[English] 日本語
Yorodumi
- PDB-4tpl: West Nile Virus Non-structural protein 1 (NS1) Form 1 crystal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tpl
TitleWest Nile Virus Non-structural protein 1 (NS1) Form 1 crystal
ComponentsWest Nile Virus NS1
KeywordsVIRAL PROTEIN / flavivirus / non-structural protein 1 / NS1
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / 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 / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / 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 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesWest Nile virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsAkey, D.L. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI055672 United States
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1.
Authors: Akey, D.L. / Brown, W.C. / Konwerski, J.R. / Ogata, C.M. / Smith, J.L.
#1: Journal: Science / Year: 2014
Title: Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system.
Authors: Akey, D.L. / Brown, W.C. / Dutta, S. / Konwerski, J. / Jose, J. / Jurkiw, T.J. / DelProposto, J. / Ogata, C.M. / Skiniotis, G. / Kuhn, R.J. / Smith, J.L.
History
DepositionJun 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Derived calculations
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 2.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 2.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: West Nile Virus NS1
B: West Nile Virus NS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,31412
Polymers85,2252
Non-polymers5,08910
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint4 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.850, 167.850, 93.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA-10 - 442
211chain BB-20 - 445

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein West Nile Virus NS1


Mass: 42612.648 Da / Num. of mol.: 2 / Fragment: UNP residues 791-1143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5SBG8

-
Sugars , 3 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 67 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100


Mass: 646.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.47 Å3/Da / Density % sol: 72.5 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3000, 5% Glycerol, 20 mM Sodium Citrate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.74625 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 11, 2013
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74625 Å / Relative weight: 1
ReflectionNumber: 6267610 / Rmerge(I) obs: 0.313 / Χ2: 1.08 / D res high: 2.9 Å / Num. obs: 33918 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
6.267.88324010.14
5.476.26322810.185
4.975.47327810.201
4.614.97329210.198
4.344.61323310.223
4.124.34330310.31
3.944.12330410.405
3.793.94322510.544
3.663.79324210.651
3.553.66308610.876
3.443.55352311.084
3.353.44327111.372
3.273.35319811.827
3.23.27306012.22
3.133.2335312.949
3.073.13312013.972
3.013.07336014.977
2.963.01298916.339
2.92.96394219
ReflectionResolution: 2.9→48.454 Å / Num. obs: 33918 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 96 % / Biso Wilson estimate: 95.55 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.313 / Rrim(I) all: 0.315 / Χ2: 1.077 / Net I/σ(I): 19.64 / Num. measured all: 6267610
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.9-2.96500.17190.69198290394639429.09199.9
2.96-3.010.6216.3391.23229277298929896.381100
3.01-3.070.7654.9771.75312973336033605.004100
3.07-3.130.8233.9722.23310757312031203.992100
3.13-3.20.8962.9493.09334621335333532.964100
3.2-3.270.9372.224.23305489306030602.231100
3.27-3.350.961.8275.16320065319831981.836100
3.35-3.440.9711.3726.87327287327132711.379100
3.44-3.550.9851.0848.76352555352335231.089100
3.55-3.660.9950.87610.69309655308630860.88100
3.66-3.790.9920.65114.07324853324232420.654100
3.79-3.940.9940.54416.85322765322532250.547100
3.94-4.120.9970.40521.79333047330433040.407100
4.12-4.340.9980.3127.46332186330333030.312100
4.34-4.610.9990.22334.91324820323332330.224100
4.61-4.970.9990.19838.21329906329232920.199100
4.97-5.470.9990.20137.78329503327832780.202100
5.47-6.260.9990.18541.05325668322832280.186100
6.26-7.880.9990.1450.84324028324032400.141100
7.8810.09466.92319865328332700.09599.6

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
SHELXphasing
DMphasing
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.14data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→48.454 Å / FOM work R set: 0.8522 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 1697 5 %
Rwork0.1703 32221 -
obs0.1723 33918 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 274.38 Å2 / Biso mean: 100.39 Å2 / Biso min: 43.94 Å2
Refinement stepCycle: final / Resolution: 2.9→48.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5471 0 234 62 5767
Biso mean--146.48 83.75 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065845
X-RAY DIFFRACTIONf_angle_d1.0087934
X-RAY DIFFRACTIONf_chiral_restr0.04879
X-RAY DIFFRACTIONf_plane_restr0.004999
X-RAY DIFFRACTIONf_dihedral_angle_d13.4312184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3197X-RAY DIFFRACTION9.321TORSIONAL
12B3197X-RAY DIFFRACTION9.321TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-2.98780.36511380.345126342772
2.9878-3.08430.32231410.253526682809
3.0843-3.19450.29631400.222826432783
3.1945-3.32240.30571400.225426732813
3.3224-3.47350.22091410.180326572798
3.4735-3.65660.19731390.154926592798
3.6566-3.88560.19491410.146526702811
3.8856-4.18550.16951410.129226912832
4.1855-4.60640.15631410.115526852826
4.6064-5.27220.15661440.121327002844
5.2722-6.63970.22541420.190827292871
6.6397-48.46090.23361490.204928122961
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)
11.6036-1.0679-0.20084.4266-2.19593.3191-0.08290.1470.8529-0.6644-0.2209-0.0552-0.09910.39490.2260.7801-0.1659-0.08290.666-0.0220.850868.9241-54.258214.1763
21.9883-1.3173-0.62233.50051.76142.3396-0.2312-0.6705-0.04560.48450.24240.378-0.1786-0.6569-0.07270.4777-0.09290.03320.71320.08690.673843.8925-38.494220.3617
33.4959-0.06930.3922.79860.20611.4771-0.1783-0.40840.1951.29830.24141.6685-0.139-0.7803-0.1060.50760.14770.1631.02290.01581.2333.2381-34.851423.3744
44.10860.68041.35333.2551-0.55022.3353-0.1454-0.5133-0.0042-0.0039-0.0317-0.4468-0.4429-0.2520.17230.67670.0520.01820.89950.06720.910147.6687-38.038317.062
55.4939-0.80770.49993.34870.26612.6615-0.2734-0.03260.5817-0.2116-0.00850.6195-0.1478-0.88960.33760.4425-0.0536-0.11610.8224-0.04340.569549.2669-52.998813.9781
63.93280.4353-1.73273.3975-2.10984.5683-0.0932-0.2964-0.3403-0.05030.26230.18680.4983-0.6512-0.13990.472-0.1928-0.0530.7339-0.00570.50341.0021-65.712126.2287
74.040.14910.71187.9421-0.31042.924-0.1840.1496-0.17040.88790.51721.37350.182-1.1993-0.36620.6883-0.20670.03271.32310.09960.768830.2144-68.22635.4254
82.75410.0731-1.40660.90141.43213.7705-0.3796-0.8915-1.18151.13490.74851.04020.22130.8517-0.1870.85190.0766-0.08231.02910.13751.014868.0599-65.32526.5919
91.58130.62282.28446.42870.46823.28760.33050.0943-0.4754-0.0665-0.3189-1.52050.00610.1832-0.08490.564-0.071-0.00410.83180.08270.997768.955-53.594314.8906
102.77430.69410.23946.1832.12494.1673-0.0320.2314-0.57410.4558-0.1711-0.35760.50880.21340.160.7511-0.02750.01410.7143-0.21291.046274.8852-85.63679.2166
114.623-3.07541.20264.43760.71283.26090.6190.912-0.6332-0.6833-0.3587-0.24170.42980.3382-0.26280.7953-0.04580.02310.7598-0.18420.953774.3687-83.24190.1104
122.0631-0.03731.24963.34880.99073.98660.07170.6421-0.41680.13090.21911.42570.9912-0.0398-0.370.7713-0.104-0.12870.6796-0.02030.958268.0473-74.463611.8375
133.1879-0.5782-0.37783.7911-0.16674.4935-0.06160.29130.372-0.5680.04260.197-0.1165-0.37490.01340.5668-0.1565-0.04310.67250.02270.561459.4685-57.8286-4.713
144.9683-0.3113-0.86493.25080.17013.0266-0.25271.6534-0.1175-1.44820.4342-0.8301-0.3074-0.2694-0.12231.203-0.31530.11461.1103-0.0540.980164.3665-50.062-20.3321
154.5365-1.12060.06453.80470.822.82560.2561.25920.211-1.3761-0.27-0.90990.30680.215-0.0031.1019-0.08290.15511.00620.05720.582666.5177-56.9982-19.2356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 18 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 61 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 146 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 171 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 196 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 328 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 329 through 352 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid -18 through 7 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 31 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 51 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 159 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 160 through 184 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 185 through 302 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 303 through 320 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 321 through 352 )B0

+
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