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- PDB-5z0v: Structural insight into the Zika virus capsid encapsulating the v... -

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Basic information

Entry
Database: PDB / ID: 5z0v
TitleStructural insight into the Zika virus capsid encapsulating the viral genome
ComponentsExtracellular solute-binding protein family 1,viral genome protein
KeywordsVIRAL PROTEIN / Zika virus / capsid
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / outer membrane-bounded periplasmic space / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / periplasmic space / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / DNA damage response / lipid binding / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Arc Repressor Mutant, subunit A - #930 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Bacterial extracellular solute-binding protein / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B ...Arc Repressor Mutant, subunit A - #930 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Bacterial extracellular solute-binding protein / 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, 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 central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Bacterial extracellular solute-binding protein / 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 / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helicase, C-terminal / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Genome polyprotein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Zika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.913 Å
AuthorsLi, T. / Zhao, Q. / Yang, X. / Chen, C. / Yang, K. / Wu, C. / Zhang, T. / Duan, Y. / Xue, X. / Mi, K. ...Li, T. / Zhao, Q. / Yang, X. / Chen, C. / Yang, K. / Wu, C. / Zhang, T. / Duan, Y. / Xue, X. / Mi, K. / Ji, X. / Wang, Z. / Yang, H.
Funding support China, 3items
OrganizationGrant numberCountry
the National Key Basic Research Program of China2015CB859800 China
the National Natural Science Foundation of China31528006 China
the National Key Research Program of China2016YFD0500300 China
CitationJournal: Cell Res. / Year: 2018
Title: Structural insight into the Zika virus capsid encapsulating the viral genome.
Authors: Li, T. / Zhao, Q. / Yang, X. / Chen, C. / Yang, K. / Wu, C. / Zhang, T. / Duan, Y. / Xue, X. / Mi, K. / Ji, X. / Wang, Z. / Yang, H.
History
DepositionDec 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular solute-binding protein family 1,viral genome protein
B: Extracellular solute-binding protein family 1,viral genome protein
C: Extracellular solute-binding protein family 1,viral genome protein
D: Extracellular solute-binding protein family 1,viral genome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,2788
Polymers195,9094
Non-polymers1,3694
Water2,378132
1
A: Extracellular solute-binding protein family 1,viral genome protein
D: Extracellular solute-binding protein family 1,viral genome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6394
Polymers97,9552
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-34 kcal/mol
Surface area36600 Å2
MethodPISA
2
B: Extracellular solute-binding protein family 1,viral genome protein
C: Extracellular solute-binding protein family 1,viral genome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6394
Polymers97,9552
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-39 kcal/mol
Surface area36790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.104, 223.076, 85.165
Angle α, β, γ (deg.)90.00, 109.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Extracellular solute-binding protein family 1,viral genome protein


Mass: 48977.270 Da / Num. of mol.: 4 / Mutation: N293D
Source method: isolated from a genetically manipulated source
Details: The fusion protein of MBP-tag (UNP Residues 27-395) and Zika virus capsid (UNP residues 24-98).
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Zika virus
Strain: B / BL21-DE3, Mr 766 / Gene: ECBD_4002 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A140NCD0, UniProt: A0A1D9C0W3, UniProt: P0AEX9*PLUS
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.6
Details: 0.1 M sodium acetate trihydrate pH 4.6, 8% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 46037 / % possible obs: 95.9 % / Redundancy: 6.1 % / Net I/σ(I): 5.9
Reflection shellResolution: 2.9→2.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SFK, 1EZ9

1sfk

1ez9


Resolution: 2.913→46.363 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.91
RfactorNum. reflection% reflection
Rfree0.2481 2339 5.09 %
Rwork0.2039 --
obs0.2061 45996 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.913→46.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13723 0 92 132 13947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514139
X-RAY DIFFRACTIONf_angle_d0.75219164
X-RAY DIFFRACTIONf_dihedral_angle_d19.4765244
X-RAY DIFFRACTIONf_chiral_restr0.052127
X-RAY DIFFRACTIONf_plane_restr0.0052442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9131-2.97260.36091380.29782376X-RAY DIFFRACTION89
2.9726-3.03720.29991580.29692539X-RAY DIFFRACTION95
3.0372-3.10780.3041240.28162522X-RAY DIFFRACTION94
3.1078-3.18550.36731480.28112536X-RAY DIFFRACTION95
3.1855-3.27160.30331530.2682530X-RAY DIFFRACTION95
3.2716-3.36790.2771210.26282552X-RAY DIFFRACTION94
3.3679-3.47660.28391120.23122535X-RAY DIFFRACTION94
3.4766-3.60080.22461410.21672517X-RAY DIFFRACTION95
3.6008-3.74490.2641460.20452538X-RAY DIFFRACTION94
3.7449-3.91520.28291420.20232554X-RAY DIFFRACTION95
3.9152-4.12150.23261400.18652528X-RAY DIFFRACTION95
4.1215-4.37960.18931390.16992582X-RAY DIFFRACTION96
4.3796-4.71740.20041510.16112603X-RAY DIFFRACTION97
4.7174-5.19160.21761490.16692578X-RAY DIFFRACTION97
5.1916-5.94150.22371320.19772700X-RAY DIFFRACTION100
5.9415-7.48060.23451190.1972728X-RAY DIFFRACTION100
7.4806-46.3690.2271260.16252739X-RAY DIFFRACTION99
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)
11.77810.1094-0.28832.25310.65932.2729-0.23110.06450.2357-0.12650.25850.2803-0.1438-0.09980.01580.32570.03370.00320.32040.02310.337673.1462-31.3328197.977
22.1479-0.16640.05622.7126-0.51911.8263-0.0095-0.07360.05080.1018-0.0502-0.14580.03970.73520.04690.30360.03070.03090.3611-0.03290.305989.668-31.1357201.3332
31.2239-1.0046-1.76741.16760.28582.5084-0.2202-0.2354-0.33460.040.0333-0.04420.74790.46220.15720.53360.1760.06830.45640.06280.408393.7946-54.7637187.3629
41.2517-0.2351-0.08261.4641-0.23673.2026-0.111-0.1051-0.23680.29180.07190.22380.72270.36530.02240.32590.08890.04610.32150.06350.276582.3671-46.545200.6198
51.4322-0.06450.04531.3120.93011.2609-0.1015-0.1394-0.0725-0.15350.0618-0.10870.08290.5870.03120.31030.10580.02950.463-0.00040.327599.112-44.0315187.4881
60.56930.0612-0.20011.7724-0.31542.4184-0.09010.1666-0.0266-0.48930.16810.13530.4176-0.0802-0.06320.3952-0.08740.00080.4153-0.02290.38893.8993-10.6078176.9159
71.19680.2847-0.0133.2589-0.41071.3102-0.0329-0.00130.07510.17710.07410.4188-0.1136-0.0904-0.02990.22770.06640.04970.2980.03560.354488.6375-41.7351148.2896
82.042-0.010.38411.55850.01830.773-0.1152-0.20090.24270.33870.12-0.1816-0.10240.12520.01320.33280.0295-0.00950.33960.02680.2535115.066-47.1753157.8704
92.0526-0.43060.50161.4985-0.21670.7924-0.05540.02040.03640.05770.07220.0206-0.0442-0.03190.01220.2880.04210.05830.26740.00720.2376104.136-47.5107153.1469
101.46470.297-0.56431.6259-0.49510.8682-0.033-0.0133-0.1429-0.085-0.0418-0.01150.10240.22020.02550.35590.06460.02220.34-0.00970.366796.1216-13.2923133.3437
111.3187-0.40470.45781.9085-1.21.9558-0.00770.0585-0.0940.01950.08620.03460.03690.1138-0.05770.3574-0.0355-0.03120.3153-0.04160.324280.56367.4428119.1072
121.82080.46991.67110.56720.51912.5546-0.25820.17740.3848-0.0439-0.0233-0.1504-0.73950.44810.23880.5302-0.1569-0.0540.43720.06570.359890.940430.7491132.3072
131.22630.15460.35241.6508-0.10533.329-0.2072-0.03030.2555-0.42110.02740.1742-0.73550.05710.12470.2971-0.0492-0.0630.2620.02540.277179.577622.7671118.9044
140.8603-0.52870.8040.62950.7041.7142-0.0060.197-0.0713-0.27290.08210.1408-0.29520.36060.0350.3786-0.1506-0.00770.3544-0.01440.414592.610321.9126127.1601
15-0.3324-0.64110.37991.71340.00480.11870.013-0.20570.03310.4807-0.1267-0.2965-0.08520.2350.13280.37410.0291-0.01140.4593-0.02780.397698.4939-3.5639144.5603
160.64290.14690.12732.5159-1.52062.9969-1.15270.7670.0664-0.0670.00530.8887-0.7701-0.39440.03460.26080.35820.1716-0.1217-0.15470.632384.4934-11.8285134.3925
172.9195-0.2302-0.13811.7597-0.2621.72590.2359-0.18550.00730.3665-0.14950.019-0.1011-0.0358-0.06650.2692-0.0561-0.05310.3322-0.03530.303389.654924.8749179.6611
180.1543-0.566-0.21782.0273-0.36530.95090.0628-0.0074-0.1881-0.19540.02030.22390.2821-0.3173-0.06320.2657-0.0813-0.0050.34450.03170.324991.592514.7533166.1717
191.25280.2418-0.42810.93440.05190.4203-0.10160.1309-0.0766-0.21820.0984-0.1649-0.0278-0.00390.00960.2997-0.0399-0.01470.330.02670.2662117.064424.0928161.6992
200.508-0.03960.02471.5843-0.22610.7010.058-0.01990.0292-0.0019-0.0619-0.0229-0.00860.05530.02010.1945-0.0052-0.00540.24810.01090.2063104.324527.0722166.7063
212.74140.8361.49632.00771.58122.57450.1457-0.09-0.69580.1703-0.023-0.46540.85890.35150.00340.4410.02350.05120.3750.06890.5208119.32754.9087164.9343
221.32740.17770.40721.6174-0.36241.4127-0.07440.07760.0303-0.08860.00830.0185-0.04960.31330.08770.3125-0.03780.01230.3151-0.01070.335898.2777-10.4234185.562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 219 )
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 315 )
5X-RAY DIFFRACTION5chain 'A' and (resid 316 through 374 )
6X-RAY DIFFRACTION6chain 'A' and (resid 375 through 445 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 106 )
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 201 )
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 374 )
10X-RAY DIFFRACTION10chain 'B' and (resid 375 through 445 )
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 106 )
12X-RAY DIFFRACTION12chain 'C' and (resid 107 through 219 )
13X-RAY DIFFRACTION13chain 'C' and (resid 220 through 315 )
14X-RAY DIFFRACTION14chain 'C' and (resid 316 through 353 )
15X-RAY DIFFRACTION15chain 'C' and (resid 354 through 420 )
16X-RAY DIFFRACTION16chain 'C' and (resid 421 through 445 )
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 43 )
18X-RAY DIFFRACTION18chain 'D' and (resid 44 through 106 )
19X-RAY DIFFRACTION19chain 'D' and (resid 107 through 201 )
20X-RAY DIFFRACTION20chain 'D' and (resid 202 through 353 )
21X-RAY DIFFRACTION21chain 'D' and (resid 354 through 374 )
22X-RAY DIFFRACTION22chain 'D' and (resid 375 through 445 )

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