[English] 日本語
Yorodumi
- PDB-5zob: Crystal structure of Zika NS3 protease with 4-guanidinomethyl-phe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zob
TitleCrystal structure of Zika NS3 protease with 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-amidinobenzylamide
Components
  • 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-amidinobenzylamide
  • NS3 protease
  • Serine protease subunit NS2B
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 JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / double-stranded RNA binding / viral capsid / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / double-stranded RNA binding / viral capsid / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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-{[4-(carbamimidamidomethyl)phenyl]acetyl}-L-arginyl-L-arginyl-N-[(4-carbamimidoylphenyl)methyl]-L-argininamide / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 12, 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 1.2Mar 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.3Nov 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

-
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
G: Serine protease subunit NS2B
H: NS3 protease
E: Serine protease subunit NS2B
F: NS3 protease
I: 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-amidinobenzylamide
J: 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-amidinobenzylamide


Theoretical massNumber of molelcules
Total (without water)101,20010
Polymers101,20010
Non-polymers00
Water4,378243
1
A: Serine protease subunit NS2B
B: NS3 protease
G: Serine protease subunit NS2B
H: NS3 protease
I: 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-amidinobenzylamide


Theoretical massNumber of molelcules
Total (without water)50,6005
Polymers50,6005
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Serine protease subunit NS2B
F: NS3 protease

C: Serine protease subunit NS2B
D: NS3 protease
J: 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-amidinobenzylamide


Theoretical massNumber of molelcules
Total (without water)50,6005
Polymers50,6005
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)60.417, 60.417, 214.873
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 / Strain: Mr 766 / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#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 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-amidinobenzylamide


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 793.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N2-{[4-(carbamimidamidomethyl)phenyl]acetyl}-L-arginyl-L-arginyl-N-[(4-carbamimidoylphenyl)methyl]-L-argininamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.48 %
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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→42.97 Å / Num. obs: 87405 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.034 / Rrim(I) all: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4443 / CC1/2: 0.9 / Rpim(I) all: 0.376 / Rrim(I) all: 0.862 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI
Resolution: 2→42.721 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 852 1.58 %Random selection
Rwork0.2572 ---
obs0.2585 53909 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 0 243 6160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026031
X-RAY DIFFRACTIONf_angle_d0.6828180
X-RAY DIFFRACTIONf_dihedral_angle_d12.5542236
X-RAY DIFFRACTIONf_chiral_restr0.029898
X-RAY DIFFRACTIONf_plane_restr0.0021065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.12590.24251410.32058741X-RAY DIFFRACTION98
2.1259-2.290.31521410.34078670X-RAY DIFFRACTION97
2.29-2.52050.31171420.3098829X-RAY DIFFRACTION98
2.5205-2.88510.31851410.30348825X-RAY DIFFRACTION98
2.8851-3.63450.34761390.24858846X-RAY DIFFRACTION98
3.6345-39.70570.21461450.1989103X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8726-1.3281-0.6431.18270.5910.29480.0383-0.0794-0.38670.21890.0378-0.09770.07480.0443-0.0440.39560.0839-0.08920.24320.0030.22898.35242.233940.3094
20.0853-0.1018-0.18050.5141-0.02530.3398-0.0122-0.23550.15870.42640.1161-0.0636-0.08230.0855-0.0750.845-0.0048-0.04490.30910.01110.1263-0.082720.588655.1322
31.0938-0.0515-0.10921.91720.7171.2847-0.03680.22610.0312-0.078-0.0248-0.1195-0.08640.01710.02330.28130.01250.00490.28530.00570.20559.026731.681334.8717
41.65930.05310.12380.57170.1831.0628-0.12740.0412-0.27150.0578-0.10140.06120.35110.17750.13560.58190.0978-0.05690.24980.05250.09226.36465.172942.8727
50.73610.0878-0.17660.48990.2270.81840.09440.1909-0.10710.1514-0.0588-0.10120.0893-0.1878-0.00940.31530.0355-0.00360.2336-0.00450.1164-0.272812.932936.038
60.5254-0.188-0.17210.3960.29520.2505-0.031-0.11770.00440.48980.0184-0.2115-0.16320.14440.01270.63880.0114-0.09230.2044-0.04220.11714.458622.575848.95
71.3970.35280.12881.530.15770.77980.0944-0.0331-0.13140.35140.04860.1446-0.02870.3455-0.09180.52320.0395-0.07130.2696-0.0270.02711.947322.729345.3444
83.68480.3624-0.08553.1012-0.06780.13970.00090.0581-0.5235-0.0765-0.07830.22780.3473-0.22360.10440.5549-0.1774-0.05110.2898-0.03350.238921.78272.127667.6076
90.2925-0.13760.24212.16221.57781.56450.02290.04870.0703-0.17940.0314-0.2563-0.01450.1278-0.07110.5337-0.0245-0.07060.1545-0.0530.18931.9946.421856.7749
100.30170.0752-0.00660.24260.27080.3322-0.02130.095-0.0085-0.08860.00190.0477-0.03390.06420.01140.9970.02290.18760.4779-0.07830.247235.658816.844247.6501
110.5028-0.2634-0.37720.91520.39640.32860.17780.14730.0086-0.01980.12120.1908-0.0449-0.1366-0.23230.85260.1102-0.14880.39680.0180.195426.1730.058753.093
120.6472-0.0080.09491.9425-1.01130.66220.03160.0296-0.05590.005-0.04170.1406-0.20250.037-0.01320.41520.13980.05090.3116-0.01240.224622.036629.88874.3986
133.0735-2.64580.61357.1838-1.25722.466-0.01530.01280.1361-0.0679-0.07050.0988-0.128-0.08820.06910.3604-0.01110.02420.2960.08360.261719.686534.683169.3112
140.08630.3801-0.44021.6105-1.93952.4103-0.01370.1697-0.1631-0.3666-0.176-0.10190.17020.20340.12630.3927-0.0317-0.03020.2027-0.03780.098328.56313.909263.4923
150.41750.10850.36171.00180.50930.561-0.1892-0.1237-0.0861-0.1269-0.14090.04310.2304-0.41180.18370.6399-0.1297-0.03960.33440.00080.078619.6616.148265.4777
160.6117-0.1854-0.05671.00220.12760.74940.158-0.0658-0.0920.0565-0.2051-0.11560.2297-0.17930.03840.3541-0.0441-0.03220.25090.04190.131927.922810.221973.6198
170.4855-0.1005-0.07551.0201-1.36962.14510.01770.06440.1228-0.09920.02050.0299-0.15710.2772-0.01710.4741-0.12610.13580.3098-0.0463-0.278337.622620.448265.2338
180.33590.208-0.26690.1205-0.15980.215-0.01990.2609-0.216-0.4890.11610.1802-0.1077-0.0353-0.01380.6612-0.0161-0.05930.26580.02910.131326.235317.084853.0536
191.05020.0879-0.01441.3144-0.14280.4234-0.02630.02310.1428-0.31660.0159-0.147-0.3492-0.2826-0.00930.5705-0.012-0.08650.28470.06970.033927.05224.632662.5953
202.8194-0.7930.7113.5558-0.49681.7365-0.0382-0.0268-0.16880.15010.0042-0.05020.103-0.00820.0380.29960.12050.04210.5001-0.05950.0613.036.557714.0473
213.2547-1.31590.15460.77170.4241.0860.04140.1720.1805-0.0395-0.03950.067-0.15950.0055-0.02730.28410.14290.1690.597-0.0893-0.00218.586416.76173.038
220.98150.883-0.57290.86-0.61380.47410.17070.3865-0.1876-0.3816-0.08260.04640.139-0.0836-0.06260.45820.14150.03580.71910.03040.135-4.218515.8307-6.2861
231.1882-0.24290.72021.3992-0.57451.02850.0320.0963-0.097-0.0180.1072-0.00750.03420.0023-0.12340.3898-0.0841-0.1820.7928-0.0351-0.2362-19.958310.60744.2144
240.3450.0699-0.32940.24740.1030.44170.03810.0261-0.0286-0.0532-0.0997-0.01980.1275-0.06010.01190.3376-0.18590.0390.44650.08410.2206-18.00928.232418.485
251.0090.04692.40330.0334-0.18248.41850.01450.0065-0.11190.0675-0.0328-0.00680.15640.0098-0.00310.5192-0.0334-0.03490.4022-0.08480.1723-11.57616.153322.0543
261.3694-1.4217-0.67621.47330.70130.3334-0.02380.0699-0.1085-0.0140.00970.11440.0309-0.11010.0140.5518-0.08530.01510.56060.01910.187-21.27474.239316.4454
270.68250.3797-0.17510.67660.17841.2757-0.01420.4903-0.06940.07440.0375-0.05640.0545-0.0686-0.01220.17820.03350.01510.3512-0.02240.14464.423513.268214.8756
280.67560.053-0.23610.5253-0.13310.57650.02960.5185-0.1449-0.01170.03930.06280.1759-0.1922-0.04650.2532-0.00570.0060.6694-0.0470.0989-7.66411.87136.5416
292.363-0.37480.25912.6287-0.17490.7412-0.03960.0053-0.18340.0876-0.0764-0.09740.12680.06450.0980.36230.14190.07710.5897-0.06740.011543.185236.759314.0108
301.409-0.90890.91120.7677-0.83310.88990.09030.25410.0104-0.27190.07160.142-0.0096-0.011-0.11340.29290.18290.20550.75710.049-0.116933.174948.4826-2.133
312.33222.4733-1.05422.9215-1.56671.14840.00790.277-0.0578-0.31390.1028-0.06960.23940.0748-0.07040.5350.0843-0.08660.6851-0.09230.229121.631940.6655-6.5398
320.5364-0.1830.3480.5592-0.21180.37010.03750.0331-0.04720.00710.06680.02780.0356-0.0822-0.07910.3244-0.1411-0.17590.8129-0.044-0.248510.1940.91914.2155
33-0.0008-0.0043-0.0007-0.0025-0.00040.00040.02920.10290.0023-0.0471-0.0624-0.02830.0187-0.1406-0.00080.3477-0.2370.05480.40370.04680.225612.158938.427718.4919
341.2175-0.34231.37740.57660.36216.90750.04920.0511-0.09450.06-0.03720.01250.135-0.0146-0.02170.4996-0.18580.01280.2792-0.05490.206318.686336.442322.0707
351.5009-1.4763-0.40581.44910.39870.1095-0.0658-0.0793-0.11940.04460.07950.09520.001-0.1438-0.00780.6398-0.13970.03560.64110.01840.21558.993934.373716.4434
360.43770.1710.33921.7205-1.08771.7471-0.02480.13380.0350.0313-0.0903-0.1013-0.2510.10280.01170.26680.19360.18190.4942-0.09150.11841.067243.13479.3724
370.60650.0116-0.29511.85090.89570.9758-0.00250.2881-0.025-0.08890.0132-0.05510.16590.108-0.02340.16770.01490.00550.3699-0.04370.142236.55738.80513.8261
381.204-0.3197-1.49410.08160.38881.8673-0.0154-0.1520.13490.042-0.0235-0.1479-0.13290.20970.0310.41920.0874-0.05440.4691-0.11990.17243.357440.999619.4548
390.53220.6729-0.07740.91160.11670.87240.12310.4101-0.15570.11050.0121-0.0186-0.3259-0.1457-0.1690.2060.0160.02480.2879-0.02210.161627.306248.697617.0445
400.0725-0.06690.14960.5389-0.31030.37560.09520.4368-0.214-0.26570.022-0.04130.1782-0.0803-0.16250.1263-0.0302-0.0160.6376-0.01950.218524.747542.2231.1741
414.0192-0.1473-3.81352.10640.41064.42660.1909-0.1223-0.01450.27620.0738-0.0447-0.135-0.0379-0.23190.24660.0270.0030.484-0.00270.197911.956145.65616.0404
420.79560.1424-0.31680.6872-0.08651.23810.05310.35920.0894-0.3570.1102-0.03690.3313-0.0633-0.09060.21740.0485-0.00330.6319-0.06870.057224.946642.56326.3042
430.7694-0.124-0.19260.2642-0.42410.86920.03360.1239-0.46590.0244-0.03320.36280.2636-0.2433-0.02710.3539-0.0071-0.00610.612-0.085-0.014518.945939.698610.4234
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 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 88 )
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 42 )
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 93 )
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 136 )
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 170 )
8X-RAY DIFFRACTION8chain 'C' and (resid 50 through 54 )
9X-RAY DIFFRACTION9chain 'C' and (resid 55 through 59 )
10X-RAY DIFFRACTION10chain 'C' and (resid 60 through 64 )
11X-RAY DIFFRACTION11chain 'C' and (resid 65 through 74 )
12X-RAY DIFFRACTION12chain 'C' and (resid 75 through 83 )
13X-RAY DIFFRACTION13chain 'C' and (resid 84 through 88 )
14X-RAY DIFFRACTION14chain 'D' and (resid 15 through 27 )
15X-RAY DIFFRACTION15chain 'D' and (resid 28 through 42 )
16X-RAY DIFFRACTION16chain 'D' and (resid 43 through 79 )
17X-RAY DIFFRACTION17chain 'D' and (resid 80 through 93 )
18X-RAY DIFFRACTION18chain 'D' and (resid 94 through 112 )
19X-RAY DIFFRACTION19chain 'D' and (resid 113 through 170 )
20X-RAY DIFFRACTION20chain 'G' and (resid 50 through 54 )
21X-RAY DIFFRACTION21chain 'G' and (resid 55 through 59 )
22X-RAY DIFFRACTION22chain 'G' and (resid 60 through 69 )
23X-RAY DIFFRACTION23chain 'G' and (resid 70 through 74 )
24X-RAY DIFFRACTION24chain 'G' and (resid 75 through 79 )
25X-RAY DIFFRACTION25chain 'G' and (resid 80 through 84 )
26X-RAY DIFFRACTION26chain 'G' and (resid 85 through 87 )
27X-RAY DIFFRACTION27chain 'H' and (resid 17 through 94 )
28X-RAY DIFFRACTION28chain 'H' and (resid 95 through 170 )
29X-RAY DIFFRACTION29chain 'E' and (resid 50 through 54 )
30X-RAY DIFFRACTION30chain 'E' and (resid 55 through 64 )
31X-RAY DIFFRACTION31chain 'E' and (resid 65 through 69 )
32X-RAY DIFFRACTION32chain 'E' and (resid 70 through 74 )
33X-RAY DIFFRACTION33chain 'E' and (resid 75 through 79 )
34X-RAY DIFFRACTION34chain 'E' and (resid 80 through 84 )
35X-RAY DIFFRACTION35chain 'E' and (resid 85 through 87 )
36X-RAY DIFFRACTION36chain 'F' and (resid 17 through 27 )
37X-RAY DIFFRACTION37chain 'F' and (resid 28 through 53 )
38X-RAY DIFFRACTION38chain 'F' and (resid 54 through 66 )
39X-RAY DIFFRACTION39chain 'F' and (resid 67 through 93 )
40X-RAY DIFFRACTION40chain 'F' and (resid 94 through 117 )
41X-RAY DIFFRACTION41chain 'F' and (resid 118 through 125 )
42X-RAY DIFFRACTION42chain 'F' and (resid 126 through 155 )
43X-RAY DIFFRACTION43chain 'F' and (resid 156 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://pdbjlvh1.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