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- PDB-7nab: Crystal structure of human neutralizing mAb CV3-25 binding to SAR... -

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Basic information

Entry
Database: PDB / ID: 7nab
TitleCrystal structure of human neutralizing mAb CV3-25 binding to SARS-CoV-2 S MPER peptide 1140-1165
Components
  • CV3-25 Fab Heavy Chain
  • CV3-25 Fab Light Chain
  • Spike protein S2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / human neutralizing mAb / MPER-targeting / SARS-CoV-2 / spike / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Similarity search - Domain/homology
CITRIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, Y. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentStart-up funds from the Uniformed Services University of the Health Sciences United States
Citation
Journal: Cell Rep / Year: 2022
Title: Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern.
Authors: Wenwei Li / Yaozong Chen / Jérémie Prévost / Irfan Ullah / Maolin Lu / Shang Yu Gong / Alexandra Tauzin / Romain Gasser / Dani Vézina / Sai Priya Anand / Guillaume Goyette / Debashree ...Authors: Wenwei Li / Yaozong Chen / Jérémie Prévost / Irfan Ullah / Maolin Lu / Shang Yu Gong / Alexandra Tauzin / Romain Gasser / Dani Vézina / Sai Priya Anand / Guillaume Goyette / Debashree Chaterjee / Shilei Ding / William D Tolbert / Michael W Grunst / Yuxia Bo / Shijian Zhang / Jonathan Richard / Fei Zhou / Rick K Huang / Lothar Esser / Allison Zeher / Marceline Côté / Priti Kumar / Joseph Sodroski / Di Xia / Pradeep D Uchil / Marzena Pazgier / Andrés Finzi / Walther Mothes /
Abstract: Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating ...Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here, we elucidate the structural basis and mode of action for two potent SARS-CoV-2 spike (S)-neutralizing monoclonal antibodies, CV3-1 and CV3-25, which remain effective against emerging variants of concern in vitro and in vivo. CV3-1 binds to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggers potent shedding of the S1 subunit. In contrast, CV3-25 inhibits membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among β-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in the RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.
#1: Journal: bioRxiv / Year: 2021
Title: A protective broadly cross-reactive human antibody defines a conserved site of vulnerability on beta-coronavirus spikes.
Authors: Zhou, P. / Yuan, M. / Song, G. / Beutler, N. / Shaabani, N. / Huang, D. / He, W.T. / Zhu, X. / Callaghan, S. / Yong, P. / Anzanello, F. / Peng, L. / Ricketts, J. / Parren, M. / Garcia, E. / ...Authors: Zhou, P. / Yuan, M. / Song, G. / Beutler, N. / Shaabani, N. / Huang, D. / He, W.T. / Zhu, X. / Callaghan, S. / Yong, P. / Anzanello, F. / Peng, L. / Ricketts, J. / Parren, M. / Garcia, E. / Rawlings, S.A. / Smith, D.M. / Nemazee, D. / Teijaro, J.R. / Rogers, T.F. / Wilson, I.A. / Burton, D.R. / Andrabi, R.
History
DepositionJun 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Jan 19, 2022Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 26, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CV3-25 Fab Heavy Chain
L: CV3-25 Fab Light Chain
A: CV3-25 Fab Heavy Chain
B: CV3-25 Fab Light Chain
D: Spike protein S2
C: Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,89523
Polymers101,3356
Non-polymers56017
Water8,989499
1
H: CV3-25 Fab Heavy Chain
L: CV3-25 Fab Light Chain
C: Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,89713
Polymers50,6673
Non-polymers23010
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-131 kcal/mol
Surface area21010 Å2
MethodPISA
2
A: CV3-25 Fab Heavy Chain
B: CV3-25 Fab Light Chain
D: Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,99810
Polymers50,6673
Non-polymers3307
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-90 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.762, 85.241, 87.067
Angle α, β, γ (deg.)90.000, 114.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 2 molecules DC

#3: Protein/peptide Spike protein S2


Mass: 3094.363 Da / Num. of mol.: 2 / Fragment: SARS-CoV-2 S2 peptide (1140-1165) / Source method: obtained synthetically / Details: GeneScript synthezied peptide
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Antibody , 2 types, 4 molecules HALB

#1: Antibody CV3-25 Fab Heavy Chain


Mass: 24457.557 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 CV3-25 Fab Light Chain


Mass: 23115.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 516 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10mg/mL CV3-25 Fab mixed with 10-fold (molar-ratio) of S2 peptide (1140-1165), 0.1M Na citrate pH 5.6, 20% PEG4000, 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2021
RadiationMonochromator: M1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 57884 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 38.72 Å2 / CC1/2: 0.942 / CC star: 0.985 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.119 / Rrim(I) all: 0.221 / Χ2: 1.113 / Net I/av σ(I): 6.18 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.14-2.2230.4892.3356530.7140.9130.3290.5921.07196.3
2.22-2.313.40.42957460.7560.2770.5131.15898.6
2.31-2.413.40.37458230.8120.2420.4481.13798.6
2.41-2.543.40.32658280.840.210.3891.14799
2.54-2.73.30.27457750.8750.1760.3271.17398.3
2.7-2.93.20.22857030.9040.1480.2731.21996.5
2.9-3.23.50.20958120.9260.1310.2471.13598.9
3.2-3.663.40.1958700.910.1210.2261.10299
3.66-4.613.30.16657440.9350.1090.1990.99297
4.61-103.40.15859300.9470.1010.1881.00198.1

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SABPred model

Resolution: 2.15→38.56 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 2006 3.47 %
Rwork0.1852 55812 -
obs0.187 57818 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.98 Å2 / Biso mean: 45.1477 Å2 / Biso min: 24.91 Å2
Refinement stepCycle: final / Resolution: 2.15→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7022 0 29 499 7550
Biso mean--57.34 46.34 -
Num. residues----920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20.27611080.2462778288667
2.2-2.260.29441490.23314026417598
2.26-2.320.26351420.22184050419298
2.32-2.40.25491420.21794100424299
2.4-2.490.27651520.22764130428299
2.49-2.590.28951570.22464092424999
2.59-2.70.31431450.22454039418498
2.7-2.840.28061360.21413987412396
2.85-3.020.26361490.21214067421699
3.02-3.260.23871440.20034105424999
3.26-3.580.21041480.17494150429899
3.58-4.10.22691340.16764041417597
4.1-5.170.20351490.13664116426598
5.17-38.560.21431510.17244131428297
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)
11.32230.6525-0.8622.5833-0.80424.97310.0696-0.0503-0.09320.29080.0523-0.0035-0.06890.0946-0.06130.30570.0131-0.04150.33730.02020.2886-12.519627.4098-17.1297
20.94090.52060.4951.91781.89111.8733-0.0598-0.031-0.07690.1230.2375-0.4122-0.2950.5102-0.11830.5189-0.006-0.11870.56840.04170.4211-5.879824.8026-10.7961
32.275-0.2826-1.22242.47780.22331.89780.0695-0.08090.21380.2350.11270.11460.04780.2125-0.20040.34050.0389-0.02090.3527-0.01550.3296-9.365328.4355-17.7239
41.534-0.8976-1.1321.88690.4051.25290.0252-0.30880.0110.20610.09680.0041-0.04110.22480.68970.3133-0.0145-0.02240.3765-0.02620.3073-55.9961-12.2891-17.9057
52.6296-0.99111.07752.45581.8323.6858-0.15330.45460.6769-0.935-0.3223-0.9569-0.91050.00190.480.7101-0.0418-0.0260.460.04880.7074-61.611333.7144-19.7286
61.5738-0.7296-1.419920.13554.3584-0.13290.1363-0.21720.05530.00950.3550.3739-0.6540.13350.3042-0.0850.01110.3809-0.03990.3759-66.656822.0591-19.1507
70.8370.6637-0.56722.0698-0.34741.25950.206-0.09770.1228-0.1531-0.0674-0.2504-0.22380.167500.36070.00410.0110.354-0.0240.3503-43.3047-4.411-33.621
83.24861.28031.47911.132.03044.005-0.2495-0.26830.1576-0.72680.05990.22530.1694-0.0682-0.57920.41130.07220.08040.28140.02640.2322-46.487816.6467-35.0141
91.33250.7531-0.72691.6480.07123.18760.0166-0.3526-0.03750.3213-0.0718-0.14170.27160.42280.06570.39880.0076-0.01530.4422-0.00850.3301-51.655626.9132-15.563
101.92380.3041-1.26981.3457-0.58931.97020.1242-0.37530.14340.2486-0.0351-0.04240.13060.3412-0.0450.38840.0063-0.01110.4047-0.00950.4195-50.512428.9182-17.7492
115.6852.1091-1.26273.8689-1.44145.336-0.5270.2455-1.37230.4690.37831.52781.8197-0.65660.40710.7307-0.16210.16890.5529-0.02960.9791-58.1574-35.7107-26.7339
125.8669-1.06081.21694.6139-0.33897.9339-0.1050.89580.3027-0.6712-0.35640.4893-0.3447-0.08660.44790.43510.0285-0.06420.4123-0.05250.4442-50.3308-26.4287-32.1304
136.65180.42160.3153.6693-3.64763.70330.30310.2183-1.42250.84580.28230.3111.049-1.2052-0.18090.9203-0.15950.18890.497-0.13490.6928-15.5099-34.6948-27.5604
148.5681-0.3393-0.99725.09852.6482.92370.5961.3695-0.3134-0.7302-0.44580.2919-0.5409-0.02250.02210.51860.14210.09630.45280.02850.5132-7.9042-26.0738-32.4788
151.1802-0.2534-0.37391.98230.09341.3632-0.02950.0638-0.04120.16690.04340.04550.1319-0.1227-0.04210.2905-0.0063-0.00460.30340.02580.2585-14.9589-12.3467-18.3152
163.1953-1.3180.98232.43362.04794.6106-0.11330.24550.5739-0.7965-0.0789-1.0904-1.26310.4890.05490.6199-0.04510.04670.44670.15940.6636-20.276933.8081-20.5575
171.7291-0.1998-0.50612.4796-0.4631.4603-0.05380.1982-0.04580.14430.07320.52070.0157-0.28230.01410.30380.0141-0.02030.40290.05140.4459-25.535522.3463-20.5172
180.26510.092-0.00530.129-0.0960.0734-0.039-0.30280.1425-0.093-0.0762-0.2725-0.05330.21930.00030.4306-0.00130.03640.3628-0.01390.391.86883.0204-32.3355
190.55440.6369-0.03950.8171-0.28630.64450.06210.0961-0.1573-0.0063-0.05750.0291-0.03430.00280.00010.3360.01040.00740.3045-0.00340.2997-2.8771-6.8759-33.955
200.40820.3757-0.08520.42790.1920.6856-0.0196-0.09240.0581-0.15290.035-0.1997-0.01210.0378-0.00010.32170.0006-0.0070.3026-0.0110.363-0.8711-4.5246-32.5532
213.5203-1.16131.39510.47580.0332.9344-0.0565-0.0760.2695-0.16840.1674-0.1283-0.2418-0.2351-0.30190.2366-0.01920.04360.22230.02940.0802-4.18916.7364-34.6394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 114 through 150 )L114 - 150
2X-RAY DIFFRACTION2chain 'L' and (resid 151 through 163 )L151 - 163
3X-RAY DIFFRACTION3chain 'L' and (resid 164 through 212 )L164 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 119 )A1 - 119
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 134 )A120 - 134
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 214 )A135 - 214
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 101 )B1 - 101
8X-RAY DIFFRACTION8chain 'B' and (resid 102 through 113 )B102 - 113
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 163 )B114 - 163
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 213 )B164 - 213
11X-RAY DIFFRACTION11chain 'D' and (resid 1146 through 1155 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 1156 through 1165 )D0
13X-RAY DIFFRACTION13chain 'C' and (resid 1146 through 1156 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1157 through 1165 )C0
15X-RAY DIFFRACTION15chain 'H' and (resid 1 through 119 )H1 - 119
16X-RAY DIFFRACTION16chain 'H' and (resid 120 through 134 )H120 - 134
17X-RAY DIFFRACTION17chain 'H' and (resid 135 through 214 )H135 - 214
18X-RAY DIFFRACTION18chain 'L' and (resid 1 through 18 )L1 - 18
19X-RAY DIFFRACTION19chain 'L' and (resid 19 through 61 )L19 - 61
20X-RAY DIFFRACTION20chain 'L' and (resid 62 through 101 )L62 - 101
21X-RAY DIFFRACTION21chain 'L' and (resid 102 through 113 )L102 - 113

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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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