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- PDB-5u0b: Structure of full-length Zika virus NS5 -

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Basic information

Entry
Database: PDB / ID: 5u0b
TitleStructure of full-length Zika virus NS5
ComponentsGenome polyprotein
KeywordsTRANSFERASE / Viral RNA polymerase
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 / 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 ...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 / 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 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 / 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
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 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 / Vaccinia Virus protein VP39 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhao, B. / Du, F.
CitationJournal: Nat Commun / Year: 2017
Title: Structure and function of the Zika virus full-length NS5 protein.
Authors: Zhao, B. / Yi, G. / Du, F. / Chuang, Y.C. / Vaughan, R.C. / Sankaran, B. / Kao, C.C. / Li, P.
History
DepositionNov 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all / _struct_ref_seq_dif.details
Revision 1.3Oct 4, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,90414
Polymers206,2972
Non-polymers1,60712
Water00
1
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9527
Polymers103,1491
Non-polymers8036
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9527
Polymers103,1491
Non-polymers8036
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.500, 197.000, 95.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Genome polyprotein


Mass: 103148.688 Da / Num. of mol.: 2
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: Q32ZE1, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: 1.0 M ammonium sulfate plus 1% PE G 3350, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→85.775 Å / Num. obs: 50661 / % possible obs: 97.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.103 / Net I/σ(I): 6.4
Reflection shellRmerge(I) obs: 0.715 / Rpim(I) all: 0.475

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k6m

4k6m


Resolution: 3→85.775 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.6
RfactorNum. reflection% reflection
Rfree0.268 2521 4.99 %
Rwork0.2308 --
obs0.2327 50511 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→85.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14196 0 86 0 14282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214608
X-RAY DIFFRACTIONf_angle_d0.51119740
X-RAY DIFFRACTIONf_dihedral_angle_d22.2728698
X-RAY DIFFRACTIONf_chiral_restr0.042066
X-RAY DIFFRACTIONf_plane_restr0.0042528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05770.38771430.34322620X-RAY DIFFRACTION98
3.0577-3.12010.37031140.33342695X-RAY DIFFRACTION98
3.1201-3.1880.39651420.32382663X-RAY DIFFRACTION98
3.188-3.26210.30261280.30962662X-RAY DIFFRACTION97
3.2621-3.34370.32241510.29212610X-RAY DIFFRACTION97
3.3437-3.43410.30211390.28622636X-RAY DIFFRACTION97
3.4341-3.53520.32231560.28772597X-RAY DIFFRACTION95
3.5352-3.64930.35611160.26062627X-RAY DIFFRACTION96
3.6493-3.77970.29311210.25212595X-RAY DIFFRACTION95
3.7797-3.9310.29711530.24192591X-RAY DIFFRACTION95
3.931-4.10990.22821410.21552678X-RAY DIFFRACTION98
4.1099-4.32660.22151390.19812673X-RAY DIFFRACTION97
4.3266-4.59770.23081320.17592701X-RAY DIFFRACTION98
4.5977-4.95260.231510.17682666X-RAY DIFFRACTION97
4.9526-5.4510.24341230.18842691X-RAY DIFFRACTION96
5.451-6.23950.221500.19212727X-RAY DIFFRACTION98
6.2395-7.86030.2371590.19482768X-RAY DIFFRACTION98
7.8603-85.80960.1861630.17422790X-RAY DIFFRACTION95
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)
10.7410.1791-0.24390.13720.2071.9360.0112-0.1107-0.0108-0.0114-0.10030.1448-0.0723-0.10150.03820.90190.00010.21480.1821-0.00240.38530.5918103.932337.2374
20.4496-0.2653-0.11010.4187-0.46861.03640.060.0437-0.0323-0.0574-0.0783-0.02740.20880.06030.01310.7121-0.04480.17980.17250.00580.354136.2085106.397926.8414
31.7294-0.00091.32040.32540.29371.2779-0.15360.17240.22060.0185-0.04380.1808-0.04480.1872-0.39010.79010.03280.29640.25780.00990.308132.8414116.5078-15.5074
41.5091-0.13440.46360.94080.37421.2835-0.06140.08590.0025-0.0193-0.11820.14090.3109-0.08260.13940.7501-0.040.24220.2429-0.02370.30130.4945112.5022-6.9181
50.2038-0.49090.05752.94910.75951.897-0.00580.1063-0.0047-0.0124-0.15670.33630.258-0.45140.13490.3538-0.03040.1750.4454-0.06490.386811.2126134.5445.7328
60.74840.03011.580.43950.68744.4219-0.0123-0.04740.0164-0.0282-0.15740.1486-0.2408-0.30710.14590.34840.01850.19520.23520.01160.311230.698364.492210.4429
70.3310.1751-0.10080.11230.17691.71350.01810.0281-0.0346-0.0963-0.0391-0.0174-0.2610.18740.00980.1402-0.00920.12940.2179-0.03150.328137.679256.947333.6322
80.6070.1925-0.13580.51660.20241.01650.0247-0.11460.0628-0.0979-0.07250.1961-0.2179-0.0668-0.01690.1897-0.05630.15290.1919-0.00570.307124.105957.833553.8584
92.1674-0.0757-0.07712.33960.16592.4925-0.08830.08480.0184-0.05390.10010.02320.4154-0.1038-0.01590.3076-0.09460.19240.1687-0.02830.270512.139430.720540.806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 368 )
3X-RAY DIFFRACTION3chain 'A' and (resid 369 through 414 )
4X-RAY DIFFRACTION4chain 'A' and (resid 415 through 695 )
5X-RAY DIFFRACTION5chain 'A' and (resid 696 through 887 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 174 )
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 462 )
8X-RAY DIFFRACTION8chain 'B' and (resid 463 through 724 )
9X-RAY DIFFRACTION9chain 'B' and (resid 725 through 887 )

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