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- PDB-7lgo: Crystal structure of the nucleic acid binding domain (NAB) of Nsp... -

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Basic information

Entry
Database: PDB / ID: 7lgo
TitleCrystal structure of the nucleic acid binding domain (NAB) of Nsp3 from SARS-CoV-2
ComponentsNon-structural protein 3
KeywordsRNA BINDING PROTEIN / VIRAL PROTEIN / SARS-COV-2 / NON-STRUCTURAL PROTEIN / NSP3 / NUCLEIC ACID BINDING DOMAIN / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS INFECTIOUS DISEASES / CSGID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / snRNP Assembly ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / snRNP Assembly / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / 5'-3' DNA helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host ISG15-protein conjugation / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA helicase / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated suppression of host NF-kappaB cascade / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lyase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-terminal / : / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus Nsp3 ectodomain (3Ecto) profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Microbiol Spectr / Year: 2025
Title: Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5' UTR of the viral genome.
Authors: Lemak, S. / Skarina, T. / Patel, D.T. / Stogios, P.J. / Savchenko, A.
History
DepositionJan 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 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 1.2Jul 29, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _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: Non-structural protein 3
B: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)26,5662
Polymers26,5662
Non-polymers00
Water2,558142
1
A: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)13,2831
Polymers13,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)13,2831
Polymers13,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.672, 76.672, 204.146
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-279-

HOH

21B-241-

HOH

31B-244-

HOH

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Components

#1: Protein Non-structural protein 3 / nsp3


Mass: 13283.150 Da / Num. of mol.: 2 / Fragment: nucleic acid binding domain (NAB)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P0DTD1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M ammonium sulfate, 2% hexanediol. Cryoprotectant paratone.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→25 Å / Num. obs: 13937 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.04 / Net I/σ(I): 17.7
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 10 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 666 / CC1/2: 0.633 / Rpim(I) all: 0.386 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K87

2k87


Resolution: 2.45→24.91 Å / SU ML: 0.3412 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.8502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3175 1022 5.03 %RANDOM
Rwork0.2608 19299 --
obs0.2636 12684 81.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.62 Å2
Refinement stepCycle: LAST / Resolution: 2.45→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 142 1954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411872
X-RAY DIFFRACTIONf_angle_d0.83792553
X-RAY DIFFRACTIONf_chiral_restr0.0662273
X-RAY DIFFRACTIONf_plane_restr0.0073326
X-RAY DIFFRACTIONf_dihedral_angle_d16.1104680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.570.4179730.35981262X-RAY DIFFRACTION37.55
2.57-2.730.3956990.35252054X-RAY DIFFRACTION60.53
2.73-2.940.39661400.33882677X-RAY DIFFRACTION78.89
2.94-3.240.33891710.30713209X-RAY DIFFRACTION96
3.24-3.710.34071780.26353359X-RAY DIFFRACTION99.58
3.71-4.670.29211780.21543365X-RAY DIFFRACTION99.77
4.67-24.910.27161830.23043373X-RAY DIFFRACTION99.83
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)
13.86310008082-0.972567160471-0.1473117098130.2451674003080.03689940548180.00513282136736-0.103720351957-0.502119194083-1.33909888474-0.022579919470.0122561750569-0.001700516225631.20445491729-0.2404099796560.08166602285481.01440587428-0.318126470480.01451105692770.3724578304430.08745377955930.498237531591-17.5914516993-15.49851262356.16743025907
21.96143986181.73011241483-0.03879279354542.24828048104-1.154043928711.742011093030.160377145071-0.2082462277430.9852770643660.537238711874-0.02175834994460.671501757536-1.08630383407-0.862482385194-0.3480303149060.4908130636340.2573100563340.0752421722760.1928339858620.03805477781960.317690057858-21.83502343869.298638517058.44624669299
30.3707139042370.1894835421170.304822229080.216603619702-0.1491267270491.025481949410.0680276588448-0.3421746883490.05571819883370.270465974625-0.2841822027970.2245817441520.300885739914-0.5814754249940.161866482870.49229229052-0.352519478370.1355725957660.560824818483-0.2184904780350.259324628968-24.3349136506-0.72018448029123.1999247699
41.93470853585-0.447968973551-1.169038108290.1430553390050.2737558249360.705936085345-0.233265512092-0.1604639939760.09431719526230.2749863317660.2458006984620.08964917992210.16641923654-0.1827925903-0.03730325492620.4955900818390.1190183750240.09734253512431.49227917987-0.200910393680.434943625668-30.03695793479.2343069241720.3951869733
51.184113427390.930895284952-0.8072858518222.15795957473-0.8164567605570.6608704318570.00140584076342-0.142711043352-0.1520582887860.111386293977-0.05734884559790.03541677778570.616259344554-0.546971895241-0.01323831125260.53499941476-0.507709146995-0.02013233428260.214343905430.09806107459560.247449372362-19.8084197512-6.8235578981611.7286322004
61.450067488651.12757316544-0.382749365963.04541236328-0.454590221670.5041708623860.123831217017-0.0955828822115-0.2084464981870.105159246937-0.0561563790882-0.0445262006750.42845759521-0.286039058646-0.09899834368770.360637101925-0.499597151097-0.0583891146443-0.04204977048390.03296611707850.19803886219-16.4931442923-2.0422935299614.870271146
76.60153242842-0.2921555655891.666701172291.99907396108-6.895725644355.628086569961.640509552562.504062509641.359898739-1.67133175486-1.773277999963.8213379843-1.50900895454-2.403068028550.1677464288460.919141770690.6215475807290.1419391635111.16811577412-0.1975633133811.35313845917-26.233192412210.33065697426.74354544192
82.47081207242-0.777957215193-1.796420621080.2445706065820.5647222969661.305189187750.4976975006230.6595055731411.11282723673-0.2958171597010.9028194109251.16597824295-0.353064884887-1.11151439916-1.418515636331.62058138691-0.6803531465820.1817673606871.165235099640.2999539019681.01104811773-39.0282670488-20.008474780422.1054049008
93.327483003642.54701142542-2.359144901022.50549688154-2.021740574071.753919528960.0947319607415-0.80251437333-1.911259801340.868485626619-0.594376849421-0.933282845298-0.01545176876520.3641805985220.4486164473551.48705199207-0.555533944846-0.3678859186720.7109318485920.2429915120221.07834888065-25.6212709919-35.234588614735.1901778239
102.16982172952-1.863328021820.8887911888444.9403607531-0.2222142610560.4518287882080.0825898038421-0.220753346435-0.3317828590670.335022861564-0.05215271540740.2299690958190.009481549003440.0363613856533-0.03881289481011.15092576693-0.420704654923-0.189623766620.490179483220.1884968619680.744823911076-16.6383569152-22.267100105925.0831613541
113.493393709821.57633928544-1.314733721982.87896932347-1.041517901930.6468580313230.281999629606-0.455158658956-1.088268232771.04446802038-0.278271911895-0.6280592789080.56749730624-0.006633069410910.09997072829781.13046300368-0.550404200094-0.2631035662320.4937511409960.1021602945630.780978831207-14.5711426843-25.033128993831.8819995435
120.2476966685930.146780657086-0.01160738820740.4576338876510.08562800670130.1654836415910.0692088584347-0.133956598087-0.09637655971330.126016006779-0.04920747924770.02653875764830.0898217901197-0.1194278883180.004220803176991.31443770449-1.20036020736-3.84181797171E-50.344573934344-0.00847783571620.378522890461-29.2172260049-21.017715268827.5538191736
133.168433839582.4675396184-2.245164291973.86832096746-2.943165958992.65528762684-0.206341389454-0.0697565577328-0.500142968465-0.038056140629-0.010702076676-0.09113190350280.36258700159-0.03334747922420.1955567728941.44672646324-0.670606627691-0.1526472387860.7668824246790.208218945520.614207590698-26.715855605-27.846891126836.4272189302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 38 )
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 47 )
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 79 )
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 107 )
7X-RAY DIFFRACTION7chain 'A' and (resid 108 through 113 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 10 )
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 22 )
10X-RAY DIFFRACTION10chain 'B' and (resid 23 through 28 )
11X-RAY DIFFRACTION11chain 'B' and (resid 29 through 47 )
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 96 )
13X-RAY DIFFRACTION13chain 'B' and (resid 97 through 110 )

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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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