[English] 日本語
Yorodumi
- PDB-7jz0: Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jz0
TitleCrystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).
Components
  • 2'-O-methyltransferase
  • Non-structural protein 10
  • RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*U)-3')
KeywordsVIRAL PROTEIN/RNA / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / nsp16 / nsp10 / complex / VIRAL PROTEIN / SAH / Cap-1 / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / G-quadruplex RNA binding / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host ISG15-protein conjugation / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / viral transcription / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host TRAF activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / thiol-dependent deubiquitinase / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / : / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 14, betacoronavirus / 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 profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus 2'-O-methyltransferase / Non-structural protein NSP15, middle domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus proofreading exoribonuclease / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP1 superfamily, betacoronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / Lipocalin signature. / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP4, C-terminal / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, C-terminal, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus-like / RNA synthesis protein NSP10, coronavirus / Coronavirus main protease (M-pro) domain profile. / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein 6, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Coronavirus endopeptidase C30 / Non-structural protein NSP8 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal
Similarity search - Domain/homology
FORMIC ACID / RNA / S-ADENOSYL-L-HOMOCYSTEINE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Citation
Journal: Sci.Signal. / Year: 2020
Title: High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.
Authors: Rosas-Lemus, M. / Minasov, G. / Shuvalova, L. / Inniss, N.L. / Kiryukhina, O. / Brunzelle, J. / Satchell, K.J.F.
#1: Journal: Biorxiv / Year: 2020
Title: Structure of SARS-CoV-2 2′- O -methyltransferase heterodimer with RNA Cap analog and sulfates bound reveals new strategies for structure-based inhibitor design
Authors: Rosas-Lemus, M. / Minasov, G. / Shuvalova, L. / Inniss, N. / Kiryukhina, O. / Brunzelle, J. / Satchell, K.J.F.
History
DepositionSep 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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*(A2M)P*UP*U)-3')
F: RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,53931
Polymers101,8006
Non-polymers1,73925
Water7,080393
1
A: 2'-O-methyltransferase
B: Non-structural protein 10
E: RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,80816
Polymers50,9003
Non-polymers90813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2'-O-methyltransferase
D: Non-structural protein 10
F: RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,73115
Polymers50,9003
Non-polymers83112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)167.238, 167.238, 98.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein 2'-O-methyltransferase / NSP16


Mass: 33556.426 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) / Variant (production host): (DE3)magic
References: UniProt: P0DTD1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Non-structural protein 10 / NSP10


Mass: 15004.114 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) / Variant (production host): (DE3)magic / References: UniProt: P0DTD1

-
RNA chain , 1 types, 2 molecules EF

#3: RNA chain RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*U)-3')


Mass: 2339.452 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

-
Non-polymers , 6 types, 418 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein: 4.7mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: Anions (E6), 0.1M Sodium acetate pH 4.6, 0.5M Sodium succinate; Soak: ...Details: Protein: 4.7mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: Anions (E6), 0.1M Sodium acetate pH 4.6, 0.5M Sodium succinate; Soak: 17 hours, 0.2mM [M7Gppp]rArUrUrArArA, 5mM SAM, 5mM Manganese chloride, Cryo: 4M Sodium formate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2020 / Details: BE
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 86204 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.036 / Rrim(I) all: 0.097 / Rsym value: 0.09 / Χ2: 1.387 / Net I/σ(I): 26.6
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.239 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4265 / CC1/2: 0.735 / Rpim(I) all: 0.493 / Rrim(I) all: 1.335 / Rsym value: 1.239 / Χ2: 0.999 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w4h
Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.181 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 4338 5 %RANDOM
Rwork0.1733 ---
obs0.1745 81799 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.9 Å2 / Biso mean: 55.875 Å2 / Biso min: 27.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.65 Å2-0 Å2
2--1.29 Å20 Å2
3----4.19 Å2
Refinement stepCycle: final / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 188 91 398 7173
Biso mean--60.53 56.93 -
Num. residues----850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137087
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176475
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.6529650
X-RAY DIFFRACTIONr_angle_other_deg0.3811.59814954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7885868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.65123.98304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7471521
X-RAY DIFFRACTIONr_chiral_restr0.060.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.028032
X-RAY DIFFRACTIONr_gen_planes_other0.0470.021589
LS refinement shellResolution: 2.152→2.208 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 313 -
Rwork0.271 5927 -
all-6240 -
obs--99.13 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.59020.08120.47011.3564-0.14342.6454-0.04850.1177-0.0275-0.27780.0910.06440.2104-0.1106-0.04250.2599-0.00170.0110.02620.01310.170185.325323.3048-2.5945
21.67560.2868-0.30651.60890.01953.5306-0.0855-0.0564-0.0859-0.03620.1191-0.10650.40670.2186-0.03360.24930.06110.01250.0318-0.01460.170793.576220.53124.3963
32.09050.05421.20351.13110.0923.4623-0.0873-0.02250.2039-0.10690.0849-0.0066-0.19840.04280.00240.20370.03440.01050.02110.020.203189.212532.4162.3019
44.1378-0.9441-0.14355.3363-2.21197.2525-0.14890.4224-0.1952-0.53450.024-0.84540.2711.05870.12490.27340.05050.17330.2766-0.06440.1984107.048321.7456-15.5131
54.57076.5795-2.7349.9281-4.76673.2162-0.13160.1187-0.1877-0.35170.081-0.2090.30910.13560.05070.47180.05340.06190.083-0.0640.235191.06142.7991-9.7133
61.5968-3.54210.13469.537-0.28960.0888-0.1524-0.2145-0.0991-0.20950.25390.25760.0402-0.0282-0.10150.28560.0137-0.0230.19840.01590.260780.797714.55192.6362
70.673-1.48440.144811.47015.33933.99350.0253-0.0514-0.0534-0.032-0.05620.19090.0199-0.05110.03090.097-0.0963-0.00320.20380.02850.329754.99773.0322-13.4608
83.22-0.42530.46073.1947-0.10851.90040.02190.5157-0.3752-0.6219-0.02450.59210.2575-0.3480.00260.3648-0.1132-0.22210.1963-0.02780.23666.431419.6749-17.0999
90.75050.10961.14867.9501-8.050410.29560.1182-0.1562-0.3895-0.63930.1835-0.38140.8108-0.4165-0.30170.49660.0509-0.06920.3792-0.01270.331559.289830.8798-35.9
104.5551-0.0502-2.10992.0951.13213.5691-0.10780.2296-0.4244-0.18210.0715-0.10080.22750.26450.03630.36180.0353-0.02030.0792-0.08070.19689.7874-37.1428-24.8645
111.33930.17830.06221.62280.03642.81480.05180.02020.1306-0.13250.02770.1282-0.3538-0.041-0.07950.33940.03660.00850.00560.00090.226281.5861-20.051-10.7843
121.56060.0863-0.00970.99720.56983.05020.04090.1585-0.0699-0.26250.1282-0.1557-0.18250.5213-0.16910.3407-0.00050.04140.1104-0.04790.209794.0927-25.9767-19.1572
134.03042.93312.43023.08762.26255.15910.2205-0.1285-0.45270.22210.087-0.22630.25130.0823-0.30750.28680.0321-0.00340.0506-0.0030.220385.8137-30.0764-1.0221
141.7389-2.1041.05155.8835-1.1793.5034-0.1547-0.06420.08890.30390.1427-0.3453-0.35580.65880.0120.2296-0.09190.00250.1877-0.05770.198996.9154-16.1248-1.1827
150.32821.8704-0.100310.9485-0.34150.21320.03010.00230.03440.1320.02240.1428-0.03150.0116-0.05240.25610.0278-0.02070.14750.01870.199380.8616-15.745-19.1212
160.1149-0.8523-0.5459.5343.09922.87720.0610.01330.0582-0.11020.2548-0.0939-0.3841-0.1575-0.31580.19850.19620.02520.21770.00360.396152.6699-5.3225-8.755
172.59460.83010.55643.259-0.63453.5970.1839-0.11520.26350.0887-0.06030.6014-0.2147-0.8462-0.12370.24420.07170.0280.2172-0.00470.367263.8794-22.9404-5.155
1811.79692.70985.35594.67421.00255.3567-0.1001-0.89140.54010.631-0.1770.5190.0081-0.21340.27710.48140.12460.11510.1273-0.09930.463165.4854-4.1086-0.343
193.29650.6579-1.51863.9216-0.9136.06570.043-0.32750.4030.32770.10440.8304-0.4303-1.3362-0.14740.19540.12770.13770.4483-0.05590.42357.9942-20.41591.1781
201.7349-5.00064.455414.459-12.874711.47380.0663-0.0375-0.0843-0.08820.13430.28040.0864-0.0961-0.20060.2367-0.01120.05380.23350.03110.272181.794825.623116.4175
214.9206-6.6694-7.177729.925328.089626.61260.06170.2262-0.20890.3118-0.57470.50860.2496-0.57560.5130.3532-0.09420.01040.3822-0.02290.256479.114220.49838.1266
222.483-4.79492.73049.3302-5.31843.03860.3638-0.1518-0.4384-0.90280.16880.83220.5331-0.1115-0.53260.7280.0882-0.00370.56240.16020.567174.90920.22965.2478
2327.35033.861-15.38170.55-2.17138.6508-0.5095-0.2483-0.9775-0.0289-0.0459-0.09980.27960.13330.55530.87610.0293-0.12490.3255-0.06290.837370.967626.98235.1053
240.10860.1115-0.29420.1283-0.31980.82280.0019-0.046-0.0205-0.0609-0.02380.01750.09660.10480.0220.425-0.005-0.10170.20780.02190.266683.5713-26.9649-32.6985
2512.240812.3791-1.271719.734-9.31999.0784-0.902-0.23490.28310.57410.68420.0722-1.5675-0.99770.21780.53490.1776-0.08980.17310.01920.144979.8488-21.5871-24.9956
2610.1411-7.3052-3.11597.12752.51241.00230.0546-0.14920.7252-0.27810.2247-0.6378-0.04670.0511-0.27930.41460.03950.06550.18030.04810.317775.4905-20.9294-22.9497
2712.7896-4.62717.13381.6774-2.58183.98060.2210.3831-0.0637-0.1115-0.16260.04140.13120.2132-0.05840.55650.0179-0.08510.3392-0.09020.325571.1456-27.1592-23.8284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6798 - 6931
2X-RAY DIFFRACTION2A6932 - 7014
3X-RAY DIFFRACTION3A7015 - 7052
4X-RAY DIFFRACTION4A7053 - 7079
5X-RAY DIFFRACTION5A7080 - 7096
6X-RAY DIFFRACTION6A7101
7X-RAY DIFFRACTION7B4264 - 4289
8X-RAY DIFFRACTION8B4290 - 4375
9X-RAY DIFFRACTION9B4376 - 4392
10X-RAY DIFFRACTION10C6799 - 6832
11X-RAY DIFFRACTION11C6833 - 6938
12X-RAY DIFFRACTION12C6939 - 7037
13X-RAY DIFFRACTION13C7038 - 7062
14X-RAY DIFFRACTION14C7063 - 7096
15X-RAY DIFFRACTION15C7101
16X-RAY DIFFRACTION16D4271 - 4286
17X-RAY DIFFRACTION17D4287 - 4332
18X-RAY DIFFRACTION18D4333 - 4342
19X-RAY DIFFRACTION19D4343 - 4385
20X-RAY DIFFRACTION20E0
21X-RAY DIFFRACTION21E1
22X-RAY DIFFRACTION22E2
23X-RAY DIFFRACTION23E3
24X-RAY DIFFRACTION24F0
25X-RAY DIFFRACTION25F1
26X-RAY DIFFRACTION26F2
27X-RAY DIFFRACTION27F3 - 4

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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

Read more