[English] 日本語
Yorodumi
- PDB-7ult: Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer Apo-Form. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ult
TitleCrystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer Apo-Form.
Components
  • 2'-O-methyltransferase
  • Non-structural protein 10
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / SARS-CoV-2 / nsp16/10
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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 / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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 / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / 5'-3' DNA helicase activity / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent 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 / : / : / 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 / Lipocalin signature. / (+) 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 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 / Coronavirus 3Ecto domain profile. / 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
Similarity search - Domain/homology
FORMIC ACID / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer Apo-Form.
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,34933
Polymers97,1214
Non-polymers1,22829
Water13,836768
1
A: 2'-O-methyltransferase
B: Non-structural protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,10515
Polymers48,5612
Non-polymers54513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-46 kcal/mol
Surface area20390 Å2
MethodPISA
2
C: 2'-O-methyltransferase
D: Non-structural protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,24418
Polymers48,5612
Non-polymers68316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-51 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.681, 166.681, 98.550
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) / 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


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) / Strain (production host): BL21(DE3) / References: UniProt: P0DTD1

-
Non-polymers , 4 types, 797 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 768 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 5.3 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 5% Glycerol; Screen: ComPAS (F10), 0.4M Potassium/Sodium tartrate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2021
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 123235 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 35.8 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.041 / Rrim(I) all: 0.137 / Rsym value: 0.13 / Χ2: 1.024 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 10 % / Rmerge(I) obs: 1.403 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5985 / CC1/2: 0.577 / CC star: 0.855 / Rpim(I) all: 0.458 / Rsym value: 1.403 / Χ2: 1.005 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w4h
Resolution: 1.9→29.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.593 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 6205 5 %RANDOM
Rwork0.1644 ---
obs0.1656 117003 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.34 Å2 / Biso mean: 35.067 Å2 / Biso min: 17.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å2-0 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.9→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 63 784 7237
Biso mean--50.33 44.97 -
Num. residues----827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156311
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.649242
X-RAY DIFFRACTIONr_angle_other_deg0.3421.58314565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1415872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.424.013304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.899151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.2251521
X-RAY DIFFRACTIONr_chiral_restr0.060.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.027912
X-RAY DIFFRACTIONr_gen_planes_other0.0480.021566
LS refinement shellResolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 528 -
Rwork0.264 8329 -
all-8857 -
obs--98.33 %
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)
12.4163-0.33391.22230.7605-0.21573.2025-0.1175-0.13350.35040.09240.007-0.0535-0.27780.1230.11050.1599-0.01230.00080.0247-0.01460.104393.15535.73049.7375
21.324-0.01210.51761.44220.26690.9595-0.02390.0282-0.1276-0.13180.07590.05750.1219-0.052-0.05210.1826-0.00780.00110.03680.01080.052584.964619.1836-4.2721
31.12710.21150.02971.32450.61342.0326-0.0479-0.0516-0.07140.00150.1161-0.12450.16020.2245-0.06820.13360.02360.00750.0758-0.00340.074396.665923.67484.0557
41.1404-0.23510.26621.64790.34914.1146-0.15560.00720.2704-0.18250.12410.1217-0.32590.11630.03150.1743-0.0149-0.04620.03090.03260.113982.646235.6609-6.4261
56.2471-0.28691.15434.0472-1.55074.6318-0.02570.3285-0.1128-0.43350.0186-0.76610.03240.61710.00710.2164-0.01040.150.2728-0.05970.1883108.597322.4032-14.9944
61.67643.3732-0.63197.6141-1.95440.8136-0.01760.0819-0.1548-0.13530.1103-0.13570.08630.0462-0.09270.24480.03640.05850.0896-0.03820.10293.94115.2736-10.4125
71.1747-0.9763-2.22998.7731-0.17224.84210.08640.0602-0.1833-0.4087-0.23990.53380.0188-0.1650.15340.1138-0.0882-0.12350.13340.02150.361655.29056.6642-12.3998
82.4032-0.1020.35822.6374-0.09031.485-0.0370.1774-0.0472-0.28150.0810.31020.0099-0.1106-0.0440.1954-0.0396-0.09020.06180.01590.077169.369422.8538-14.9891
94.07894.518-0.645511.3355-0.39870.93930.00550.3474-0.4072-0.6065-0.090.05820.19120.15850.08450.30610.0313-0.08040.1688-0.07450.207571.26487.4011-19.0305
101.56790.3490.05581.6846-0.68663.1467-0.00790.2205-0.1327-0.2940.06280.38490.1993-0.1836-0.05490.236-0.0499-0.14670.08110.00150.157663.239320.4315-19.4115
113.0627-2.08015.07595.9806-1.27179.58730.1885-0.0405-0.0395-0.6725-0.16290.40070.2653-0.1276-0.02560.3233-0.0167-0.21050.183-0.00170.140860.222425.0483-30.7886
1211.91581.05763.498624.377-8.02184.66460.5844-1.3144-0.6751-0.2952-0.5547-0.08640.6211-0.0398-0.02980.29710.1105-0.00690.28080.07530.091161.960337.3926-43.3927
133.9503-0.3098-0.43441.34950.68591.630.02090.24-0.37690.0033-0.0318-0.10030.14950.2770.01090.21060.04510.01060.1179-0.06080.134691.3215-37.9057-24.4052
141.26440.2723-0.07870.91450.20791.44480.02030.03520.103-0.0076-0.00630.0898-0.0915-0.0027-0.01390.15790.0140.0160.02790.00220.070181.8787-20.6062-9.8027
153.0822-3.2093-3.09333.58282.04179.28190.30320.4125-0.0243-0.2904-0.32650.0223-0.7-0.78270.02330.24220.02080.02570.23090.01890.011889.7573-18.6855-32.6911
161.0679-0.0606-0.17710.59370.33491.7688-0.01020.1259-0.0506-0.0710.0672-0.05690.01120.237-0.05710.15440.02170.0210.0833-0.01040.065192.7874-27.8524-17.5732
179.90753.33084.20732.41251.9383.3590.0073-0.0351-0.34450.16970.1663-0.1720.10550.2479-0.17350.12710.02810.01020.0723-0.01550.020892.4717-26.4573.5066
180.8694-1.3980.89395.4281-2.06783.1179-0.0525-0.03990.15550.1556-0.0204-0.3466-0.15560.39020.07290.0758-0.03750.00330.0955-0.02810.039997.6114-16.8024-1.223
190.57442.0023-0.06527.7523-1.25821.39670.0884-0.02480.07550.3976-0.08420.263-0.1598-0.0285-0.00420.09070.05860.00430.059-0.00460.233655.3744-0.93-7.3249
2010.72064.7329-2.74864.2679-0.07514.730.05060.21340.1914-0.2841-0.14890.34380.0994-0.08260.09830.06850.0441-0.04720.08790.03780.162351.4421-11.0705-15.8161
211.68830.23340.21323.029-0.11081.2030.0494-0.11340.16620.0999-0.02120.3781-0.0433-0.2234-0.02820.11570.01230.03880.0694-0.02240.147565.2614-21.9307-4.5716
223.9819-0.4846-0.25869.639-2.37813.2566-0.0441-0.31190.36870.5959-0.03580.3227-0.2626-0.05630.07990.19450.01560.03920.0484-0.09370.241867.6039-5.3815-0.6875
232.12550.4072-1.74072.9066-1.2593.470.0316-0.06930.13170.15170.11690.5497-0.2146-0.3279-0.14850.12490.04030.07490.091-0.03620.222159.5846-18.4879-1.335
248.192.4384-0.55765.1245-2.40829.49610.3858-0.40280.19690.4646-0.10680.6055-0.1606-0.3736-0.2790.18220.00840.16380.1614-0.04150.190253.7054-21.82028.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6799 - 6826
2X-RAY DIFFRACTION2A6827 - 6947
3X-RAY DIFFRACTION3A6948 - 7032
4X-RAY DIFFRACTION4A7033 - 7052
5X-RAY DIFFRACTION5A7053 - 7077
6X-RAY DIFFRACTION6A7078 - 7096
7X-RAY DIFFRACTION7B4271 - 4289
8X-RAY DIFFRACTION8B4290 - 4332
9X-RAY DIFFRACTION9B4333 - 4348
10X-RAY DIFFRACTION10B4349 - 4374
11X-RAY DIFFRACTION11B4375 - 4386
12X-RAY DIFFRACTION12B4387 - 4392
13X-RAY DIFFRACTION13C6799 - 6827
14X-RAY DIFFRACTION14C6828 - 6930
15X-RAY DIFFRACTION15C6931 - 6945
16X-RAY DIFFRACTION16C6946 - 7046
17X-RAY DIFFRACTION17C7047 - 7063
18X-RAY DIFFRACTION18C7064 - 7096
19X-RAY DIFFRACTION19D4271 - 4282
20X-RAY DIFFRACTION20D4283 - 4289
21X-RAY DIFFRACTION21D4290 - 4332
22X-RAY DIFFRACTION22D4333 - 4346
23X-RAY DIFFRACTION23D4347 - 4374
24X-RAY DIFFRACTION24D4375 - 4385

+
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