[English] 日本語
Yorodumi
- PDB-6vxs: Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vxs
TitleCrystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / SARS Corona virus / macro domain / ADP-ribose / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / 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, hydrolytic mechanism / 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 / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / copper ion binding / symbiont-mediated activation of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / cysteine-type endopeptidase activity / viral RNA genome replication / DNA clamp loader activity / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / : / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKim, Y. / Jedrzejczak, R. / Maltseva, N. / Endres, M. / Mesecar, A. / Michalska, K. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Iucrj / Year: 2020
Title: Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes.
Authors: Michalska, K. / Kim, Y. / Jedrzejczak, R. / Maltseva, N.I. / Stols, L. / Endres, M. / Joachimiak, A.
History
DepositionFeb 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.plasmid_name / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_related_exp_data_set / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _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.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 2.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.3Oct 14, 2020Group: Source and taxonomy / Structure summary / Category: entity_name_com / entity_src_gen / struct
Item: _entity_name_com.name / _entity_src_gen.plasmid_name / _struct.pdbx_descriptor
Revision 2.4Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_ec / _entity_name_com.name
Revision 2.5Aug 18, 2021Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.6Oct 11, 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: Non-structural protein 3
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4129
Polymers36,5522
Non-polymers8617
Water2,504139
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6754
Polymers18,2761
Non-polymers3993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7375
Polymers18,2761
Non-polymers4614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.391, 37.896, 65.400
Angle α, β, γ (deg.)84.368, 82.110, 90.114
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Non-structural protein 3 / Nsp3 / ADP ribose phosphatase / PL2-PRO / Papain-like protease / Papain-like proteinase / PL-PRO


Mass: 18275.771 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: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5, 30 %(w/v) PEG3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 16545 / % possible obs: 90.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 23.07 Å2 / CC1/2: 0.971 / Net I/σ(I): 8.44
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.76 / Num. unique obs: 820 / CC1/2: 0.804 / % possible all: 91.2

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 2ACF

2acf


Resolution: 2.03→37.71 Å / SU ML: 0.2423 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.5194
RfactorNum. reflection% reflection
Rfree0.2335 770 4.88 %
Rwork0.1864 --
obs0.1886 15779 84.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.57 Å2
Refinement stepCycle: LAST / Resolution: 2.03→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 14 139 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272615
X-RAY DIFFRACTIONf_angle_d0.51343552
X-RAY DIFFRACTIONf_chiral_restr0.04418
X-RAY DIFFRACTIONf_plane_restr0.0029450
X-RAY DIFFRACTIONf_dihedral_angle_d14.35931551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.190.29571340.23632376X-RAY DIFFRACTION67.55
2.19-2.410.26231730.21542906X-RAY DIFFRACTION83.22
2.41-2.750.27581630.20943281X-RAY DIFFRACTION91.94
2.75-3.470.25441550.19043204X-RAY DIFFRACTION90.34
3.47-37.710.17411450.1573242X-RAY DIFFRACTION91.1
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)
12.45323060693-1.139828536771.350370844923.72736709229-0.4650147162233.662236199420.104261593386-0.585908078967-0.04431031373770.205195384468-0.00959405845060.169014134133-0.139483163004-0.293531044829-0.1896796666280.1628573763170.007014031384340.02127844630430.211337883509-0.04816165007750.184938346327-7.613460649373.2221138989611.4161084424
22.546006241210.2150026711531.24167180392.464676138541.771536006073.208245195790.113058001437-0.249912122046-0.4923095023990.3868363423550.04438155549530.05892180699610.3555491397030.163720026821-0.1555540733980.15108052708-0.01855526993080.008437687239570.1487691843060.01594312723710.17523113087-1.21583088996-4.170888266587.87138218908
32.108018598260.51955572523-0.1609488442253.82814419439-0.9761533819912.823744369870.247515667491-0.02646143410610.09154160690670.161621825606-0.2511066232920.1410023753440.1169282369670.3292445051450.08225958766350.107216016777-0.0104702070255-0.01631772386560.1404422427150.0007205264349910.1523513641147.2060987511-10.7482417613-3.58464921684
43.69191339949-1.257200702511.369153857412.89202501876-1.784634003935.25636437407-0.1562170253130.15773149307-0.3431055571710.111032473157-0.1113600042770.1600784791130.476708380474-0.1659836025450.07286545672510.174430060729-0.0128264499880.03625619740090.112680335412-0.05092060405050.239379463911.47398060176-13.981066536-11.7095643436
51.416080040190.0212458459973-0.6436207832271.263532556360.2991026894242.071942074680.08448651312250.1023639323550.0744102979103-0.0298317193151-0.003081476207880.1885193342960.0471375101630.0983572239844-0.2003357398310.121724904688-0.0112372441616-0.04986135543290.1899958897940.01732829389380.183930055151-1.99006736268-7.82590954921-7.01110532707
60.451065066754-0.7594368787960.7681100604922.10927875246-0.4318612226992.677934508450.02975999412820.9597358057510.117247965114-0.02382001847850.177874510950.05848318598760.01341228675190.0580065723189-0.0034117953190.1154683097830.0097263226566-0.008895381050570.2289620440230.0218768629480.2036594097155.254144623691.66224486247-8.7645014906
71.14310968557-0.072070847598-1.127069797052.52497110486-1.414720825222.983483009470.01198787770740.272146676991-0.04907524413410.1246590472990.0430952139105-0.138167739156-0.1401194813080.1000058644-0.05103184994260.1942540552150.0166883512526-0.01085559749280.136619200566-0.02274118780040.119328447923-0.3187897862434.62002778689-3.63645145522
84.139337269171.084930953840.6420515526514.59249682161-0.7474168853774.34653024901-0.02828475605930.308294740603-0.1008563010660.3232975820430.02996928015380.403209457564-0.595024016229-0.247935861184-0.1495669336370.1796217590660.02884364513250.02726054403760.167025987001-0.00633328698780.1315777644210.7242720671812.27321079330.660744275244
91.4697680261.900646707110.8258470077342.821987057710.8636992313973.51839806715-0.127793290894-0.2824976419880.01278708383510.1154113026250.0403766866809-0.0780902878665-0.3862559732020.1485436979060.1152118164380.157745554827-0.02278916469230.03197740112240.138184538576-0.00078076609280.1734160470091.935052518147.586097904779.34293765911
102.78455601025-1.36715850242-1.091940435642.634028831090.7250593790724.861307625130.101578836750.4239966943050.197749042288-0.329896936915-0.155193801555-0.0972431513756-0.122863615193-0.3057746507270.05250057965880.143711127275-0.0167890898459-0.02137863520570.2142227363520.01589728244070.169946834262-18.6311537138-18.8094974183-38.9943067486
112.229010259410.8907183369241.170217037171.848757045631.136779365073.15386785959-0.0421648985602-0.008998331645190.157986354709-0.09041341206560.0209711648519-0.123768062407-0.385891082575-0.0362185287578-0.03488590661740.1359421059790.02465783159930.0002863923674410.124384614774-0.02342677476210.178124983991-10.2963936222-8.22681593083-22.8539528891
121.21565002480.867525485093-0.2546508077320.873907692123-0.05087976954542.091749479840.00211111261653-0.09623129172770.0916618251954-8.4382351366E-50.008214012170880.173923949066-0.112685613245-0.0718125319693-0.09274415248090.1336409994630.0331234977684-0.01111040510760.171341066568-0.01532764324220.226330745289-17.1906078437-12.4979508342-22.9392654895
130.1547529863740.354438218989-0.5291461875073.41547639986-0.4476647976632.6650725886-0.0688468892392-0.45379223268-0.04833444747480.3720809711350.0192367902702-0.4457777754620.04886679219830.2123870310650.1448430837220.147240353675-0.0142116870002-0.01186640977570.2422834617970.0300008988720.165206524011-9.93082659182-22.0962574882-21.1450899631
141.542359571330.4183483805080.8185056616262.30791543468-0.7769887454233.073230662310.086407904672-0.319164661413-0.03176710894550.131411433723-0.0729297347523-0.04036113179920.00554680911656-0.04523743590790.04856510629790.153250849544-0.00636593307945-0.0001376771377690.137893336367-0.03159951366730.108632626331-15.4730024743-25.0442544304-26.1518425282
152.76319945909-2.140211239711.879804333152.97760271648-0.1737918634473.749269134510.0278672810152-0.168170044179-0.254856216853-0.07942239504040.0186842057499-0.06015412316180.514946302345-0.18389332001-0.02199758670070.193944949515-0.00460738815302-0.007984121877240.138303274361-0.01950353885280.174676991443-16.1558438393-28.2442736027-33.1199305828
162.288004923121.945107794812.16794327826.986782473654.008640873792.959622219630.375753503847-0.0772748554419-0.1629806586830.0101629744131-0.131998431882-0.4795343232160.293713205409-0.156093659451-0.02010802641210.3576331729940.0345471449563-0.01308298934840.242775557549-0.01140969197170.199885235002-9.12804780568-31.7813150839-42.1096473126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 105 )
7X-RAY DIFFRACTION7chain 'A' and (resid 106 through 135 )
8X-RAY DIFFRACTION8chain 'A' and (resid 136 through 146 )
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 169 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 72 )
12X-RAY DIFFRACTION12chain 'B' and (resid 73 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 105 )
14X-RAY DIFFRACTION14chain 'B' and (resid 106 through 135 )
15X-RAY DIFFRACTION15chain 'B' and (resid 136 through 157 )
16X-RAY DIFFRACTION16chain 'B' and (resid 158 through 169 )

+
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