[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


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / TRAF3-dependent IRF activation pathway / 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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Lipocalin signature. / 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. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus
Similarity search - Domain/homology
FORMIC ACID / 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: 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: 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.
#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
Revision 1.2Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

-
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)103,53731
Polymers101,7986
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)51,80716
Polymers50,8993
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)51,73015
Polymers50,8993
Non-polymers83112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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: 2338.444 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

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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