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- PDB-6z6i: SARS-CoV-2 Macrodomain in complex with ADP-HPD -

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Basic information

Entry
Database: PDB / ID: 6z6i
TitleSARS-CoV-2 Macrodomain in complex with ADP-HPD
ComponentsReplicase polyprotein 1ab
KeywordsVIRAL PROTEIN / Viral Macrodomain / ADP-ribose binding module / ADP-ribosylhydrolase / ADP-ribosylation / ADP-HPD
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Lipocalin signature. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus
Similarity search - Domain/homology
Chem-A1R / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZorzini, V. / Rack, J. / Ahel, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101794 and 210634 United Kingdom
CitationJournal: Open Biology / Year: 2020
Title: Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.
Authors: Rack, J.G.M. / Zorzini, V. / Zhu, Z. / Schuller, M. / Ahel, D. / Ahel, I.
History
DepositionMay 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1ab
B: Replicase polyprotein 1ab
C: Replicase polyprotein 1ab
D: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,85238
Polymers75,9154
Non-polymers4,93834
Water15,943885
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A: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3889
Polymers18,9791
Non-polymers1,4098
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9076
Polymers18,9791
Non-polymers9295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,52612
Polymers18,9791
Non-polymers1,54711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,03111
Polymers18,9791
Non-polymers1,05310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.816, 83.096, 84.363
Angle α, β, γ (deg.)90.000, 94.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 208 through 215 or resid 217...
21(chain B and (resid 208 through 215 or resid 217...
31(chain C and (resid 208 through 215 or resid 217...
41(chain D and (resid 208 through 215 or resid 217...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYS(chain A and (resid 208 through 215 or resid 217...AA208 - 2155 - 12
12THRTHRASPASP(chain A and (resid 208 through 215 or resid 217...AA217 - 21814 - 15
13VALVALLYSLYS(chain A and (resid 208 through 215 or resid 217...AA220 - 25917 - 56
14GLYGLYGLYGLY(chain A and (resid 208 through 215 or resid 217...AA307104
15VALVALGLUGLU(chain A and (resid 208 through 215 or resid 217...AA207 - 3784 - 175
16VALVALGLUGLU(chain A and (resid 208 through 215 or resid 217...AA207 - 3784 - 175
17VALVALGLUGLU(chain A and (resid 208 through 215 or resid 217...AA207 - 3784 - 175
18VALVALGLUGLU(chain A and (resid 208 through 215 or resid 217...AA207 - 3784 - 175
19VALVALGLUGLU(chain A and (resid 208 through 215 or resid 217...AA207 - 3784 - 175
21ASNASNLYSLYS(chain B and (resid 208 through 215 or resid 217...BB208 - 2155 - 12
22THRTHRASPASP(chain B and (resid 208 through 215 or resid 217...BB217 - 21814 - 15
23VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB220 - 23217 - 29
24VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
25VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
26VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
27VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
28VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
29VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
210VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
211VALVALLYSLYS(chain B and (resid 208 through 215 or resid 217...BB207 - 3794 - 176
31ASNASNLYSLYS(chain C and (resid 208 through 215 or resid 217...CC208 - 2155 - 12
32THRTHRASPASP(chain C and (resid 208 through 215 or resid 217...CC217 - 21814 - 15
33VALVALLYSLYS(chain C and (resid 208 through 215 or resid 217...CC220 - 23217 - 29
34GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
35GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
36GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
37GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
38GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
39GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
310GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
311GLUGLULYSLYS(chain C and (resid 208 through 215 or resid 217...CC206 - 3793 - 176
41ASNASNLYSLYS(chain D and (resid 208 through 215 or resid 217...DD208 - 2155 - 12
42THRTHRASPASP(chain D and (resid 208 through 215 or resid 217...DD217 - 21814 - 15
43VALVALLYSLYS(chain D and (resid 208 through 215 or resid 217...DD220 - 23217 - 29
44LYSLYSLYSLYS(chain D and (resid 208 through 215 or resid 217...DD23330
45GLUGLUGLUGLU(chain D and (resid 208 through 215 or resid 217...DD206 - 3783 - 175
46GLUGLUGLUGLU(chain D and (resid 208 through 215 or resid 217...DD206 - 3783 - 175
47GLUGLUGLUGLU(chain D and (resid 208 through 215 or resid 217...DD206 - 3783 - 175
48GLUGLUGLUGLU(chain D and (resid 208 through 215 or resid 217...DD206 - 3783 - 175
49GLUGLUGLUGLU(chain D and (resid 208 through 215 or resid 217...DD206 - 3783 - 175
410GLUGLUGLUGLU(chain D and (resid 208 through 215 or resid 217...DD206 - 3783 - 175
411GLUGLUGLUGLU(chain D and (resid 208 through 215 or resid 217...DD206 - 3783 - 175

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Replicase polyprotein 1ab / pp1ab / ORF1ab polyprotein


Mass: 18978.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 6 types, 919 molecules

#2: Chemical
ChemComp-A1R / 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE


Mass: 542.332 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H24N6O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 885 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.9 M DL-Malic Acid 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 24, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2→83.1 Å / Num. obs: 55826 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.176 / Rrim(I) all: 0.348 / Net I/σ(I): 2.6 / Num. measured all: 208136 / Scaling rejects: 681
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.053.71.4621505540770.5330.8681.7060.899.4
8.94-83.13.80.06925226680.9940.040.086.199.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z5T

6z5t


Resolution: 2→59.631 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 2847 5.14 %
Rwork0.2289 52569 -
obs0.2315 55416 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.82 Å2 / Biso mean: 25.9534 Å2 / Biso min: 4.75 Å2
Refinement stepCycle: final / Resolution: 2→59.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 314 896 6339
Biso mean--28.48 32.3 -
Num. residues----692
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2760X-RAY DIFFRACTION5.321TORSIONAL
12B2760X-RAY DIFFRACTION5.321TORSIONAL
13C2760X-RAY DIFFRACTION5.321TORSIONAL
14D2760X-RAY DIFFRACTION5.321TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03450.37321500.33822590100
2.0345-2.07150.36221580.3144260399
2.0715-2.11130.35551510.29642618100
2.1113-2.15440.32541630.2803258799
2.1544-2.20130.32261620.2643259099
2.2013-2.25250.33141710.2633256699
2.2525-2.30880.30971460.2524262999
2.3088-2.37130.3311240.24322658100
2.3713-2.4410.26971290.256262499
2.441-2.51980.33081390.25352604100
2.5198-2.60990.30821490.2477262799
2.6099-2.71440.27831270.22972645100
2.7144-2.83790.31051020.2362658100
2.8379-2.98750.29181260.22652653100
2.9875-3.17470.30291510.22272623100
3.1747-3.41980.23291230.19232657100
3.4198-3.76390.24971410.18572651100
3.7639-4.30840.22181670.17622630100
4.3084-5.42760.19991290.18172681100
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)
11.4205-1.1444-0.21431.6796-0.74681.74970.00340.06920.0460.1312-0.0245-0.0059-0.06590.08730.00850.2588-0.0203-0.10330.2153-0.0130.41611.1345-10.6453.8655
21.5980.0322-0.56811.4933-0.48352.53870.03330.01610.1034-0.09-0.05350.0640.05510.01960.01860.24670.004-0.11030.212-0.00510.444230.864-5.0314-3.6236
30.25940.11140.03950.0746-0.0150.12260.0233-0.0080.03560.04910.0052-0.0145-0.04150.02760.07120.0394-0.0286-0.10990.056-0.01120.32544.549815.0983-38.4221
40.1739-0.01890.01630.1197-0.01310.02280.00570.0402-0.0254-0.077-0.00610.00510.01230.011-0.01040.0694-0.0355-0.06660.0251-0.00160.377634.355320.0412-45.5771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A207 - 378
2X-RAY DIFFRACTION2chain 'B'B207 - 379
3X-RAY DIFFRACTION3chain 'C'C206 - 379
4X-RAY DIFFRACTION4chain 'D'D206 - 378

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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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