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- PDB-7kbk: Ricin bound to VHH antibody V6E11 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7kbk
TitleRicin bound to VHH antibody V6E11
Components
  • (Ricin) x 2
  • VHH antibody V6E11
KeywordsTOXIN / ribosome inactivating protein / VHH antibody
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil ...Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca)
Ricinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.091 Å
AuthorsRudolph, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface.
Authors: Rudolph, M.J. / Poon, A.Y. / Kavaliauskiene, S. / Myrann, A.G. / Reynolds-Peterson, C. / Davis, S.A. / Sandvig, K. / Vance, D.J. / Mantis, N.J.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: Ricin
C: VHH antibody V6E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,14217
Polymers73,7063
Non-polymers2,43614
Water11,313628
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-35 kcal/mol
Surface area27220 Å2
Unit cell
Length a, b, c (Å)58.664, 186.583, 234.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21C-341-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Ricin


Mass: 29936.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Catalytic subunit, glycosidase / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase
#2: Protein Ricin


Mass: 28989.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Lectin / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase
#3: Protein VHH antibody V6E11


Mass: 14779.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 3 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 639 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 200 mM sodium chloride 100 mM CHES pH 9.5, and 1.26 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 74803 / % possible obs: 97.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.75 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.04 / Rrim(I) all: 0.09 / Χ2: 0.957 / Net I/σ(I): 7.9 / Num. measured all: 332599
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.09-2.132.80.5232550.7530.350.6320.93886.2
2.13-2.163.20.46436580.8070.2950.5530.94397
2.16-2.213.60.42437490.8380.2540.4970.93798
2.21-2.253.90.37937530.8780.2150.4381.02298.6
2.25-2.33.90.37837190.8990.2130.4370.9998.9
2.3-2.354.10.33437870.9060.1860.3840.9498.5
2.35-2.414.10.29637190.9340.1640.340.93898.8
2.41-2.484.20.27637480.950.1490.3150.92298.8
2.48-2.554.30.24638050.9570.1320.2810.93499
2.55-2.634.30.21837630.9660.1150.2480.93298.8
2.63-2.734.50.1937370.9770.0980.2150.96198.6
2.73-2.844.70.15837610.9820.080.1780.93298.7
2.84-2.974.80.12837450.990.0630.1430.92697.8
2.97-3.1250.09937560.9940.0480.1110.92997.4
3.12-3.325.20.07537330.9960.0350.0830.95497.3
3.32-3.575.30.05737080.9970.0260.0631.00996.8
3.57-3.935.40.04937620.9980.0220.0541.16797
3.93-4.55.30.03838230.9980.0180.0421.0597.9
4.5-5.675.20.03338690.9990.0150.0370.8398.7
5.67-5050.0339530.9990.0140.0330.84996.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AAI

2aai


Resolution: 2.091→21.672 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 3700 4.95 %
Rwork0.1724 71027 -
obs0.1739 74727 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.44 Å2 / Biso mean: 35.5342 Å2 / Biso min: 8.76 Å2
Refinement stepCycle: final / Resolution: 2.091→21.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5028 0 151 628 5807
Biso mean--65.98 43.05 -
Num. residues----643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015344
X-RAY DIFFRACTIONf_angle_d0.9437289
X-RAY DIFFRACTIONf_chiral_restr0.056828
X-RAY DIFFRACTIONf_plane_restr0.006935
X-RAY DIFFRACTIONf_dihedral_angle_d4.3514304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0915-2.1190.26881340.2293247790
2.119-2.1480.28421510.2201262697
2.148-2.17870.24791330.2153271997
2.1787-2.21110.2461410.2114269899
2.2111-2.24570.23831350.1982274299
2.2457-2.28240.25511420.2027274099
2.2824-2.32180.23971550.2003270699
2.3218-2.36390.2221530.1985271498
2.3639-2.40930.22751710.1908270599
2.4093-2.45840.23051300.197276299
2.4584-2.51180.25021420.1996272799
2.5118-2.57020.2751480.2021272699
2.5702-2.63430.25061390.1924278099
2.6343-2.70540.20951430.1905271599
2.7054-2.78490.22171380.1836277699
2.7849-2.87460.18051340.1805271898
2.8746-2.97710.25591240.1879274398
2.9771-3.09590.21581360.1761275097
3.0959-3.23640.19381420.1713270197
3.2364-3.40640.19661330.1612273497
3.4064-3.61890.18791570.1473270797
3.6189-3.89690.18061560.1493272597
3.8969-4.28630.16871440.1365272397
4.2863-4.90030.13421420.1315281498
4.9003-6.15030.19731400.1687283799
6.1503-21.6720.18491370.1792296298
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5975-2.19252.91816.3076-1.01031.7492-0.32480.25890.0029-0.6897-0.3721-1.39030.17250.73310.63390.30020.030.12090.30340.02860.27059.412421.313322.0213
28.3129-5.21386.27387.0281-7.82062.3564-0.3418-0.53720.20560.70280.1831-0.2906-0.7625-0.21080.11750.31650.02990.07060.2563-0.00350.17344.427224.514229.8176
32.4307-0.7582-1.83812.77261.68423.02580.07550.04590.1339-0.34060.0175-0.338-0.27880.1392-0.09530.27650.00620.03990.2050.02820.17081.292428.978319.6849
4-0.1872-0.57620.68233.08710.48745.8161-0.070.06540.0527-0.12860.0215-0.27740.0102-0.02620.06390.27310.00060.10270.19170.02280.2065-1.162821.445810.393
55.25912.68540.15016.1313-1.246.0914-0.05050.2213-0.0303-0.06330.12-0.0699-0.37860.0254-0.06640.29410.00850.08640.1816-0.00120.1340.272922.53214.6512
66.21170.91363.44327.78712.64274.0608-0.1147-0.2562-0.5385-0.18360.10580.54520.1269-0.52420.01140.21-0.00080.09460.20630.01080.2387-12.865310.968719.3915
75.6955-3.1596-1.02474.51633.58046.27190.21370.339-0.3634-0.5046-0.1728-0.37220.31480.3014-0.05360.3630.06440.12470.19560.01730.35262.68477.223815.895
80.1665-0.22050.8150.5252-1.08412.6417-0.1151-0.1402-0.17510.02810.02590.07010.2007-0.06730.07760.23970.04110.06950.24460.03110.2444-5.273414.985327.8599
93.101-3.1768-0.44397.95072.12922.00450.09610.1225-0.0789-0.3413-0.32930.5732-0.4108-0.29260.2280.25670.0963-0.01380.2705-0.01030.173-17.394931.18927.5856
106.23565.4977-3.09877.43060.90146.56870.28-0.17780.08760.3131-0.82630.77170.311-0.40920.55120.17130.0439-0.02370.2632-0.07180.2586-20.669925.364834.8723
113.9767-1.88311.77691.5547-2.42364.72180.12160.3710.2673-0.1105-0.17060.0724-0.581-0.03050.08040.42210.10590.030.2525-0.00010.1916-9.950735.536926.2004
123.7361-1.453-0.41192.94840.64531.96830.26850.47750.1396-0.6229-0.23190.1186-0.29-0.2511-0.09420.29520.0683-0.01480.2385-0.06570.2603-27.069442.365839.3472
133.00920.80182.56657.8545-2.27114.22220.1460.1671-0.4672-0.1457-0.0940.7569-0.0423-0.5276-0.06680.1250.05880.01370.3131-0.07820.3131-36.417343.840546.4162
146.04753.36150.83119.6383-1.32012.24980.04250.39860.0533-0.6791-0.0420.1452-0.1972-0.20020.01770.35090.1503-0.04730.3351-0.05570.1816-29.512649.383935.793
153.1261-1.2972-0.46543.28980.67411.19460.18170.24340.1236-0.333-0.13110.0149-0.2025-0.1183-0.03840.21830.04470.01830.1773-0.0120.1636-22.441251.018246.922
165.8584-6.5213.01377.8796-2.51652.11040.2750.1731-0.7809-0.2245-0.06010.66590.0516-0.2202-0.42370.17280.0099-0.00980.2116-0.04360.2457-12.807922.757546.9328
174.6814-4.7755-0.53545.25771.4541.1953-0.0862-0.17-0.52070.29010.05870.49440.2060.04610.06140.1794-0.02520.010.179-0.00190.232-12.10920.595152.4672
183.25391.922.84676.48942.10014.73080.0648-0.1569-0.02280.1223-0.14720.27770.0654-0.14590.09020.15170.01410.03930.1215-0.00960.1079-10.596430.474657.0897
191.26690.2281-1.25281.2248-0.29224.46440.1159-0.00170.08710.0232-0.05230.0512-0.1327-0.113-0.03560.1714-0.00040.00110.199-0.03730.2039-10.572434.148351.5062
204.5433-5.3880.69372.5303-1.67873.15940.0695-0.32210.33160.1984-0.0877-0.6091-0.18110.01720.10670.1714-0.0278-0.02460.1996-0.04170.2139-1.493233.417351.2604
212.9532-1.712.16813.2722-0.31338.7430.33620.1213-0.1283-0.2272-0.1744-0.26280.29430.2735-0.21150.130.02130.02020.1598-0.02280.2035-0.034426.060649.1135
224.28220.49154.57274.0933-0.39688.58530.0816-0.10140.64660.1039-0.9434-2.3929-0.79630.76890.36950.2484-0.244-0.45220.64170.02630.991625.0095.705754.9985
235.5786-1.3236-0.16623.0097-0.58640.16210.01972.01751.0852-0.8224-0.4929-1.1249-0.85790.96320.25070.45060.08570.17220.90550.29770.833320.10736.59242.2462
249.2192-4.51174.2288.2808-3.27488.16840.0212-0.1288-0.10450.2891-0.0683-0.52610.34290.40540.07360.1169-0.0077-0.00870.20480.00270.247211.11433.843451.588
258.63160.2856-2.04785.4361-2.96622.3017-0.37060.5331.2760.39950.3915-0.9389-0.5182-0.16130.15220.3845-0.0472-0.14570.40260.02720.639815.546611.778753.2694
269.0271-1.93474.05334.4828-1.59513.7197-0.1933-0.13330.15090.4296-0.1046-0.7109-0.08490.41760.2190.1920.0031-0.03580.2350.05040.275614.91741.280153.1743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 17 )A4 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 32 )A18 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 75 )A33 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 97 )A76 - 97
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 122 )A98 - 122
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 140 )A123 - 140
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 160 )A141 - 160
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 201 )A161 - 201
9X-RAY DIFFRACTION9chain 'A' and (resid 202 through 229 )A202 - 229
10X-RAY DIFFRACTION10chain 'A' and (resid 230 through 248 )A230 - 248
11X-RAY DIFFRACTION11chain 'A' and (resid 249 through 261 )A249 - 261
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 26 )B2 - 26
13X-RAY DIFFRACTION13chain 'B' and (resid 27 through 47 )B27 - 47
14X-RAY DIFFRACTION14chain 'B' and (resid 48 through 62 )B48 - 62
15X-RAY DIFFRACTION15chain 'B' and (resid 63 through 134 )B63 - 134
16X-RAY DIFFRACTION16chain 'B' and (resid 135 through 155 )B135 - 155
17X-RAY DIFFRACTION17chain 'B' and (resid 156 through 180 )B156 - 180
18X-RAY DIFFRACTION18chain 'B' and (resid 181 through 202 )B181 - 202
19X-RAY DIFFRACTION19chain 'B' and (resid 203 through 223 )B203 - 223
20X-RAY DIFFRACTION20chain 'B' and (resid 224 through 238 )B224 - 238
21X-RAY DIFFRACTION21chain 'B' and (resid 239 through 262 )B239 - 262
22X-RAY DIFFRACTION22chain 'C' and (resid 2 through 17 )C2 - 17
23X-RAY DIFFRACTION23chain 'C' and (resid 18 through 30 )C18 - 30
24X-RAY DIFFRACTION24chain 'C' and (resid 31 through 60 )C31 - 60
25X-RAY DIFFRACTION25chain 'C' and (resid 61 through 82 )C61 - 82
26X-RAY DIFFRACTION26chain 'C' and (resid 83 through 126 )C83 - 126

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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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