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- PDB-5w8t: Crystal structure of MERS-CoV papain-like protease in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5w8t
TitleCrystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain of human ISG15
Components
  • ORF1ab
  • Ubiquitin-like protein ISG15
KeywordsSIGNALING PROTEIN / Hydrolase / papain-like protease / ISG15
Function / homology
Function and homology information


positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / response to type I interferon / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of bone mineralization ...positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / response to type I interferon / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of bone mineralization / RSV-host interactions / positive regulation of interleukin-10 production / 7-methylguanosine mRNA capping / host cell membrane / negative regulation of protein ubiquitination / positive regulation of erythrocyte differentiation / positive regulation of interferon-beta production / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / positive regulation of type II interferon production / Termination of translesion DNA synthesis / response to virus / PKR-mediated signaling / integrin binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / modification-dependent protein catabolic process / ISG15 antiviral mechanism / protein tag activity / cytosolic ribosome / Interferon alpha/beta signaling / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / defense response to virus / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / 5'-3' DNA helicase activity / G-quadruplex RNA binding / symbiont-mediated suppression of host ISG15-protein conjugation / mRNA guanylyltransferase activity / omega peptidase activity / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / defense response to bacterium / lyase activity / RNA helicase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / structural constituent of ribosome / symbiont-mediated suppression of host gene expression / viral translational frameshifting / innate immune response / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / DNA-templated transcription / nucleoplasm / extracellular region / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / : / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Coronavirus replicase NSP2, C-terminal / Helicase, Ruva Protein; domain 3 ...Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / : / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Coronavirus replicase NSP2, C-terminal / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Nonstructural protein 14, betacoronavirus / Ubiquitin domain profile. / Ubiquitin-like domain / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / 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 profile. / (+) RNA virus helicase core domain / Betacoronavirus single-stranded poly(A) binding domain / 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 / 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 (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / 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 / Peptidase family C16 domain profile. / : / : / Coronavirus Nsp3 ectodomain (3Ecto) profile.
Similarity search - Domain/homology
prop-2-en-1-amine / ORF1ab polyprotein / ORF1ab polyprotein / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesHomo sapiens (human)
Human betacoronavirus 2c EMC/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.758 Å
AuthorsDaczkowski, C.M. / Goodwin, O.Y. / Dzimianski, J.V. / Farhat, J.J. / Pegan, S.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109008 United States
United States Department of Agriculture (USDA)58-5030-5-034 United States
CitationJournal: J. Virol. / Year: 2017
Title: Structurally Guided Removal of DeISGylase Biochemical Activity from Papain-Like Protease Originating from Middle East Respiratory Syndrome Coronavirus.
Authors: Daczkowski, C.M. / Goodwin, O.Y. / Dzimianski, J.V. / Farhat, J.J. / Pegan, S.D.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 29, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 2.0Apr 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin-like protein ISG15
A: ORF1ab
D: Ubiquitin-like protein ISG15
C: ORF1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,59018
Polymers89,3754
Non-polymers1,21614
Water55831
1
B: Ubiquitin-like protein ISG15
A: ORF1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,30810
Polymers44,6872
Non-polymers6208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-83 kcal/mol
Surface area18050 Å2
MethodPISA
2
D: Ubiquitin-like protein ISG15
C: ORF1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2838
Polymers44,6872
Non-polymers5956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-103 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.342, 86.342, 223.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 4 molecules BDAC

#1: Protein Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein / hUCRP


Mass: 8870.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: P05161
#2: Protein ORF1ab


Mass: 35817.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Gene: orf1ab / Production host: Escherichia coli (E. coli) / References: UniProt: K0BWD0, UniProt: M4STU1*PLUS

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Non-polymers , 4 types, 45 molecules

#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.66 Å3/Da / Density % sol: 73.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM CaCl2, 100 mM NaO2C2H3 pH 4.6, 28% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.2837 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2837 Å / Relative weight: 1
ReflectionResolution: 2.758→50 Å / Num. obs: 41920 / % possible obs: 99.73 % / Redundancy: 8.5 % / CC1/2: 0.999 / Net I/σ(I): 24.1
Reflection shellResolution: 2.758→2.81 Å / Mean I/σ(I) obs: 1.5 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.758→41.232 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.61
RfactorNum. reflection% reflection
Rfree0.2237 2034 4.86 %
Rwork0.1872 --
obs0.189 41878 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.758→41.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 0 62 31 6293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116398
X-RAY DIFFRACTIONf_angle_d0.7788640
X-RAY DIFFRACTIONf_dihedral_angle_d3.173770
X-RAY DIFFRACTIONf_chiral_restr0.047996
X-RAY DIFFRACTIONf_plane_restr0.0041086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.758-2.8220.39671230.30842636X-RAY DIFFRACTION100
2.822-2.89260.35791340.29672673X-RAY DIFFRACTION100
2.8926-2.97080.32321090.27992680X-RAY DIFFRACTION100
2.9708-3.05820.36231440.27192628X-RAY DIFFRACTION100
3.0582-3.15680.29981040.24282660X-RAY DIFFRACTION100
3.1568-3.26960.27191440.22912655X-RAY DIFFRACTION100
3.2696-3.40050.24751360.22032656X-RAY DIFFRACTION100
3.4005-3.55510.26411390.22262646X-RAY DIFFRACTION100
3.5551-3.74250.27041580.19882663X-RAY DIFFRACTION100
3.7425-3.97680.1971490.17882619X-RAY DIFFRACTION100
3.9768-4.28350.19031520.15672661X-RAY DIFFRACTION100
4.2835-4.7140.16441270.13582674X-RAY DIFFRACTION100
4.714-5.39490.19931540.1492649X-RAY DIFFRACTION100
5.3949-6.79210.19591310.18352671X-RAY DIFFRACTION100
6.7921-41.23650.20261300.17352673X-RAY DIFFRACTION99
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)
12.25592.52212.26117.55463.34012.4606-0.6092-0.47980.9238-0.4509-0.21640.5612-0.7478-1.02730.83050.3837-0.0284-0.00690.96190.04540.6268112.577627.0855157.3406
22.7347-1.50424.95159.8653-4.18549.2164-0.554-1.30930.8770.7963-0.15370.6455-1.3478-1.41430.52510.51640.1935-0.01330.9194-0.06610.7395108.342927.4615164.8909
34.0664-3.24054.92562.6759-4.04816.6282-0.3823-1.03390.54570.91330.30280.7756-0.5032-0.61230.04710.50890.14060.0910.8752-0.04510.9202101.234524.2718157.1598
48.79311.03511.46242.02283.43082.80831.2537-0.9533-0.2150.4553-0.82290.67180.1608-1.1325-0.54530.59150.04110.04221.051-0.10580.6724105.798214.831163.3653
59.92843.96776.34055.93332.08074.0865-0.32370.4129-0.2115-0.07040.0849-0.4406-0.48970.4130.18230.33280.0580.07060.7990.02470.5037107.837319.7979158.4139
65.1024-2.1106-5.18537.93063.07035.3549-0.9027-0.3871-0.73430.33540.09870.61731.1348-0.01130.84950.43390.03390.00690.82340.05590.641769.635515.1811164.1172
77.9144-1.7007-2.82314.9158-2.56983.2179-0.2742.1871-0.8172-0.9704-0.15690.92551.3561-1.25880.19140.6311-0.327-0.04541.173-0.10350.826963.303216.6381156.3924
83.7532-0.4851-2.39387.6758-3.95783.9239-0.06390.8003-0.4997-0.08680.6270.47190.5468-0.0073-0.48190.4171-0.1252-0.08360.7984-0.11830.684860.038821.794165.2236
98.9334-1.53793.73988.3115-2.03728.5957-0.08270.0289-0.5811-0.2196-0.31260.2263-0.8788-0.26490.30140.390.06430.06090.7486-0.05230.605667.707225.5622157.0431
103.9902-3.9919-4.93767.21083.61266.6221-0.6484-1.6049-0.29980.22230.77070.28430.95310.5078-0.10630.5938-0.05420.07540.7540.0590.51458.148222.1495169.7519
115.1999-1.5542-4.57862.89021.95767.3207-0.46630.05950.03680.60990.43330.2370.8457-0.88070.02230.66370.0079-0.03730.67920.1660.55784.05195.9937171.6494
124.07341.4492-0.59742.6273-0.61774.3503-0.08430.8088-0.3077-0.18230.346-0.12390.3581-0.0951-0.25880.47890.1066-0.01560.6483-0.01030.4502104.47427.5334148.9766
133.88381.26844.01453.05872.21677.899-0.26810.3593-0.0274-0.65960.28740.2024-0.6809-0.92660.01090.784-0.1134-0.01810.75820.17420.619838.02235.4873146.0432
143.6567-1.11740.90592.7893-0.81145.0118-0.0851-0.72050.19430.16270.3236-0.015-0.4539-0.4232-0.23410.4654-0.07210.02990.6201-0.00170.425858.99636.7249172.0687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 80 through 92 )
2X-RAY DIFFRACTION2chain 'B' and (resid 93 through 114 )
3X-RAY DIFFRACTION3chain 'B' and (resid 115 through 126 )
4X-RAY DIFFRACTION4chain 'B' and (resid 127 through 136 )
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 156 )
6X-RAY DIFFRACTION6chain 'D' and (resid 80 through 98 )
7X-RAY DIFFRACTION7chain 'D' and (resid 99 through 114 )
8X-RAY DIFFRACTION8chain 'D' and (resid 115 through 131 )
9X-RAY DIFFRACTION9chain 'D' and (resid 132 through 146 )
10X-RAY DIFFRACTION10chain 'D' and (resid 147 through 156 )
11X-RAY DIFFRACTION11chain 'A' and (resid 2 through 142 )
12X-RAY DIFFRACTION12chain 'A' and (resid 143 through 320 )
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 104 )
14X-RAY DIFFRACTION14chain 'C' and (resid 105 through 320 )

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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

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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

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