[English] 日本語
Yorodumi
- PDB-5zmq: Crystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zmq
TitleCrystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-Arg-COOH inhibitor
Components
  • Serine protease NS3
  • Serine protease subunit NS2B
  • peptide PAC-DLY-DLY-DAR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Viral protease / Serine protease / non-structural protein 3 / Zika protease / VIRAL PROTEIN / HYDROLASE-HYDROLASE 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 / protein-macromolecule adaptor activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / viral envelope / lipid binding / symbiont entry into host cell / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 / Trypsin-like serine proteases / 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 / 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
N2-(phenylacetyl)-D-lysyl-D-lysyl-D-arginine / polypeptide(D) / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.987 Å
AuthorsPhoo, W.W. / Wirawan, M.
Funding support Singapore, Germany, 5items
OrganizationGrant numberCountry
start up grant Singapore
CBRG15May045 Singapore
NRF2016NRF-CRP001-063 Singapore
Ministry of Education (Singapore)MOE2016-T2-2-097 Singapore
DZIF-TTU 01.902 Germany
CitationJournal: Antiviral Res. / Year: 2018
Title: Structures of Zika virus NS2B-NS3 protease in complex with peptidomimetic inhibitors.
Authors: Phoo, W.W. / Zhang, Z. / Wirawan, M. / Chew, E.J.C. / Chew, A.B.L. / Kouretova, J. / Steinmetzer, T. / Luo, D.
History
DepositionApr 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease subunit NS2B
B: Serine protease NS3
C: Serine protease subunit NS2B
D: Serine protease NS3
E: Serine protease subunit NS2B
F: Serine protease NS3
G: Serine protease subunit NS2B
H: Serine protease NS3
I: peptide PAC-DLY-DLY-DAR
K: peptide PAC-DLY-DLY-DAR


Theoretical massNumber of molelcules
Total (without water)100,64710
Polymers100,64710
Non-polymers00
Water8,989499
1
A: Serine protease subunit NS2B
B: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)24,8872
Polymers24,8872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-26 kcal/mol
Surface area8950 Å2
MethodPISA
2
C: Serine protease subunit NS2B
D: Serine protease NS3
I: peptide PAC-DLY-DLY-DAR


Theoretical massNumber of molelcules
Total (without water)25,4373
Polymers25,4373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-22 kcal/mol
Surface area9090 Å2
MethodPISA
3
E: Serine protease subunit NS2B
F: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)24,8872
Polymers24,8872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-27 kcal/mol
Surface area8860 Å2
MethodPISA
4
G: Serine protease subunit NS2B
H: Serine protease NS3
K: peptide PAC-DLY-DLY-DAR


Theoretical massNumber of molelcules
Total (without water)25,4373
Polymers25,4373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-20 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.150, 60.330, 214.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe authors states the assemblies are heterodimers.

-
Components

#1: Protein
Serine protease subunit NS2B


Mass: 5865.384 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Protein
Serine protease NS3


Mass: 19021.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: H8XX12, UniProt: Q32ZE1*PLUS
#3: Polypeptide(D) peptide PAC-DLY-DLY-DAR


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 549.687 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: N2-(phenylacetyl)-D-lysyl-D-lysyl-D-arginine
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.987→60.33 Å / Num. obs: 53862 / % possible obs: 98.4 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.066 / Rrim(I) all: 0.117 / Net I/σ(I): 10.3
Reflection shellResolution: 1.987→2.04 Å / Redundancy: 5 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3829 / CC1/2: 0.796 / Rpim(I) all: 0.231 / Rrim(I) all: 0.541 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 1.987→57.907 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 2649 4.93 %Random selection
Rwork0.1705 ---
obs0.175 53779 98.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.987→57.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 0 499 6187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035795
X-RAY DIFFRACTIONf_angle_d0.6857867
X-RAY DIFFRACTIONf_dihedral_angle_d11.9982007
X-RAY DIFFRACTIONf_chiral_restr0.027883
X-RAY DIFFRACTIONf_plane_restr0.0021014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9894-2.02550.27661170.23562526X-RAY DIFFRACTION89
2.0255-2.06450.211130.23912531X-RAY DIFFRACTION90
2.0645-2.10660.24521380.2252542X-RAY DIFFRACTION89
2.1066-2.15240.28721360.22892570X-RAY DIFFRACTION90
2.1524-2.20250.24541350.21382580X-RAY DIFFRACTION92
2.2025-2.25750.23451390.20812650X-RAY DIFFRACTION93
2.2575-2.31860.27031460.20732683X-RAY DIFFRACTION94
2.3186-2.38680.2571280.20052672X-RAY DIFFRACTION95
2.3868-2.46380.2741290.21042693X-RAY DIFFRACTION95
2.4638-2.55180.26041250.20662720X-RAY DIFFRACTION95
2.5518-2.6540.2431420.20252715X-RAY DIFFRACTION95
2.654-2.77470.23181340.18632727X-RAY DIFFRACTION95
2.7747-2.92090.19811260.1862738X-RAY DIFFRACTION96
2.9209-3.10380.20361440.16362708X-RAY DIFFRACTION95
3.1038-3.34330.19751660.15672749X-RAY DIFFRACTION94
3.3433-3.67940.16761530.15062713X-RAY DIFFRACTION95
3.6794-4.21110.16511510.1382784X-RAY DIFFRACTION95
4.2111-5.30250.16561590.11922796X-RAY DIFFRACTION95
5.3025-34.92070.17211280.16252982X-RAY DIFFRACTION96
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)
11.85611.0611-0.48393.678-1.56942.38370.02570.13950.0607-0.11090.0893-0.1414-0.15650.13550.00570.18110.04540.01270.2548-0.06840.1615-21.180819.8742-7.8053
20.1067-0.0773-0.31750.05650.28133.24270.0264-0.29820.19870.15840.0054-0.0439-0.27070.1351-0.04720.3335-0.0118-0.01610.38640.07570.1872-34.259710.40464.5241
30.36120.0329-0.01390.4422-0.18760.69850.0399-0.0479-0.00870.01380.00310.2032-0.0893-0.0470.04010.26850.06970.01240.35410.01880.0103-47.771823.025-10.8916
40.93680.23210.11642.5650.26940.83630.0272-0.0465-0.0059-0.2170.055-0.2366-0.09710.2844-0.00540.2624-0.02460.02430.3292-0.05430.1034-20.782320.7226-8.7105
50.907-0.38430.06160.77850.04631.01610.045-0.09230.0846-0.24920.013-0.0767-0.05570.1792-0.01760.18240.01130.00310.2147-0.00330.055-27.829319.3614-13.5925
60.5796-0.21250.02380.59950.33671.13970.1233-0.08980.1555-0.00950.0706-0.0795-0.06430.21190.01530.3011-0.03490.08160.4514-0.01420.0481-22.641219.548-20.6645
70.2009-0.0782-0.12080.1482-0.02050.19590.03040.0389-0.0197-0.0396-0.02480.0223-0.0073-0.0523-0.02910.24630.0953-0.10980.28560.02-0.1327-33.56919.4421-20.5525
81.31910.0428-1.09590.2707-0.07791.0041-0.02170.0077-0.171-0.112-0.02860.11830.25680.05250.06340.225-0.006-0.03420.20620.00470.1724-38.05919.2278-11.5544
91.59051.3715-0.34511.992-0.17740.1287-0.0246-0.20150.08850.22060.0867-0.05190.00330.0706-0.01660.2150.01330.00180.232-0.05280.0792-31.160820.37350.3599
100.9178-0.32930.20940.6108-0.48051.138-0.0508-0.0633-0.1338-0.01440.00470.010.0511-0.0686-0.00370.1998-0.0130.01920.2421-0.00150.0678-44.802417.1503-4.1174
110.5161-0.0678-0.10780.5486-0.01610.338-0.09430.07120.0153-0.12440.02590.0403-0.0813-0.09040.02670.184-0.01670.00740.23-0.04680.0918-41.73221.5579-8.8839
122.37220.3735-0.67023.3479-1.21861.84850.0322-0.0892-0.30120.02920.01370.09820.2616-0.11660.01790.1818-0.0175-0.03230.24580.04090.1459-36.82668.6222-4.2767
130.62930.12040.53781.2758-0.73791.0247-0.0281-0.03550.0237-0.00650.07740.0167-0.0378-0.13180.01420.1833-0.01670.00890.2133-0.00820.046-40.879121.611-9.8198
140.86090.53450.25480.7642-0.11291.3788-0.06130.01910.0471-0.10620.02250.03580.01460.0040.00020.1752-0.0003-0.0040.2121-0.00330.1027-42.004820.893-10.6742
152.98020.49772.16620.29560.54262.59290.08230.04820.04380.0563-0.0164-0.07010.0160.0257-0.00310.3510.04360.03060.2865-0.01870.133-25.077532.5547-41.0035
160.03360.27310.17622.31351.47640.94410.07540.16960.0366-0.11790.0950.0471-0.1593-0.068-0.07490.3023-0.0024-0.00980.37460.04250.1239-34.15422.3789-56.3558
170.2913-0.00210.35580.6311-0.28140.97680.09760.0243-0.1422-0.03080.1516-0.13790.1367-0.01730.02990.33180.10780.030.3204-0.02010.1359-22.67254.1189-43.0671
180.2333-0.2976-0.23290.47120.20540.30930.0226-0.07680.3842-0.09490.05490.1223-0.17280.09770.00230.3350.0340.04750.2630.02330.1954-30.868832.4341-42.437
191.1373-0.3616-0.55630.67250.03670.5234-0.0133-0.0605-0.0426-0.08270.0405-0.0034-0.1188-0.0096-0.02670.26380.03650.00750.2377-0.02580.0786-28.738823.468-38.5123
201.6231-0.183-0.49030.9040.03280.77250.13730.02170.2451-0.07470.0632-0.0885-0.33730.1049-0.01660.3696-0.00820.04270.3536-0.0510.0524-29.291827.5774-30.8224
210.3859-0.2764-0.08150.3980.31020.5335-0.01920.0054-0.0763-0.022-0.00250.07360.0426-0.02390.00360.22920.01830.03120.23010.0030.0931-28.688313.373-45.6253
223.2555-0.32970.79782.23320.12431.52450.00040.05820.1053-0.06920.02390.1259-0.0727-0.12760.02050.25310.04880.00730.3075-0.02470.1552-9.369628.5742-66.2182
230.95221.0314-0.05321.70261.00372.20640.03140.0344-0.02220.05240.0785-0.11930.07520.0877-0.01490.2683-0.0591-0.00750.2785-0.00490.0771.521624.2642-56.6974
240.6781-0.32730.62531.41520.10360.80960.017-0.0919-0.01250.14490.0440.0365-0.0689-0.0230.01790.3933-0.0801-0.08280.42460.03130.15594.171914.3733-48.3862
250.32840.3030.45261.5391.54132.45260.0605-0.05-0.01920.0746-0.02670.05550.06870.08140.01320.38440.04240.05850.31830.05270.1017-4.70090.7794-52.7655
260.6944-0.11490.11290.9547-0.23290.6729-0.01390.1162-0.0242-0.11140.06540.02520.06010.00620.02570.3878-0.1087-0.03710.42590.02560.0621-9.6101-0.5747-72.3166
271.942-0.35920.34490.9926-0.09261.06070.04260.16940.23070.0930.07630.1372-0.28120.0587-0.00760.2508-0.01890.01970.20240.00110.1343-4.797226.4942-63.0125
280.1090.0955-0.08860.61180.06890.66160.0070.08770.0591-0.0231-0.00860.0691-0.1325-0.1165-0.01790.2458-0.00420.02550.22820.01160.0827-7.312121.9253-67.0085
290.6222-0.32540.18831.17950.56871.45360.112-0.02040.2589-0.07280.06140.0364-0.17380.0573-0.01540.35970.01550.0210.2698-0.0110.1456-7.273827.4401-72.2107
300.95330.164-0.54860.2030.30021.49380.115-0.08760.0950.0418-0.00830.0081-0.1702-0.07370.00620.3098-0.0730.04810.3365-0.0079-0.0507-1.157821.9291-76.6296
310.07040.1379-0.150.4727-0.52880.5859-0.02550.0336-0.0909-0.0535-0.0119-0.15870.0110.10920.02650.2075-0.01570.01340.2517-0.01560.07772.654511.676-68.7392
321.7853-1.26860.4271.6382-0.3710.1310.0475-0.12150.06930.26650.17020.0758-0.01590.0040.00140.2855-0.0110.02520.30230.0110.0884-4.757615.9585-53.2119
330.994-0.09580.23491.50440.76711.7161-0.0345-0.0576-0.17580.06870.0458-0.029-0.01480.064-0.04130.22440.02520.02620.22850.01450.0731-2.15893.9124-56.6529
340.57410.29080.150.4129-0.30360.7885-0.0150.1147-0.0907-0.12180.0830.0054-0.06120.06760.01630.28070.00370.01770.2551-0.00460.091-6.32895.7443-62.1064
355.3948-0.48911.93212.2174-0.60551.7166-0.0678-0.0764-0.10410.1858-0.121-0.44440.05570.27030.0120.23460.0356-0.0210.23660.0360.12375.294412.0433-57.3855
360.9599-0.36550.22091.19910.2341.19460.03120.0279-0.12270.0222-0.00570.13520.1438-0.0469-0.01250.21420.00020.01180.28460.0337-0.0182-6.61366.0049-62.877
371.4604-0.14110.18890.44540.39031.26750.06460.11740.0847-0.08720.1395-0.1835-0.12480.1792-0.0250.23660.00910.00120.3072-0.05040.150813.8749-11.6358-9.3315
384.9669-0.2975-4.15230.748-1.16466.237-0.0036-0.31890.23490.16730.0832-0.1173-0.35670.3562-0.07040.3631-0.0086-0.03250.30150.02110.21561.4305-20.27745.1873
390.7339-0.0154-0.03170.7934-0.47911.74050.0955-0.06880.057-0.0408-0.07880.13950.0044-0.16630.03240.28710.06510.01140.3203-0.05720.0911-12.7523-6.9544-9.877
400.8784-0.3653-0.45810.15190.190.2412-0.0244-0.07530.22520.0527-0.0596-0.0371-0.2316-0.09270.01620.25920.02480.00490.26780.00490.164819.1228-27.3752-10.5739
410.5278-0.1319-0.2490.03350.07740.60760.0811-0.05310.2099-0.02180.0439-0.1792-0.24520.1983-0.01620.2257-0.0231-0.0220.2724-0.08320.170213.3338-5.9953-9.8779
420.5872-0.39360.06140.77410.29710.67270.0535-0.09090.0302-0.04850.0539-0.0378-0.01280.1101-0.02320.20850.03840.02410.2404-0.010.02236.532-12.9329-14.4586
432.1935-0.6160.05421.30230.46330.82630.02220.0468-0.0139-0.06360.1027-0.12560.04270.0892-0.03690.3591-0.09850.03790.3783-0.08860.184314.1504-10.9708-20.9801
440.3748-0.0213-0.07420.2519-0.0670.17080.0430.0651-0.2209-0.0478-0.14780.0693-0.0269-0.0834-0.01020.260.0143-0.00750.22420.00020.0528-1.0226-17.9919-16.1571
451.78881.1079-0.2092.6473-0.12120.1940.028-0.09960.07730.2048-0.0022-0.21330.02570.1318-0.02920.20810.0495-0.01750.3107-0.0576-0.02854.6321-10.1009-0.1585
460.61980.0698-0.20510.82420.03470.69280.0318-0.0086-0.0418-0.0327-0.06080.0520.0615-0.15170.01920.19470.0024-0.01020.2435-0.04290.0963-7.3108-10.5363-5.5851
472.3494-0.1374-0.94222.8623-1.28132.4648-0.0647-0.1211-0.38760.0257-0.10250.14590.2667-0.19590.03650.2242-0.01190.01270.2213-0.0170.1243-1.6388-22.0202-3.3795
480.5013-0.1884-0.01741.00890.11650.4328-0.03950.0442-0.0032-0.0823-0.01970.0933-0.0373-0.04420.02860.1880.0042-0.00630.2104-0.02060.0536-6.4465-9.3675-9.3693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 87 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 33 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 71 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 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 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 145 )
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 156 )
14X-RAY DIFFRACTION14chain 'B' and (resid 157 through 170 )
15X-RAY DIFFRACTION15chain 'C' and (resid 51 through 55 )
16X-RAY DIFFRACTION16chain 'C' and (resid 56 through 65 )
17X-RAY DIFFRACTION17chain 'C' and (resid 66 through 87 )
18X-RAY DIFFRACTION18chain 'D' and (resid 13 through 34 )
19X-RAY DIFFRACTION19chain 'D' and (resid 35 through 53 )
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 71 )
21X-RAY DIFFRACTION21chain 'D' and (resid 72 through 170 )
22X-RAY DIFFRACTION22chain 'E' and (resid 50 through 54 )
23X-RAY DIFFRACTION23chain 'E' and (resid 55 through 59 )
24X-RAY DIFFRACTION24chain 'E' and (resid 60 through 64 )
25X-RAY DIFFRACTION25chain 'E' and (resid 65 through 74 )
26X-RAY DIFFRACTION26chain 'E' and (resid 75 through 87 )
27X-RAY DIFFRACTION27chain 'F' and (resid 18 through 28 )
28X-RAY DIFFRACTION28chain 'F' and (resid 29 through 53 )
29X-RAY DIFFRACTION29chain 'F' and (resid 54 through 62 )
30X-RAY DIFFRACTION30chain 'F' and (resid 63 through 71 )
31X-RAY DIFFRACTION31chain 'F' and (resid 72 through 93 )
32X-RAY DIFFRACTION32chain 'F' and (resid 94 through 106 )
33X-RAY DIFFRACTION33chain 'F' and (resid 107 through 118 )
34X-RAY DIFFRACTION34chain 'F' and (resid 119 through 136 )
35X-RAY DIFFRACTION35chain 'F' and (resid 137 through 145 )
36X-RAY DIFFRACTION36chain 'F' and (resid 146 through 168 )
37X-RAY DIFFRACTION37chain 'G' and (resid 50 through 59 )
38X-RAY DIFFRACTION38chain 'G' and (resid 60 through 64 )
39X-RAY DIFFRACTION39chain 'G' and (resid 65 through 88 )
40X-RAY DIFFRACTION40chain 'H' and (resid 12 through 20 )
41X-RAY DIFFRACTION41chain 'H' and (resid 21 through 34 )
42X-RAY DIFFRACTION42chain 'H' and (resid 35 through 53 )
43X-RAY DIFFRACTION43chain 'H' and (resid 54 through 66 )
44X-RAY DIFFRACTION44chain 'H' and (resid 67 through 94 )
45X-RAY DIFFRACTION45chain 'H' and (resid 95 through 106 )
46X-RAY DIFFRACTION46chain 'H' and (resid 107 through 137 )
47X-RAY DIFFRACTION47chain 'H' and (resid 138 through 145 )
48X-RAY DIFFRACTION48chain 'H' and (resid 146 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