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- PDB-5yxa: Crystal structure of the C-terminal fragment of NS1 protein from ... -

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Basic information

Entry
Database: PDB / ID: 5yxa
TitleCrystal structure of the C-terminal fragment of NS1 protein from yellow fever virus
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / yellow fever virus / NS1
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / 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 perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / 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 / host cell nucleus / GTP binding / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesYellow fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, H. / Song, H. / Qi, J. / Shi, Y. / Gao, G.F.
CitationJournal: Sci China Life Sci / Year: 2017
Title: Crystal structure of the C-terminal fragment of NS1 protein from yellow fever virus.
Authors: Wang, H. / Han, M. / Qi, J. / Hilgenfeld, R. / Luo, T. / Shi, Y. / Gao, G.F. / Song, H.
History
DepositionDec 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Non-structural protein 1
B: Non-structural protein 1
C: Non-structural protein 1
D: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)79,9304
Polymers79,9304
Non-polymers00
Water2,162120
1
A: Non-structural protein 1

D: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)39,9652
Polymers39,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area1280 Å2
ΔGint-8 kcal/mol
Surface area15760 Å2
MethodPISA
2
B: Non-structural protein 1

C: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)39,9652
Polymers39,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.291, 114.104, 139.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Non-structural protein 1 / NS1


Mass: 19982.557 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A161I252, UniProt: Q1X881*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.0M Tris, 1.0M Bicine pH 8.5, 0.12M of an alcohols (0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M 1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol), 18% PEG-MME 500, 18% PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 55378 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Net I/σ(I): 22.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5462 / CC1/2: 0.917 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IY3

5iy3


Resolution: 2.1→41.612 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.91
RfactorNum. reflection% reflection
Rfree0.258 2805 5.07 %
Rwork0.2228 --
obs0.2246 55274 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5420 0 0 120 5540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055592
X-RAY DIFFRACTIONf_angle_d0.9957588
X-RAY DIFFRACTIONf_dihedral_angle_d13.9832016
X-RAY DIFFRACTIONf_chiral_restr0.039816
X-RAY DIFFRACTIONf_plane_restr0.004972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0959-2.13210.35261310.31662541X-RAY DIFFRACTION98
2.1321-2.17090.35731480.30072591X-RAY DIFFRACTION100
2.1709-2.21260.30791460.2742572X-RAY DIFFRACTION100
2.2126-2.25780.3371220.28272609X-RAY DIFFRACTION100
2.2578-2.30690.33051350.27672591X-RAY DIFFRACTION100
2.3069-2.36050.34051450.272596X-RAY DIFFRACTION100
2.3605-2.41950.32091630.27772564X-RAY DIFFRACTION100
2.4195-2.4850.29541270.26492616X-RAY DIFFRACTION100
2.485-2.55810.33451280.27092621X-RAY DIFFRACTION100
2.5581-2.64060.28871390.26082593X-RAY DIFFRACTION100
2.6406-2.7350.29051410.25432607X-RAY DIFFRACTION100
2.735-2.84450.32771350.25712609X-RAY DIFFRACTION100
2.8445-2.97390.28491510.25362613X-RAY DIFFRACTION100
2.9739-3.13060.25581360.24792623X-RAY DIFFRACTION100
3.1306-3.32670.28421350.2562630X-RAY DIFFRACTION100
3.3267-3.58340.2641520.23182638X-RAY DIFFRACTION100
3.5834-3.94380.22771420.20592647X-RAY DIFFRACTION100
3.9438-4.51390.19551310.1662684X-RAY DIFFRACTION100
4.5139-5.68470.21831450.16362693X-RAY DIFFRACTION100
5.6847-41.62070.21261530.19052831X-RAY DIFFRACTION100
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)
11.81530.15-0.61850.7231-0.01891.625-0.06640.1418-0.1396-0.03690.0843-0.0050.16750.069800.36030.0195-0.01390.3065-0.02550.344127.2805-2.5055-8.1425
21.395-0.2516-0.65071.02780.79111.49760.0534-0.1153-0.06740.161-0.0693-0.05150.1362-0.208200.3385-0.0402-0.00690.4192-0.03120.36021.3747-6.4013-31.5789
31.11390.16030.09313.423-2.34591.94950.06440.13220.2069-0.22510.13930.38390.13630.14150.09760.30940.0078-0.03850.28430.07680.414615.1123.10761.7056
40.8446-0.13880.49630.5451-0.01781.2356-0.13390.02750.22970.1097-0.0238-0.1859-0.57520.4231-0.00390.6293-0.1386-0.07280.5037-0.05030.485421.182615.5662-42.4514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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