[English] 日本語
Yorodumi
- PDB-6wkq: 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wkq
Title1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer from SARS-CoV-2 in Complex with Sinefungin
Components
  • 2'-O-methyltransferase
  • Non-structural protein 10
KeywordsVIRAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / nsp16 / nsp10 / complex
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 / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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
Vaccinia Virus protein VP39 / 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 / : ...Vaccinia Virus protein VP39 / 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 / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / 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.
Similarity search - Domain/homology
FORMIC ACID / SINEFUNGIN / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: 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.
History
DepositionApr 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Jan 27, 2021Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)99,21229
Polymers97,4054
Non-polymers1,80725
Water11,458636
1
A: 2'-O-methyltransferase
B: Non-structural protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,53713
Polymers48,7032
Non-polymers83411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-33 kcal/mol
Surface area20570 Å2
MethodPISA
2
C: 2'-O-methyltransferase
D: Non-structural protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,67516
Polymers48,7032
Non-polymers97214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-32 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.247, 166.247, 98.139
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 / Non-structural protein 16 / nsp16 / SARS-CoV-2 NSP16


Mass: 33627.504 Da / Num. of mol.: 2 / Fragment: UNP residues 6799-7096
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): magic
References: UniProt: P0DTD1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Non-structural protein 10 / nsp10 / Growth factor-like peptide / GFL / SARS-CoV-2 NSP10


Mass: 15075.190 Da / Num. of mol.: 2 / Fragment: UNP residues 4254-4392
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 (bacteria) / References: UniProt: P0DTD1

-
Non-polymers , 5 types, 661 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 636 / 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: 3.95 Å3/Da / Density % sol: 68.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5.3 mg/mL 1:1 nsp10/nsp16 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen F10 (0.4 M potassium/sodium tartrate), soak and ...Details: 5.3 mg/mL 1:1 nsp10/nsp16 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen F10 (0.4 M potassium/sodium tartrate), soak and cryoprotection: 5 mM SFG, 4 M sodium formate, 3 hrs

-
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: Apr 3, 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: 1.98→30 Å / Num. obs: 108598 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.033 / Rrim(I) all: 0.078 / Rsym value: 0.071 / Χ2: 1.009 / Net I/σ(I): 22.2
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2 / Num. unique obs: 5383 / CC1/2: 0.724 / CC star: 0.916 / Rpim(I) all: 0.384 / Rrim(I) all: 0.874 / Rsym value: 0.784 / Χ2: 1.002 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6W75

6w75


Resolution: 1.98→29.922 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.237 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1799 5357 4.941 %
Rwork0.1623 --
all0.163 --
obs-108429 99.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.283 Å20.141 Å20 Å2
2--0.283 Å20 Å2
3----0.917 Å2
Refinement stepCycle: LAST / Resolution: 1.98→29.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 107 636 7151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136842
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176193
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.6519294
X-RAY DIFFRACTIONr_angle_other_deg0.3471.58614422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4635868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.64123.946299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.057151136
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.441514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.6491521
X-RAY DIFFRACTIONr_chiral_restr0.060.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.027724
X-RAY DIFFRACTIONr_gen_planes_other0.0510.021385
X-RAY DIFFRACTIONr_nbd_refined0.20.21426
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.25921
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23356
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.22446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2591
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.010.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.240
X-RAY DIFFRACTIONr_nbd_other0.2230.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.222
X-RAY DIFFRACTIONr_mcbond_it1.6032.5063430
X-RAY DIFFRACTIONr_mcbond_other1.6032.5073431
X-RAY DIFFRACTIONr_mcangle_it2.6563.744312
X-RAY DIFFRACTIONr_mcangle_other2.6553.7414313
X-RAY DIFFRACTIONr_scbond_it2.342.7853412
X-RAY DIFFRACTIONr_scbond_other2.3272.7663383
X-RAY DIFFRACTIONr_scangle_it3.464.0514982
X-RAY DIFFRACTIONr_scangle_other3.464.0524983
X-RAY DIFFRACTIONr_lrange_it6.90431.158063
X-RAY DIFFRACTIONr_lrange_other6.73530.3537894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.98-2.0310.2543990.25175610.25179600.8630.8581000.215
2.031-2.0870.2584090.22173070.22377160.8750.8911000.186
2.087-2.1470.2384100.20671070.20875170.910.9161000.171
2.147-2.2130.2113290.18369670.18472960.9320.9381000.152
2.213-2.2850.1813260.17167610.17170870.9490.9481000.141
2.285-2.3640.1923060.16165590.16268650.9490.9571000.137
2.364-2.4530.1983410.16462930.16666340.9470.9551000.139
2.453-2.5520.1813200.1660510.16163710.9530.9611000.139
2.552-2.6650.192930.16358340.16461270.9560.9621000.146
2.665-2.7940.1873670.16755300.16858970.9570.9611000.151
2.794-2.9440.1892360.17653320.17755680.9540.9531000.165
2.944-3.120.2172430.18350540.18452970.9390.9521000.176
3.12-3.3330.1852220.16547810.16650030.960.9631000.165
3.333-3.5970.1542330.14744060.14746390.9730.9731000.152
3.597-3.9340.1432020.12941090.12943110.9780.9791000.137
3.934-4.3890.1442080.12737130.12839210.9760.9791000.141
4.389-5.050.1221270.12933340.12934610.9830.981000.149
5.05-6.1410.1781780.16827920.16929700.9710.9731000.188
6.141-8.5080.191410.16922040.17123450.9660.9681000.194
8.508-29.9220.189670.18513780.18514460.9580.96599.93080.23
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)
12.1894-0.27181.34720.3208-0.01584.5154-0.1001-0.08950.2920.04470.017-0.0478-0.24610.08430.08310.1559-0.0124-0.01380.0097-0.01250.094792.766935.39849.8184
21.4012-0.00650.27911.00740.3451.2155-0.01780.0897-0.0672-0.1950.06390.09780.1677-0.0375-0.04610.2251-0.0068-0.02020.03590.00140.047884.037719.3689-6.4362
34.121-0.986-0.76873.25062.50166.88640.1255-0.256-0.42970.6369-0.03290.15130.6081-0.3935-0.09270.2852-0.01560.0340.07290.06320.078187.674615.225415.0498
41.12650.16040.26631.15160.26641.8668-0.04390.00120.0202-0.07590.0959-0.06030.07870.2287-0.0520.14190.01120.00190.0464-0.00690.050294.005725.91850.4711
52.40123.362-0.766.5049-1.19671.4693-0.15190.1455-0.3324-0.36720.1737-0.50420.14140.3226-0.02180.20080.04250.07640.1305-0.05370.0841101.862213.8732-12.2691
60.9457-1.5198-0.12219.76241.11664.07170.1437-0.0645-0.3112-0.4777-0.32910.50240.1035-0.45680.18530.176-0.1182-0.09350.16070.00610.385454.85226.4895-12.1411
72.2211-0.64810.3412.3474-0.15361.5551-0.00270.1299-0.0475-0.34450.06760.36230.1278-0.1809-0.0650.214-0.0357-0.11760.05110.01570.084668.893622.7613-14.8069
83.0262-0.57670.13064.9392-0.56842.4460.05220.4082-0.3803-0.4275-0.02470.33540.2936-0.1305-0.02750.2689-0.0543-0.13160.0771-0.03560.127367.537614.186-17.0976
90.7222-1.79670.55694.9961-2.57443.28180.19330.1278-0.1401-0.5353-0.08020.30350.3904-0.3488-0.1130.3631-0.0685-0.21630.2788-0.0320.149960.678324.9549-31.1207
103.4115-0.0005-0.47321.4770.21541.98510.08560.2728-0.40280.0097-0.0096-0.08550.1990.2772-0.0760.19330.0641-0.00450.0853-0.06580.191.1316-37.6872-24.2507
111.07580.05580.0281.10140.24011.84280.0461-0.00120.07550.0217-0.02150.1018-0.0914-0.0012-0.02460.18010.02230.01980.0121-0.00360.06181.661-20.4131-9.7791
1227.3458-11.2605-12.12819.478422.332425.63490.2661-0.70490.3924-0.4208-0.34210.0555-0.4747-0.43390.0760.24990.12540.04660.24810.07220.050385.1526-16.3385-32.309
130.9432-0.0102-0.00940.64310.38132.07930.02220.108-0.0783-0.02650.0547-0.06190.0360.2672-0.07690.15660.03110.01410.053-0.0150.043391.9935-27.402-15.7519
141.4389-1.64980.94154.8874-0.72512.806-0.0993-0.01210.17190.29250.0988-0.4135-0.110.47870.00050.1104-0.033-0.01330.1238-0.03710.047598.7253-16.6992-0.7316
151.11083.12141.20779.64481.32487.07990.0193-0.03420.40560.1868-0.03921.0966-0.3227-0.34920.01980.15520.1625-0.03590.19270.00620.504953.6705-4.5075-9.9004
162.13480.19430.25253.3991-0.36522.26450.0839-0.18240.14680.1922-0.06550.3582-0.016-0.3722-0.01840.10830.00080.04760.0786-0.02360.10565.0654-23.5545-3.7792
173.1026-0.8978-0.45226.2651-0.49052.74460.0004-0.26840.63090.54680.05920.2845-0.4875-0.1717-0.05960.21410.04110.07670.0438-0.07280.270167.1737-7.0457-2.0365
181.65110.4628-0.73423.4739-1.09334.89210.0705-0.1790.23920.39430.06330.6848-0.2546-0.728-0.13380.13240.04310.130.1861-0.04570.223356.576-19.83072.3673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA6800 - 6827
2X-RAY DIFFRACTION2ALLA6828 - 6931
3X-RAY DIFFRACTION3ALLA6932 - 6948
4X-RAY DIFFRACTION4ALLA6949 - 7059
5X-RAY DIFFRACTION5ALLA7060 - 7096
6X-RAY DIFFRACTION6ALLB4271 - 4289
7X-RAY DIFFRACTION7ALLB4290 - 4332
8X-RAY DIFFRACTION8ALLB4333 - 4362
9X-RAY DIFFRACTION9ALLB4363 - 4392
10X-RAY DIFFRACTION10ALLC6799 - 6827
11X-RAY DIFFRACTION11ALLC6828 - 6931
12X-RAY DIFFRACTION12ALLC6932 - 6939
13X-RAY DIFFRACTION13ALLC6940 - 7058
14X-RAY DIFFRACTION14ALLC7059 - 7096
15X-RAY DIFFRACTION15ALLD4271 - 4289
16X-RAY DIFFRACTION16ALLD4290 - 4328
17X-RAY DIFFRACTION17ALLD4329 - 4348
18X-RAY DIFFRACTION18ALLD4349 - 4386

+
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://pdbjlvh1.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