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- PDB-1wyk: SINDBIS VIRUS CAPSID PROTEIN (114-264) -

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Basic information

Entry
Database: PDB / ID: 1wyk
TitleSINDBIS VIRUS CAPSID PROTEIN (114-264)
ComponentsSINDBIS VIRUS CAPSID PROTEIN
KeywordsViral protein / hydrolase / COAT PROTEIN / SINDBIS / VIRUS / PROTEINASE / ALPHAVIRUS / CAPSID / DIOXANE
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / RNA binding
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / FORMYL GROUP / Structural polyprotein
Similarity search - Component
Biological speciesSindbis virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, S. / Kuhn, R.J. / Rossmann, M.G.
Citation
Journal: Proteins / Year: 1998
Title: Probing the potential glycoprotein binding site of sindbis virus capsid protein with dioxane and model building.
Authors: Lee, S. / Kuhn, R.J. / Rossmann, M.G.
#1: Journal: Structure / Year: 1996
Title: Identification of a Protein Binding Site on the Surface of the Alphavirus Nucleocapsid and its Implication in Virus Assembly
Authors: Lee, S. / Owen, K.E. / Choi, H.K. / Lee, H. / Lu, G. / Wengler, G. / Brown, D.T. / Rossmann, M.G. / Kuhn, R.J.
#2: Journal: Nature / Year: 1991
Title: Structure of Sindbis Virus Core Protein Reveals a Chymotrypsin-Like Serine Proteinase and the Organization of the Virion
Authors: Choi, H.K. / Tong, L. / Minor, W. / Dumas, P. / Boege, U. / Rossmann, M.G. / Wengler, G.
History
DepositionJan 12, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SINDBIS VIRUS CAPSID PROTEIN
B: SINDBIS VIRUS CAPSID PROTEIN
C: SINDBIS VIRUS CAPSID PROTEIN
D: SINDBIS VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,26813
Polymers66,7074
Non-polymers5619
Water8,449469
1
A: SINDBIS VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7953
Polymers16,6771
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SINDBIS VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8834
Polymers16,6771
Non-polymers2063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SINDBIS VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7953
Polymers16,6771
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SINDBIS VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7953
Polymers16,6771
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.980, 59.540, 71.050
Angle α, β, γ (deg.)109.40, 101.50, 90.14
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.779681, -0.56603, -0.267782), (-0.551434, -0.823279, 0.134653), (-0.296677, 0.042677, -0.954024)10.572, 3.2665, 59.1573
2given(0.771114, -0.56934, -0.285017), (0.554856, 0.820461, -0.137759), (0.312277, -0.051915, 0.948571)24.7411, 9.7564, 31.7661
3given(0.999996, -0.002136, -0.001906), (-0.002132, -0.999996, 0.00209), (-0.00191, -0.002086, -0.999996)-0.1281, 36.7006, 25.5119
4given(0.99981, 0.005077, 0.018823), (0.005045, -0.999986, 0.001786), (0.018831, -0.001691, -0.999821)13.041, 12.8639, 90.7193

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Components

#1: Protein
SINDBIS VIRUS CAPSID PROTEIN / SINDBIS VIRUS CORE PROTEIN


Mass: 16676.828 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sindbis virus / Genus: Alphavirus / Strain: SA-AR 86 / Cell line: BL21 / Gene: POTENTIAL / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P27285, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-FOR / FORMYL GROUP / Aldehyde


Mass: 30.026 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growpH: 6.5
Details: 20-26%(W/V) PEG 8000, 100 MM SODIUM CACODYLATE, PH6.5, 150MM SODIUM ACETATE, 6%(V/V) DIOXANE
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110.5 mg/mlprotein1drop
225 mMTris-HCl1drop
312.5 mM1dropNaCl
40.5 mMEDTA1drop
510-13 %(w/v)PEG80001drop
650 mMsodium cacodylate1drop
775 mMsodium acetate1drop
83 %(v/v)dioxane1drop
920-26 %(w/v)PEG80001reservoir
10100 mMsodium cacodylate1reservoir
11150 mMsodium acetate1reservoir
126 %(v/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 26, 1995 / Details: BENT FOCUSING MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 28851 / % possible obs: 78.3 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.028 / Net I/σ(I): 16
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 6 / Rsym value: 0.089 / % possible all: 28.8
Reflection
*PLUS
Num. measured all: 53873 / Rmerge(I) obs: 0.028

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HKLdata reduction
HKLdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SINDBIS VIRUS CAPSID PROTEIN MUTANT (S215A, 106-266) IN TRICLINIC CRYSTAL

Resolution: 2→8 Å / Rfactor Rfree error: 0.0072 / Data cutoff high absF: 304 / Data cutoff low absF: 9.7 / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1365 5 %RANDOM
Rwork0.197 ---
obs0.197 28043 78 %-
Displacement parametersBiso mean: 15.6 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 30 469 5195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.734
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.87
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.571
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: MOL1 AND MOL4, MOL2 AND MOL3 WERE RESTRAINED IN A PAIRWISE MANNER DURING REFINEMENT.
LS refinement shellResolution: 2→2.03 Å / Rfactor Rfree error: 0.074 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 24 1.3 %
Rwork0.234 473 -
obs--24 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2FORMET.PARTOPH19.PEP
X-RAY DIFFRACTION3DIO.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.878
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.571

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