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- PDB-9p6p: Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (... -

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Basic information

Entry
Database: PDB / ID: 9p6p
TitleCrystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
Components
  • 2'-O-methyltransferase
  • Non-structural protein 10
  • RNA (5'-D(*(M7G))-R(P*AP*UP*U)-3')
KeywordsTRANSFERASE / Viral Protein / Center for Structural Biology of Infectious Diseases (CSBID) / 2'-O-Methyltransferase / Structural Genomics
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / 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 / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / 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 / (+)RNA virus helicase core domain profile. / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / Betacoronavirus single-stranded poly(A) binding domain / 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 / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-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 replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Shuvalova, L. / Maltseva, N. / Kim, Y. / Kiryukhina, O. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
Authors: Minasov, G. / Shuvalova, L. / Maltseva, N. / Kim, Y. / Kiryukhina, O. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionJun 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2'-O-methyltransferase
B: Non-structural protein 10
C: 2'-O-methyltransferase
D: Non-structural protein 10
E: RNA (5'-D(*(M7G))-R(P*AP*UP*U)-3')
G: RNA (5'-D(*(M7G))-R(P*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,86443
Polymers100,0796
Non-polymers3,78537
Water9,494527
1
A: 2'-O-methyltransferase
B: Non-structural protein 10
E: RNA (5'-D(*(M7G))-R(P*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,65720
Polymers50,0393
Non-polymers1,61817
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2'-O-methyltransferase
D: Non-structural protein 10
G: RNA (5'-D(*(M7G))-R(P*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,20723
Polymers50,0393
Non-polymers2,16720
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.471, 168.471, 99.945
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein 2'-O-methyltransferase / Non-structural protein 16 / nsp16


Mass: 33627.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic
References: UniProt: P0DTD1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Non-structural protein 10 / nsp10 / Growth factor-like peptide / GFL


Mass: 15075.190 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: P0DTD1

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RNA chain , 1 types, 2 molecules EG

#3: RNA chain RNA (5'-D(*(M7G))-R(P*AP*UP*U)-3')


Mass: 1336.800 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 6 types, 564 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 3.8 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: Classics II (B3), 0.5M Magnesium formate, 0.1M HEPES pH 7.5; Soak: 0. ...Details: Protein: 3.8 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: Classics II (B3), 0.5M Magnesium formate, 0.1M HEPES pH 7.5; Soak: 0.5 hours, 0.2mM m7GpppAUU, 5mM SAH, in 2M Lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 117967 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.064 / Rsym value: 0.167 / Χ2: 1.006 / Net I/σ(I): 15.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5809 / CC1/2: 0.43 / CC star: 0.776 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.46 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.422 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 5861 5 %RANDOM
Rwork0.168 ---
obs0.1693 112081 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.3 Å2 / Biso mean: 45.607 Å2 / Biso min: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å2-0 Å2
3----1.54 Å2
Refinement stepCycle: final / Resolution: 1.95→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 182 195 538 7397
Biso mean--71.83 48.14 -
Num. residues----848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156541
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.6489904
X-RAY DIFFRACTIONr_angle_other_deg0.321.58415116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2785878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.23723.916309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.645151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7651522
X-RAY DIFFRACTIONr_chiral_restr0.0590.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.028095
X-RAY DIFFRACTIONr_gen_planes_other0.0480.021602
LS refinement shellResolution: 1.953→2.003 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.282 439 -
Rwork0.28 8092 -
obs--98.75 %
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)
13.1126-0.3390.77930.0858-0.37442.9086-0.1624-0.13930.34920.0855-0.0037-0.0274-0.36860.03770.1660.23240.0143-0.03910.0274-0.02590.123394.17636.21629.2651
20.8705-0.14110.11241.10770.09191.54990.00740.0579-0.0286-0.08190.05490.02370.125-0.0457-0.06230.16490.0271-0.02760.02420.00030.034289.806320.1152-1.7431
31.4531-0.16660.75871.0613-0.04722.4992-0.06250.02650.1542-0.0150.0655-0.093-0.19940.0848-0.0030.1540.0193-0.01650.02050.01020.091393.158831.92592.0364
41.00070.5807-0.31263.7546-1.48362.3934-0.11430.1822-0.0508-0.33360.0807-0.3080.19220.2360.03360.20160.06340.05550.1488-0.04720.0766103.176815.1132-13.4916
50.0546-0.85980.117817.35110.8023.01430.05630.00090.0616-0.4335-0.2527-0.60110.47570.09750.19640.2217-0.0975-0.0290.15190.01760.298560.9044-4.9103-18.218
63.0083-0.2407-0.09532.5096-0.00623.02670.13080.1887-0.2163-0.3675-0.05260.43940.2363-0.5024-0.07820.1874-0.0047-0.13890.18960.02090.140867.456122.2695-14.8255
74.341-0.979-0.41755.83293.714510.15410.29260.1521-0.8439-0.31080.09440.38050.79880.1716-0.3870.3262-0.0675-0.17520.0581-0.0230.23269.92785.8867-16.7757
80.9759-0.45140.29451.7917-1.58153.15330.20730.3752-0.2688-0.46870.00050.40310.3625-0.5238-0.20780.3088-0.0023-0.21760.3328-0.07190.183764.920221.4648-24.3986
94.63870.25-0.6051.14190.36261.79320.0327-0.0212-0.4097-0.1324-0.0039-0.04170.34650.2114-0.02880.29670.0360.01810.0542-0.05860.137592.3271-39.0129-23.5034
100.99960.20870.01440.88220.27781.76350.02210.0365-0.0143-0.13050.0316-0.0111-0.02750.0068-0.05360.1910.00460.01210.0134-0.01720.030488.4218-24.6535-14.5002
115.01430.0137-0.09344.1528-0.41264.3410.1125-0.2363-0.04760.0934-0.0767-0.45060.07980.6095-0.03580.13540.0003-0.02220.1244-0.00680.0529101.7963-26.00534.3547
120.06520.2553-0.04328.8151-8.67749.6001-0.0148-0.00620.0013-0.00460.45330.2598-0.0627-0.476-0.43850.2170.02120.01180.0472-0.01280.096490.8532-3.4351-5.8573
130000000000000000.1116000.111600.1116000
141.68523.5811-0.20049.45672.3194.11170.35050.03720.29120.6878-0.16480.5312-0.1029-0.3355-0.18570.16750.1218-0.03520.1743-0.0420.331955.6447-3.0356-9.2155
152.08861.01380.4393.5775-0.52753.06170.1535-0.15150.18180.1243-0.12860.5230.0499-0.6111-0.0250.067-0.0310.00930.1491-0.03890.096865.0817-23.7281-4.988
162.61121.41760.1937.12360.09965.60330.1533-0.25930.58690.4562-0.13910.4568-0.7555-0.287-0.01420.1970.060.07780.0763-0.06970.221267.6208-7.529-2.9706
171.54230.2213-2.15673.7357-0.62635.20910.13730.07310.22660.3111-0.04060.7924-0.1872-1.0382-0.09670.13360.00940.12020.4292-0.08670.308256.9582-20.78563.0392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 28
2X-RAY DIFFRACTION2A29 - 212
3X-RAY DIFFRACTION3A213 - 253
4X-RAY DIFFRACTION4A254 - 298
5X-RAY DIFFRACTION5B12 - 26
6X-RAY DIFFRACTION6B27 - 73
7X-RAY DIFFRACTION7B74 - 89
8X-RAY DIFFRACTION8B90 - 139
9X-RAY DIFFRACTION9C0 - 28
10X-RAY DIFFRACTION10C29 - 252
11X-RAY DIFFRACTION11C253 - 284
12X-RAY DIFFRACTION12C285 - 297
13X-RAY DIFFRACTION13C301
14X-RAY DIFFRACTION14D17 - 32
15X-RAY DIFFRACTION15D33 - 74
16X-RAY DIFFRACTION16D75 - 95
17X-RAY DIFFRACTION17D96 - 135

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  • 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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