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- PDB-7l7r: CCHFV Gc prefusion monomer bound to ADI-36121 and ADI-37801 Fabs -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7l7r
TitleCCHFV Gc prefusion monomer bound to ADI-36121 and ADI-37801 Fabs
Components
  • (ADI-36121 Fab ...) x 2
  • (ADI-37801 Fab ...) x 2
  • Glycoprotein C
KeywordsVIRAL PROTEIN / fusion protein / antibody / Fab complex / class II fusion
Function / homology
Function and homology information


host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc ...Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Crimean-Congo hemorrhagic fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMishra, A.K. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142777 United States
CitationJournal: Science / Year: 2022
Title: Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies.
Authors: Mishra, A.K. / Hellert, J. / Freitas, N. / Guardado-Calvo, P. / Haouz, A. / Fels, J.M. / Maurer, D.P. / Abelson, D.M. / Bornholdt, Z.A. / Walker, L.M. / Chandran, K. / Cosset, F.L. / McLellan, J.S. / Rey, F.A.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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: ADI-36121 Fab light chain
B: ADI-36121 Fab heavy chain
C: ADI-37801 Fab light chain
D: ADI-37801 Fab heavy chain
G: Glycoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,0776
Polymers157,4915
Non-polymers5871
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.200, 95.179, 323.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 4 types, 4 molecules ABCD

#1: Antibody ADI-36121 Fab light chain


Mass: 23416.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody ADI-36121 Fab heavy chain


Mass: 24663.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody ADI-37801 Fab light chain


Mass: 23473.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody ADI-37801 Fab heavy chain


Mass: 25039.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars / Non-polymers , 3 types, 398 molecules G

#5: Protein Glycoprotein C


Mass: 60898.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)
Strain: Nigeria/IbAr10200/1970 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q8JSZ3
#6: 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.: 1
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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium citrate pH 5.6, 2% (v/v) MPD, 13.4% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→43.1 Å / Num. obs: 107701 / % possible obs: 98.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 39.85 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.5
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 5342 / CC1/2: 0.697

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I19, 1HEZ

5i19

1hez


Resolution: 2.1→43.05 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 5453 5.07 %
Rwork0.2187 102079 -
obs0.22 107532 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.32 Å2 / Biso mean: 67.0727 Å2 / Biso min: 30.39 Å2
Refinement stepCycle: final / Resolution: 2.1→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9295 0 39 396 9730
Biso mean--54.13 54.09 -
Num. residues----1207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069556
X-RAY DIFFRACTIONf_angle_d0.81512994
X-RAY DIFFRACTIONf_dihedral_angle_d5.9211311
X-RAY DIFFRACTIONf_chiral_restr0.0491471
X-RAY DIFFRACTIONf_plane_restr0.0071641
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 (%)
2.1-2.120.38261840.336234403624100
2.12-2.150.34891770.338133963573100
2.15-2.180.35851820.31543365354799
2.18-2.20.33271710.30833392356399
2.2-2.230.31471820.30163406358899
2.23-2.260.32521840.29643335351997
2.26-2.290.31511600.29533205336593
2.29-2.330.26571840.28423255343995
2.33-2.370.27431700.276733743544100
2.37-2.40.3271780.28434863664100
2.4-2.450.34751640.267434283592100
2.45-2.490.30991770.266433973574100
2.49-2.540.28561740.270134153589100
2.54-2.590.27991740.25353451362599
2.59-2.650.28351720.25853447361999
2.65-2.710.26141980.25263326352498
2.71-2.770.27651890.26083292348195
2.77-2.850.31441770.26523298347595
2.85-2.930.28381990.251633913590100
2.93-3.030.2442140.2333443365799
3.03-3.140.23721820.22293444362699
3.14-3.260.24872110.22633377358899
3.26-3.410.24861930.21623464365799
3.41-3.590.23651690.20093379354897
3.59-3.820.23521700.19323371354196
3.82-4.110.21181890.18683459364899
4.11-4.520.19091800.16893504368499
4.52-5.180.17411690.15783437360697
5.18-6.520.19262000.19953443364396
6.52-43.050.23671800.20233659383996
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)
11.5725-0.02780.98745.23911.08012.5266-0.0187-0.0133-0.343-0.52990.0940.48870.4309-0.173-0.06330.5967-0.0118-0.11230.25010.03490.4603-3.1681-6.12713.2319
21.38731.6061.03735.70431.3120.66590.04180.33260.0029-1.26250.2041-0.11620.05230.4781-0.26260.75750.011-0.11690.28690.02720.5752-1.3881-12.68499.4544
30.48291.31061.41843.64561.5381.0470.4405-0.2587-0.1362-0.175-0.350.58470.4723-0.6611-0.25870.7901-0.0733-0.14290.28550.04880.6306-6.694-15.051215.309
42.59631.36160.44212.4150.3994.5554-0.222-0.0219-0.03670.16830.0680.6135-0.4138-0.1538-0.06550.43980.0122-0.040.2318-0.02230.6592-11.4039-42.557718.7774
51.70172.02011.03422.67741.42991.02230.16750.00120.80830.6479-0.14531.1532-0.6934-0.7426-0.06930.72730.1630.08250.5234-0.10070.9885-16.5112-38.729225.5016
62.9681-0.82031.42583.1292-0.81014.3667-0.0109-0.0643-0.0173-0.23630.23530.9517-0.1108-0.6511-0.0730.52940.0321-0.07680.3054-0.05720.7439-14.4414-42.128417.7509
71.55020.15820.95767.1969-0.85343.85480.2614-0.2676-0.28540.4129-0.1327-0.37530.51260.2192-0.09040.48270.0075-0.11250.25490.01860.402710.0288-9.975431.2795
80.83770.3272-0.9752.5329-1.48251.47530.1263-0.1101-0.32250.2444-0.2119-0.36710.0724-0.14390.25590.49140.0492-0.09460.25440.05640.56231.2642-41.683823.8582
90.0790.51480.97224.52074.64439.0770.0704-0.01340.3468-0.2969-0.1659-0.7617-1.34240.60.26990.4868-0.1164-0.04040.39660.11520.6037.8641-40.395218.7293
102.53360.65610.18853.4708-0.68066.9597-0.13950.1062-0.1783-0.22440.076-0.4227-0.0740.64030.24270.48890.0202-0.00160.29030.09910.60472.5229-45.328416.465
111.20510.7108-0.48712.6630.62831.5761-0.16351.1315-0.0126-0.48440.3915-0.4811-0.40931.7256-0.26330.6102-0.09770.05421.8388-0.18530.563812.165919.1688-48.5576
121.77322.10510.42373.43271.67211.5512-0.05810.67560.42-0.22650.7592-0.3911-0.76331.1134-0.57510.4859-0.29840.0592.2581-0.06050.715717.696523.0544-46.9268
130.56260.20850.33260.781-1.27152.8448-0.43152.1028-0.9119-1.6868-0.3378-1.39110.32381.9885-1.35550.2599-0.2128-0.33092.0409-0.5089-0.4388.864618.5193-49.0727
140.8842-0.1538-1.88890.3443-0.20124.80560.0523-0.0992-0.0385-0.00510.01120.14320.04580.3956-0.09661.3008-0.1601-0.08123.2124-0.33580.313311.249617.2025-71.995
152.74580.2092-1.34582.2905-0.62521.1546-0.40580.36771.205-0.17090.24240.2389-0.5740.635-0.02071.2391-0.0844-0.14262.0139-0.20070.7921-7.977217.514-80.6182
161.08560.03810.37340.86940.72670.7142-0.35640.2490.6099-0.26280.35640.25520.10190.87550.01011.0726-0.0334-0.11351.6005-0.2341.0293-7.003925.6158-75.1689
170.0220.17880.28931.83382.39544.0477-0.02250.2482-0.5002-0.11960.1436-0.16690.69130.68920.33070.96870.10640.1072.3708-0.44040.49766.39410.974-71.4333
180.82240.89960.28523.1828-1.26353.1715-0.37641.22671.6073-0.42680.79910.5438-0.35840.783-0.08781.4081-0.0573-0.34692.15810.12340.8698-13.610825.5991-83.1484
190.04390.0985-0.05980.5539-0.20770.4592-0.19310.63721.2703-0.63930.2770.02-0.72370.31650.04411.2896-0.2522-0.25782.24710.11541.1598-0.846525.0329-86.7418
202.6090.1338-0.88033.03830.8795.42810.31620.5977-0.6579-0.4161-0.24790.2320.88160.3885-0.00480.58350.0414-0.11180.57-0.24610.6576-10.23057.667-41.4038
213.4345-0.25780.05524.70762.8743.95460.17941.657-0.1926-2.0369-0.2299-0.3596-1.30041.00990.19650.10250.0854-0.11630.7682-0.1690.3901-4.009916.8556-42.8466
223.6415-1.1042-0.1783.49010.31256.00230.12180.6762-0.3351-0.3204-0.01030.3344-0.02980.3829-0.06820.25420.014-0.04830.4575-0.13950.315-6.6115.3959-37.7038
230.48530.25520.23990.8594-0.43941.0112-0.25820.19740.1856-0.42140.00660.07480.3917-0.27860.04580.96420.0522-0.23511.3512-0.25670.6501-14.721610.558-69.7394
241.211.2025-0.71051.0001-0.69470.8267-0.19820.01330.0189-0.61420.2402-0.09080.29950.54590.0041.01060.1355-0.10341.5432-0.30850.6554-9.18327.9669-73.2001
250.87680.229-0.05260.77810.33510.2917-0.10130.4151-0.3607-0.32020.09190.06410.92110.00090.00051.23640.0932-0.1841.6684-0.30720.7472-15.80961.9016-77.2926
260.34760.1432-0.55030.9839-0.0510.9294-0.0645-0.6230.0363-0.4332-0.1627-0.3761-0.35270.95580.20091.4164-0.11080.13381.55890.13690.8871-0.178310.271567.8157
271.46410.4001-0.2261.2032-0.57551.97630.3243-0.9054-0.06770.8513-0.20030.2706-0.5891-0.0503-0.19771.0259-0.12070.14890.78860.07920.41870.20511.249557.5449
280.6699-0.11840.8972-0.2064-0.69374.90720.02650.18-0.04040.0618-0.02720.05240.12870.57910.04810.45070.0185-0.00860.3001-0.0160.37024.357320.7021-3.5512
291.8812-0.3603-0.35311.9919-0.98844.58920.1735-0.9825-0.59880.69930.05450.03470.58060.1469-0.11990.8307-0.03520.0770.8360.18340.52622.91216.426455.8782
302.1833-1.71980.70481.7342-0.25163.1051-0.0265-0.06580.27830.0590.0362-0.0285-0.32550.1381-0.07620.4424-0.02060.0410.23180.00470.37035.922321.887721.2086
313.42490.60692.95561.47161.29822.89660.21371.2083-0.3753-0.40120.1812-0.39310.10691.0157-0.230.67060.00710.03170.463-0.01510.437813.658117.34611.1156
321.328-0.27251.24071.08960.8254.7131-0.18710.01240.1050.0059-0.06750.1454-0.6252-0.24720.18890.48990.0124-0.00430.1890.00630.4508-1.134128.17013.5884
332.11510.4918-0.09832.488-1.42125.94040.2781-0.41280.01120.5695-0.0569-0.0323-0.4909-0.08920.0260.6469-0.05380.03030.41340.0170.34364.64812.616546.7104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 75 )A1 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 90 )A76 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 113 )A91 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 150 )A114 - 150
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 163 )A151 - 163
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 213 )A164 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 106 )B1 - 106
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 145 )B107 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 157 )B146 - 157
10X-RAY DIFFRACTION10chain 'B' and (resid 158 through 215 )B158 - 215
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 61 )C1 - 61
12X-RAY DIFFRACTION12chain 'C' and (resid 62 through 75 )C62 - 75
13X-RAY DIFFRACTION13chain 'C' and (resid 76 through 102 )C76 - 102
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 114 )C103 - 114
15X-RAY DIFFRACTION15chain 'C' and (resid 115 through 144 )C115 - 144
16X-RAY DIFFRACTION16chain 'C' and (resid 145 through 163 )C145 - 163
17X-RAY DIFFRACTION17chain 'C' and (resid 164 through 174 )C164 - 174
18X-RAY DIFFRACTION18chain 'C' and (resid 175 through 197 )C175 - 197
19X-RAY DIFFRACTION19chain 'C' and (resid 198 through 212 )C198 - 212
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 33 )D1 - 33
21X-RAY DIFFRACTION21chain 'D' and (resid 34 through 51 )D34 - 51
22X-RAY DIFFRACTION22chain 'D' and (resid 52 through 103 )D52 - 103
23X-RAY DIFFRACTION23chain 'D' and (resid 104 through 145 )D104 - 145
24X-RAY DIFFRACTION24chain 'D' and (resid 146 through 193 )D146 - 193
25X-RAY DIFFRACTION25chain 'D' and (resid 194 through 214 )D194 - 214
26X-RAY DIFFRACTION26chain 'G' and (resid 1066 through 1098 )G0
27X-RAY DIFFRACTION27chain 'G' and (resid 1099 through 1153 )G0
28X-RAY DIFFRACTION28chain 'G' and (resid 1154 through 1229 )G0
29X-RAY DIFFRACTION29chain 'G' and (resid 1230 through 1276 )G0
30X-RAY DIFFRACTION30chain 'G' and (resid 1277 through 1320 )G0
31X-RAY DIFFRACTION31chain 'G' and (resid 1321 through 1351 )G0
32X-RAY DIFFRACTION32chain 'G' and (resid 1352 through 1390 )G0
33X-RAY DIFFRACTION33chain 'G' and (resid 1391 through 1437 )G0

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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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