Mass: 23609.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1170 / 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

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, 0.24 M ammonium acetate 26% (w/v) PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→33.717 Å / Num. obs: 92183 / % possible obs: 98.7 % / Redundancy: 2.5 % / Net I/σ(I): 14.39

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPT
Resolution: 1.762→33.717 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.49
RfactorNum. reflection% reflection
Rfree0.2035 4612 5 %
Rwork0.1773 --
obs0.1786 92155 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.27 Å2 / Biso mean: 30.9047 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 1.762→33.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6761 0 0 1170 7931
Biso mean---35.1 -
Num. residues----891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036938
X-RAY DIFFRACTIONf_angle_d0.6579443
X-RAY DIFFRACTIONf_chiral_restr0.0451064
X-RAY DIFFRACTIONf_plane_restr0.0041211
X-RAY DIFFRACTIONf_dihedral_angle_d14.8664162
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2212X-RAY DIFFRACTION6.456TORSIONAL
12L2212X-RAY DIFFRACTION6.456TORSIONAL
21A2574X-RAY DIFFRACTION6.456TORSIONAL
22H2574X-RAY DIFFRACTION6.456TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.762-1.78210.30371500.27912550270087
1.7821-1.8030.29681490.27992796294595
1.803-1.8250.30141350.262867300298
1.825-1.84810.25341500.24892902305298
1.8481-1.87240.27111460.23892943308999
1.8724-1.89810.25881420.22382903304598
1.8981-1.92520.26141410.21712895303699
1.9252-1.95390.26341750.21512929310499
1.9539-1.98450.21371360.20652910304699
1.9845-2.0170.20691670.20328803047100
2.017-2.05180.20681530.1912960311399
2.0518-2.08910.21321420.19542918306099
2.0891-2.12920.2221710.192929193090100
2.1292-2.17270.21751710.192888305999
2.1727-2.21990.20541540.18522952310699
2.2199-2.27160.2281560.17832927308399
2.2716-2.32840.23391570.17629213078100
2.3284-2.39130.21851370.181529573094100
2.3913-2.46160.2281570.171129303087100
2.4616-2.54110.22131710.177629363107100
2.5411-2.63190.21611530.175329513104100
2.6319-2.73720.22851560.181129413097100
2.7372-2.86170.24351570.178729493106100
2.8617-3.01250.21171510.170829583109100
3.0125-3.20110.17861590.165929663125100
3.2011-3.4480.17131450.163129743119100
3.448-3.79460.15281500.157529873137100
3.7946-4.34270.16481590.147329653124100
4.3427-5.46760.15751700.13682961313199
5.4676-33.72290.19641520.17173008316098
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)
11.0697-0.34960.1721.0878-0.75560.5336-0.03410.2020.31940.1353-0.2356-0.6393-0.3170.3182-0.27260.1991-0.0714-0.07050.27470.14710.389313.871421.70033.4787
22.2995-0.61450.01691.24350.71550.4838-0.04830.17470.36110.2936-0.0956-0.2972-0.2250.0310.02790.1947-0.0324-0.07510.18570.08920.21334.944123.33794.1999
31.0859-0.4036-0.0641.5239-0.25252.6758-0.10280.16270.26740.1368-0.2045-0.4208-0.42260.09510.15850.178-0.0313-0.09310.22050.09790.23039.514318.49085.7109
40.06550.11350.06190.4983-0.01210.1916-0.0929-0.01760.0780.1912-0.0587-0.351-0.13660.1581-0.13510.2471-0.0283-0.30290.14220.03470.330924.49296.543532.3494
55.44293.01710.28973.48292.5183.7919-0.50590.392-0.179-0.42250.4761-0.06420.11670.1476-0.0040.34710.07060.15460.18790.02040.211461.3237-3.935531.8004
60.6035-0.3646-0.42770.24950.41651.3876-0.115-0.0979-0.23480.14210.0920.14510.17120.07030.21620.350.08430.20310.23690.04150.230358.3118-0.187340.4627
70.4537-0.2737-0.44440.46980.44380.9523-0.04160.0282-0.06890.14490.05430.285-0.0308-0.04041.0590.32240.0080.1520.2334-0.00690.227953.92733.991126.5921
81.26890.2126-0.12062.2518-0.9972.20770.02510.2109-0.1076-0.0472-0.0520.45520.1925-0.1883-0.03310.098-0.00850.00850.2739-0.09420.282751.4941-2.86294.3799
90.4685-0.017-0.26190.0294-0.12212.7809-0.0832-0.0204-0.11980.0640.02230.1977-0.1741-0.2380.02620.3240.03750.1660.19980.00690.263544.6619.287435.8209
100.77880.2341-0.00370.22290.0331.49840.02110.0520.06370.0254-0.01160.0462-0.2570.276-0.24140.3466-0.00180.18450.2126-0.00070.203853.14221.912734.6843
110.90040.097-0.60340.30470.07752.6829-0.01730.0329-0.02770.02770.05070.0496-0.12380.10740.00150.26180.04570.18930.21210.02310.235749.043616.585833.1959
122.7261.2162.28740.73391.2252.1601-0.0254-0.0875-0.0497-0.02330.01280.5654-0.4978-0.63110.09890.28810.12510.04880.3162-0.02720.388441.562219.914412.9504
132.35620.59520.33320.1921-0.16161.50190.11960.2938-0.5162-0.0843-0.11030.16460.2791-0.1670.02630.1781-0.0138-0.0240.4317-0.11050.538940.1993-7.63310.0337
141.42170.3090.33570.4318-0.28090.41980.0019-0.1412-0.01290.1274-0.08150.31810.0141-0.4565-0.06310.1732-0.00730.05360.4706-0.07280.503333.89592.05568.7273
152.35491.45971.9966.908-0.34872.2453-0.13060.1813-0.1293-0.09130.0325-0.3372-0.2881-0.01590.09540.19550.03760.07530.2751-0.05480.294647.238714.280710.927
160.8364-0.06570.08820.0356-0.16740.88080.02610.2162-0.0563-0.1431-0.03020.43610.0582-0.4573-0.18430.16840.0036-0.03980.5945-0.10870.586830.9607-1.76942.7156
176.2907-3.60740.24234.2583-0.34192.5188-0.1424-0.2291-0.0770.24060.16790.1879-0.179-0.0919-0.04860.0644-0.01930.01960.1324-0.02230.0762-0.2624-3.06957.4889
180.92060.0025-0.17681.8193-0.10060.57950.06210.2127-0.0147-0.1192-0.1743-0.11020.01080.02680.06070.0670.01590.01090.17610.01490.09462.04783.2384-2.1515
194.552-1.7879-0.84242.88550.75750.6626-0.00080.3035-0.2033-0.2128-0.08380.09650.07820.00210.10040.08670.0140.03050.203-0.01150.0855-0.7666-3.5885-3.8773
200.6561-0.04010.59162.8521-0.45621.43530.10670.1668-0.0008-0.0252-0.0954-0.32150.01710.12510.00140.0595-0.00820.01990.17220.0140.09217.5187-1.15214.0969
210.29840.2606-0.01390.28920.17860.58550.12150.27950.0854-0.4407-0.2587-0.1178-0.13020.03560.00230.28440.04110.01130.31580.06720.1199-0.068715.9849-10.801
220.4768-0.06920.10420.16580.13180.2265-0.0904-0.03120.05190.2747-0.0134-0.1955-0.12650.0578-0.03710.2215-0.0072-0.0660.11440.00310.106510.20450.055724.8308
231.06410.21780.3130.23340.02440.7161-0.1102-0.11390.14140.28850.0289-0.0223-0.1271-0.05420.01420.2030.0102-0.04930.1088-0.00170.104711.14471.114932.2307
243.70921.44241.41934.17494.15044.3319-0.0456-0.38710.09580.4316-0.07420.0056-0.0668-0.44630.24390.31090.0096-0.01630.14470.02530.12285.4718-2.000738.4779
252.48311.2046-0.40842.10071.18971.6796-0.0982-0.4177-0.19880.44910.0291-0.2771-0.012-0.0115-0.17840.4407-0.0026-0.05710.15820.04910.145410.3063-6.040842.0209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 38 )L1 - 38
2X-RAY DIFFRACTION2chain 'L' and (resid 39 through 75 )L39 - 75
3X-RAY DIFFRACTION3chain 'L' and (resid 76 through 102 )L76 - 102
4X-RAY DIFFRACTION4chain 'L' and (resid 103 through 214 )L103 - 214
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 17 )A1 - 17
6X-RAY DIFFRACTION6chain 'A' and (resid 18 through 95 )A18 - 95
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 134 )A96 - 134
8X-RAY DIFFRACTION8chain 'A' and (resid 135 through 215 )A135 - 215
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 38 )B1 - 38
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 75 )B39 - 75
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 102 )B76 - 102
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 113 )B103 - 113
13X-RAY DIFFRACTION13chain 'B' and (resid 114 through 128 )B114 - 128
14X-RAY DIFFRACTION14chain 'B' and (resid 129 through 163 )B129 - 163
15X-RAY DIFFRACTION15chain 'B' and (resid 164 through 174 )B164 - 174
16X-RAY DIFFRACTION16chain 'B' and (resid 175 through 211 )B175 - 211
17X-RAY DIFFRACTION17chain 'H' and (resid 1 through 17 )H1 - 17
18X-RAY DIFFRACTION18chain 'H' and (resid 18 through 63 )H18 - 63
19X-RAY DIFFRACTION19chain 'H' and (resid 64 through 82 )H64 - 82
20X-RAY DIFFRACTION20chain 'H' and (resid 83 through 95 )H83 - 95
21X-RAY DIFFRACTION21chain 'H' and (resid 96 through 100 )H96 - 100
22X-RAY DIFFRACTION22chain 'H' and (resid 101 through 134 )H101 - 134
23X-RAY DIFFRACTION23chain 'H' and (resid 135 through 188 )H135 - 188
24X-RAY DIFFRACTION24chain 'H' and (resid 189 through 203 )H189 - 203
25X-RAY DIFFRACTION25chain 'H' and (resid 204 through 216 )H204 - 216

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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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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