[English] 日本語
Yorodumi
- PDB-6jpw: Crystal structure of Zika NS2B-NS3 protease with compound 1C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jpw
TitleCrystal structure of Zika NS2B-NS3 protease with compound 1C
Components
  • NS3 protease
  • SER-C0F-GLY-LYS-ARG-LYS
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / Viral protease / Protease inhibitor complex
Function / homology
Function and homology information


symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity ...symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / protein-macromolecule adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...Thrombin, subunit H - #120 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsQuek, J.P.
Funding support Singapore, 3items
OrganizationGrant numberCountry
Other governmentStart up grant Singapore
Other governmentCBRG15May045 Singapore
Other governmentNRF2016NRF-CRP001-063 Singapore
CitationJournal: Org.Lett. / Year: 2019
Title: Biocompatible Macrocyclization between Cysteine and 2-Cyanopyridine Generates Stable Peptide Inhibitors.
Authors: Nitsche, C. / Onagi, H. / Quek, J.P. / Otting, G. / Luo, D. / Huber, T.
History
DepositionMar 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease subunit NS2B
B: NS3 protease
C: Serine protease subunit NS2B
D: NS3 protease
E: Serine protease subunit NS2B
F: NS3 protease
G: Serine protease subunit NS2B
H: NS3 protease
J: SER-C0F-GLY-LYS-ARG-LYS
K: SER-C0F-GLY-LYS-ARG-LYS
L: SER-C0F-GLY-LYS-ARG-LYS


Theoretical massNumber of molelcules
Total (without water)102,17411
Polymers102,17411
Non-polymers00
Water5,459303
1
A: Serine protease subunit NS2B
B: NS3 protease


Theoretical massNumber of molelcules
Total (without water)24,9032
Polymers24,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-27 kcal/mol
Surface area9080 Å2
MethodPISA
2
C: Serine protease subunit NS2B
D: NS3 protease
J: SER-C0F-GLY-LYS-ARG-LYS


Theoretical massNumber of molelcules
Total (without water)25,7573
Polymers25,7573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-28 kcal/mol
Surface area10190 Å2
MethodPISA
3
E: Serine protease subunit NS2B
F: NS3 protease
K: SER-C0F-GLY-LYS-ARG-LYS


Theoretical massNumber of molelcules
Total (without water)25,7573
Polymers25,7573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-27 kcal/mol
Surface area9020 Å2
MethodPISA
4
G: Serine protease subunit NS2B
H: NS3 protease
L: SER-C0F-GLY-LYS-ARG-LYS


Theoretical massNumber of molelcules
Total (without water)25,7573
Polymers25,7573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-29 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.107, 60.473, 215.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Serine protease subunit NS2B / NS2B cofactor


Mass: 5865.384 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Protein
NS3 protease


Mass: 19037.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142IX72, UniProt: Q32ZE1*PLUS
#3: Protein/peptide SER-C0F-GLY-LYS-ARG-LYS


Mass: 854.013 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate Trihydrate pH 4.6, 25% Peg 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.951→46.261 Å / Num. obs: 57894 / % possible obs: 99.41 % / Redundancy: 2 % / Net I/σ(I): 15.69
Reflection shellResolution: 1.951→2.02 Å / Num. unique obs: 5412

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 1.951→46.261 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 1997 3.45 %
Rwork0.1688 --
obs0.1701 57870 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.951→46.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5684 0 177 303 6164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076020
X-RAY DIFFRACTIONf_angle_d0.9528194
X-RAY DIFFRACTIONf_dihedral_angle_d12.7053444
X-RAY DIFFRACTIONf_chiral_restr0.064922
X-RAY DIFFRACTIONf_plane_restr0.0061055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.951-1.99970.27181300.23853616X-RAY DIFFRACTION92
1.9997-2.05380.2381400.18783931X-RAY DIFFRACTION100
2.0538-2.11430.2461440.1763967X-RAY DIFFRACTION100
2.1143-2.18250.22171390.1743961X-RAY DIFFRACTION100
2.1825-2.26050.23291450.16533942X-RAY DIFFRACTION100
2.2605-2.3510.24081450.17313987X-RAY DIFFRACTION100
2.351-2.4580.23681400.17183975X-RAY DIFFRACTION100
2.458-2.58760.22711440.17343999X-RAY DIFFRACTION100
2.5876-2.74970.18341430.16744030X-RAY DIFFRACTION100
2.7497-2.96190.19761440.16273966X-RAY DIFFRACTION100
2.9619-3.25990.17641370.16074033X-RAY DIFFRACTION100
3.2599-3.73150.18321450.15574088X-RAY DIFFRACTION100
3.7315-4.70060.18361440.14624098X-RAY DIFFRACTION100
4.7006-46.27420.21911570.19414280X-RAY DIFFRACTION100
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)
16.0575-0.89861.94498.7609-8.2549.59720.09670.380.58440.5364-0.1542-1.2813-0.65071.4280.12910.2457-0.05860.10630.4631-0.15620.51610.368724.7941-11.3535
29.78433.6257-5.5236.9671-2.46835.0898-0.2746-1.0815-0.41560.40880.2664-0.13340.41030.34740.02440.27760.0849-0.05970.33720.03040.244-0.207511.59910.8326
36.6933-0.03511.84491.3404-0.85437.2528-1.7535-1.16651.07531.80031.0648-0.6714-0.83792.03580.63690.54760.0469-0.07980.6195-0.08670.3695-12.277518.57616.0745
49.579-3.29147.8595.3047-1.50167.0397-0.0396-0.41-0.10770.4193-0.22540.3890.2192-1.26180.22310.20790.05960.02380.3824-0.08990.387-23.5120.3873-4.8275
57.658-0.9347-3.72267.50123.59595.13690.34960.90810.3352-0.6398-0.33350.0117-0.4521-0.86820.00530.35030.1371-0.00830.3989-0.00570.2048-18.570225.5274-19.5491
65.61572.20360.38236.9114-0.84135.3688-0.14860.02440.2886-0.00150.3195-0.7691-0.1240.7144-0.120.1491-0.02970.01390.2873-0.06860.25266.671522.0914-9.2048
76.3386-2.5882-0.70644.10660.81244.65150.15840.30490.2498-0.32910.0826-0.3883-0.19270.3727-0.15240.1902-0.00240.04040.2215-0.04220.18262.472619.1205-19.0999
89.1073-0.6103-7.28581.9112-0.40126.4506-0.38740.2385-0.7557-0.0416-0.05380.3020.4944-0.2720.44370.23460.002-0.03690.2259-0.05910.3397-8.82659.009-11.624
99.60156.6265-1.93454.6233-1.16331.76470.2492-0.11950.15580.7860.10160.08560.05230.0418-0.33050.18690.035-0.01080.2579-0.04580.2288-1.959320.39350.4122
109.2579-3.92264.66914.9408-3.29798.13620.1784-0.2122-0.1568-0.0665-0.03120.29430.3527-0.2296-0.06910.09990.02050.02480.1525-0.03650.1906-15.404617.258-3.9743
114.838-0.41510.1814.9289-0.16594.33120.05580.17-0.0413-0.1215-0.08630.1677-0.0172-0.30710.01430.1191-0.00730.02520.2144-0.04570.1668-11.429918.9532-8.8844
126.5147-1.88691.16435.0137-1.38963.40310.17910.1627-0.7930.37040.3278-0.39450.67840.7126-0.61230.27750.162-0.21750.5679-0.22380.638615.015537.278713.791
137.1904-5.04441.40517.3898-1.90270.7940.1430.05770.6672-0.7792-0.0316-0.6602-0.11770.2956-0.15090.2881-0.08570.10040.38920.01070.26695.312149.2861-0.7146
145.37116.2492-5.25647.2387-6.11155.1809-0.13170.2708-0.847-0.1543-0.3913-0.1798-0.05420.13960.51660.22140.0293-0.01260.4723-0.06010.3144-12.649740.5076-1.2929
153.5387-0.46364.97457.4116-0.00957.15880.2763-1.1429-0.20950.8221-0.0610.32780.3944-1.1921-0.11970.3255-0.08750.06030.4315-0.03890.2348-14.086534.862818.1749
169.90267.7845.74296.11214.54863.9274-0.40110.7946-2.15570.59220.0088-0.99671.55860.28080.44520.5849-0.05430.05130.4875-0.08330.792318.067857.638810.4835
175.3798-2.2272-0.72087.7128-3.17396.1925-0.03690.0572-0.74270.2836-0.0847-1.09550.70461.00680.16340.28670.1126-0.11080.4696-0.11130.509913.749634.437410.7438
185.4582.83561.62583.38144.67099.17020.00180.01640.0866-0.1403-0.0613-0.1157-0.37620.5461-0.02390.1455-0.0236-0.03870.2746-0.03240.18337.469545.195711.4787
196.7871.66310.79183.3669-0.62832.1349-0.038-0.2463-0.4720.78090.2713-0.80180.52530.8821-0.08670.28510.0432-0.15060.3797-0.10340.29458.128940.463717.8443
204.37931.6298-2.60135.4567-0.82226.16260.1142-0.0729-0.1320.39150.0958-0.5237-0.16730.382-0.14090.23180.0026-0.07080.2458-0.06480.19954.068343.837322.2313
216.0252.13385.29892.92610.81296.9582-0.5307-0.07880.68930.0727-0.01180.179-0.9235-0.24650.48190.19270.05020.00590.2619-0.0720.2682-4.679652.008910.5953
225.8953-2.27821.61085.7098-0.81412.01840.1210.43320.0216-0.2244-0.0471-0.55390.10590.1358-0.09750.1426-0.0164-0.00470.3112-0.03090.29913.679740.31150.0551
235.29233.8892-1.80835.4648-2.91618.1763-0.09270.43040.1103-0.05560.13580.4002-0.1619-0.716-0.06520.09950.0043-0.01020.2064-0.06210.215-9.9942.94992.8633
243.60090.79430.31314.6113-0.52823.19710.1475-0.02380.11030.1459-0.17650.14940.0007-0.2888-0.020.1102-0.0023-0.00340.2154-0.06070.1662-5.704242.44757.4231
258.55996.14014.90649.45165.54876.1677-0.020.1201-0.00250.39220.0383-0.07970.3308-0.03770.00370.14750.01540.02250.2077-0.03930.1506-8.764838.91399.2994
264.96533.2356-2.0324.7007-5.45097.3991-1.06320.1912-1.3682-0.2099-0.461-1.98281.80960.49081.61140.68250.131-0.02370.3177-0.00870.66739.021130.777440.392
271.52210.27280.52660.24250.34630.63970.1018-0.6517-0.27421.7717-0.3388-0.061-0.1347-0.0903-0.01191.0938-0.0036-0.05850.41070.04580.2753-1.157744.112556.495
286.22880.4583-2.67662.8863-0.68842.1447-0.06870.35340.6410.47370.6184-0.7786-0.00570.5269-0.38170.4823-0.0309-0.14050.2693-0.02730.37767.964761.397239.4349
292.2073-1.71490.55533.2622-0.61894.8318-0.11620.0135-0.38220.3640.2019-0.3530.29360.312-0.03130.39520.0646-0.09230.2088-0.03870.31646.177234.428443.6064
304.24212.1069-0.36397.0423-2.21765.66030.04340.1136-0.45610.0357-0.0696-0.42180.46410.34750.03450.26830.0593-0.0490.2476-0.0450.22.952639.389834.0335
311.97180.62450.19192.1788-0.39261.92170.0865-0.25050.00721.0354-0.0247-0.0627-0.1574-0.0449-0.06390.58360.0249-0.07260.2395-0.00480.2215-0.417949.259548.8779
325.24911.143-0.978.1901-0.0293.4777-0.03510.00330.12270.82880.0214-0.2805-0.34470.09480.00550.46950.0474-0.1370.2271-0.0540.20983.372752.651245.1595
331.90780.6692-3.63118.48670.38147.98130.21340.4511-0.6553-0.2554-0.1335-0.70952.1849-0.02030.0950.71110.0693-0.05040.3907-0.10150.2676-23.1859-2.162538.0676
343.02022.7448-0.52154.8961-0.6564.58920.355-0.55390.00971.0309-0.2077-0.22430.024-0.072-0.16040.3934-0.0331-0.03340.384-0.03360.2644-29.477215.754.8229
352.5401-0.62691.73922.65532.35524.3169-0.18670.46890.5439-1.04650.25-0.5649-1.01580.5944-0.11320.516-0.18030.03010.4225-0.02170.3654-21.929227.384735.2498
368.2648-0.8594-0.64277.28440.76877.3706-0.00470.3839-0.70810.43330.22520.25011.3888-0.2839-0.17270.5074-0.1107-0.08410.2615-0.00350.2474-28.15440.108642.8227
378.0761-0.0362-0.19043.647-1.03427.07250.12730.253-0.45170.1984-0.0666-0.15250.56320.4175-0.06670.3273-0.0386-0.06440.2198-0.06470.1915-26.23255.464538.6408
388.3045-1.64911.83319.1041-2.01796.52560.36170.312-1.0302-0.02450.0475-0.14611.39160.2081-0.36090.4897-0.0015-0.08750.3487-0.10320.2804-29.54192.562631.2676
392.39760.3217-2.03676.05284.80427.8414-0.03830.00690.07720.1595-0.0280.2370.1886-0.35440.09560.1799-0.0114-0.07080.22650.02160.2023-34.719115.900239.9235
406.9984-5.6357-5.47444.62884.87846.0061-0.3169-0.7043-0.3771.02680.2614-0.22850.34060.17940.06270.402-0.0483-0.07660.2906-0.00640.3178-24.78928.164252.7184
414.11661.1437-1.83062.7114-2.88053.6344-0.0323-0.00670.26740.22660.03440.0304-0.1892-0.06820.02210.4656-0.0555-0.03140.3188-0.06560.2032-28.120522.142551.1113
427.4739-1.1645-0.34587.08212.92493.01040.08330.12840.4703-0.11410.0811-0.2829-0.13390.2193-0.08440.2914-0.0944-0.04370.2485-0.01320.2293-24.550919.647545.2073
436.96263.5324-0.63746.9872-0.52164.04530.04840.0391-0.01950.22070.10040.0208-0.02360.0757-0.14010.288-0.0063-0.05410.2219-0.05480.159-28.877118.569545.7464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 42 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 106 )
10X-RAY DIFFRACTION10chain 'B' and (resid 107 through 118 )
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 170 )
12X-RAY DIFFRACTION12chain 'C' and (resid 50 through 54 )
13X-RAY DIFFRACTION13chain 'C' and (resid 55 through 64 )
14X-RAY DIFFRACTION14chain 'C' and (resid 65 through 74 )
15X-RAY DIFFRACTION15chain 'C' and (resid 75 through 87 )
16X-RAY DIFFRACTION16chain 'D' and (resid 12 through 20 )
17X-RAY DIFFRACTION17chain 'D' and (resid 21 through 34 )
18X-RAY DIFFRACTION18chain 'D' and (resid 35 through 44 )
19X-RAY DIFFRACTION19chain 'D' and (resid 45 through 62 )
20X-RAY DIFFRACTION20chain 'D' and (resid 63 through 79 )
21X-RAY DIFFRACTION21chain 'D' and (resid 80 through 94 )
22X-RAY DIFFRACTION22chain 'D' and (resid 95 through 106 )
23X-RAY DIFFRACTION23chain 'D' and (resid 107 through 118 )
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 155 )
25X-RAY DIFFRACTION25chain 'D' and (resid 156 through 170 )
26X-RAY DIFFRACTION26chain 'E' and (resid 50 through 54 )
27X-RAY DIFFRACTION27chain 'E' and (resid 55 through 69 )
28X-RAY DIFFRACTION28chain 'E' and (resid 70 through 87 )
29X-RAY DIFFRACTION29chain 'F' and (resid 17 through 42 )
30X-RAY DIFFRACTION30chain 'F' and (resid 43 through 79 )
31X-RAY DIFFRACTION31chain 'F' and (resid 80 through 117 )
32X-RAY DIFFRACTION32chain 'F' and (resid 118 through 170 )
33X-RAY DIFFRACTION33chain 'G' and (resid 50 through 54 )
34X-RAY DIFFRACTION34chain 'G' and (resid 55 through 74 )
35X-RAY DIFFRACTION35chain 'G' and (resid 75 through 87 )
36X-RAY DIFFRACTION36chain 'H' and (resid 17 through 28 )
37X-RAY DIFFRACTION37chain 'H' and (resid 29 through 53 )
38X-RAY DIFFRACTION38chain 'H' and (resid 54 through 71 )
39X-RAY DIFFRACTION39chain 'H' and (resid 72 through 94 )
40X-RAY DIFFRACTION40chain 'H' and (resid 95 through 106 )
41X-RAY DIFFRACTION41chain 'H' and (resid 107 through 118 )
42X-RAY DIFFRACTION42chain 'H' and (resid 119 through 137 )
43X-RAY DIFFRACTION43chain 'H' and (resid 138 through 170 )

+
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