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- PDB-1sfk: Core (C) protein from West Nile Virus, subtype Kunjin -

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Basic information

Entry
Database: PDB / ID: 1sfk
TitleCore (C) protein from West Nile Virus, subtype Kunjin
ComponentsCore proteinCapsid
KeywordsVIRAL PROTEIN / ALPHA HELIX
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #930 / : / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Arc Repressor Mutant, subunit A - #930 / : / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 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 / 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 / Arc Repressor Mutant, subunit A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesKunjin virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsDokland, T. / Walsh, M. / Mackenzie, J.M. / Khromykh, A.A. / Ee, K.-H. / Wang, S.
CitationJournal: Structure / Year: 2004
Title: West nile virus core protein; tetramer structure and ribbon formation
Authors: Dokland, T. / Walsh, M. / Mackenzie, J.M. / Khromykh, A.A. / Ee, K.-H. / Wang, S.
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2 This entry contains the crystallographic asymmetric unit which consists of 8 ...BIOMOLECULE: 1, 2 This entry contains the crystallographic asymmetric unit which consists of 8 chain(s). the biological molecule may be dimer or tetramer.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core protein
B: Core protein
C: Core protein
D: Core protein
E: Core protein
F: Core protein
G: Core protein
H: Core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,09721
Polymers68,9238
Non-polymers1,17413
Water48627
1
A: Core protein
B: Core protein
C: Core protein
D: Core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,09611
Polymers34,4614
Non-polymers6347
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: Core protein
F: Core protein
G: Core protein
H: Core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,00110
Polymers34,4614
Non-polymers5406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Core protein
B: Core protein
hetero molecules

A: Core protein
B: Core protein
hetero molecules

C: Core protein
D: Core protein
hetero molecules

C: Core protein
D: Core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,19122
Polymers68,9238
Non-polymers1,26914
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
crystal symmetry operation3_655-y+1,x+1/2,z+1/41
crystal symmetry operation8_455y-1,-x+1/2,z+1/41
Buried area22060 Å2
ΔGint-264 kcal/mol
Surface area25670 Å2
MethodPISA
4
E: Core protein
F: Core protein
hetero molecules

E: Core protein
F: Core protein
hetero molecules

G: Core protein
H: Core protein
hetero molecules

G: Core protein
H: Core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,00220
Polymers68,9238
Non-polymers1,07912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+1,x+1/2,z+1/41
crystal symmetry operation8_565y,-x+3/2,z+1/41
Buried area21190 Å2
ΔGint-225 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.655, 85.655, 214.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-101-

CA

21D-102-

CA

31F-103-

CA

41G-104-

CA

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31D
41E
51F
61G
71A
81B
91C
101D
111E
121F
131G
141H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLY6AA24 - 393 - 18
21LEULEUGLYGLY6CC24 - 393 - 18
31LEULEUGLYGLY6DD24 - 393 - 18
41LEULEUGLYGLY6EE24 - 393 - 18
51LEULEUGLYGLY6FF24 - 393 - 18
61LEULEUGLYGLY6GG24 - 393 - 18
72ARGARGARGARG2AA40 - 9619 - 75
82ARGARGARGARG2BB40 - 9619 - 75
92ARGARGARGARG2CC40 - 9619 - 75
102ARGARGARGARG2DD40 - 9619 - 75
112ARGARGARGARG2EE40 - 9619 - 75
122ARGARGARGARG2FF40 - 9619 - 75
132ARGARGARGARG2GG40 - 9619 - 75
142ARGARGARGARG2HH40 - 9619 - 75

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Core protein / Capsid


Mass: 8615.314 Da / Num. of mol.: 8 / Fragment: Tryptic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kunjin virus / Genus: Flavivirus / Species: West Nile virus / Strain: MRM61C / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14335

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Non-polymers , 5 types, 40 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.16 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: PEG3350, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97956, 0.97976, 0.8856
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979561
20.979761
30.88561
ReflectionResolution: 3.2→30 Å / Num. all: 12515 / Num. obs: 12515 / % possible obs: 99.4 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→10 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 33.609 / SU ML: 0.532 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.629 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3112 607 5 %RANDOM
Rwork0.24909 ---
all0.25209 11589 --
obs0.25209 11589 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.026 Å2
Baniso -1Baniso -2Baniso -3
1-8.03 Å20 Å20 Å2
2--8.03 Å20 Å2
3----16.06 Å2
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 41 27 4448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224479
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9716007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3175545
X-RAY DIFFRACTIONr_chiral_restr0.0950.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023146
X-RAY DIFFRACTIONr_nbd_refined0.2530.22397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.29
X-RAY DIFFRACTIONr_mcbond_it0.5251.52743
X-RAY DIFFRACTIONr_mcangle_it0.9424397
X-RAY DIFFRACTIONr_scbond_it1.0131736
X-RAY DIFFRACTIONr_scangle_it1.7134.51610
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A228tight positional0.040.05
8B228tight positional0.050.05
2C228tight positional0.040.05
3D228tight positional0.050.05
4E228tight positional0.040.05
5F228tight positional0.050.05
6G228tight positional0.050.05
14H228tight positional0.050.05
1A232medium positional0.980.5
8B232medium positional0.950.5
2C232medium positional1.020.5
3D232medium positional0.870.5
4E232medium positional0.870.5
5F232medium positional0.780.5
6G232medium positional0.830.5
14H232medium positional1.050.5
1A228tight thermal0.080.5
8B228tight thermal0.140.5
2C228tight thermal0.060.5
3D228tight thermal0.090.5
4E228tight thermal0.060.5
5F228tight thermal0.10.5
6G228tight thermal0.080.5
14H228tight thermal0.190.5
1A232medium thermal0.512
8B232medium thermal1.042
2C232medium thermal0.552
3D232medium thermal0.622
4E232medium thermal0.492
5F232medium thermal0.532
6G232medium thermal0.482
14H232medium thermal0.692
LS refinement shellResolution: 3.2→3.327 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.427 74
Rwork0.373 1257
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)
12.01873.7396-2.335217.0291-5.366515.21410.2532-0.2479-0.6647-0.0315-0.5244-0.05730.64471.36330.27120.31260.33830.03250.73740.10020.6316.754552.291462.4324
29.2586-1.11190.077522.4256-1.676113.2460.7019-1.06090.63662.5424-0.9320.0156-1.45331.03140.230.6901-0.1280.01860.71270.13990.52096.789863.900964.9331
310.75980.58043.0519.49784.287723.10330.3431.94310.0909-2.7388-1.0724-0.04331.10181.69340.72940.90720.4206-0.05650.80750.20410.65657.318466.083835.2932
43.5834-1.28941.40916.252-5.561317.76470.2848-0.25410.4646-0.0776-0.7062-0.1682-0.15691.48620.42140.22760.05720.020.39010.04370.72896.726576.214641.0066
512.8871-2.06454.80222.6677-0.932114.08640.7155-2.3234-0.41143.4437-0.6559-0.05261.5892-2.2121-0.05961.0048-0.50830.02051-0.09990.702935.412465.854977.7622
62.27531.14040.293919.13116.240917.49070.60890.53520.38630.2138-1.12420.0661-0.0902-1.59130.51530.13-0.13640.02290.4142-0.02120.783436.134876.150572.304
72.3407-2.5307-2.649819.66512.914914.65940.5354-0.0437-0.7308-0.238-0.6449-0.13480.5476-1.41150.10950.3412-0.28410.04970.7214-0.10420.635536.101852.274650.9214
89.04430.2197-1.299519.62093.439610.93530.38381.12350.2619-2.315-0.8778-0.0404-1.9935-1.06130.4940.8940.10480.06770.8659-0.1190.568336.01264.023748.3188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 963 - 75
2X-RAY DIFFRACTION2BB41 - 9620 - 75
3X-RAY DIFFRACTION3CC24 - 963 - 75
4X-RAY DIFFRACTION4DD24 - 963 - 75
5X-RAY DIFFRACTION5EE24 - 963 - 75
6X-RAY DIFFRACTION6FF24 - 963 - 75
7X-RAY DIFFRACTION7GG24 - 963 - 75
8X-RAY DIFFRACTION8HH41 - 9620 - 75

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