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- PDB-4har: Crystal Structure of Rubella virus capsid protein (residues 127-277) -

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Basic information

Entry
Database: PDB / ID: 4har
TitleCrystal Structure of Rubella virus capsid protein (residues 127-277)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / partial beta barrel / capsid protein
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / metal ion binding / membrane
Similarity search - Function
Rubella virus capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 ...Rubella virus capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella capsid protein / Chitinase A; domain 3 / Roll / Alpha Beta
Similarity search - Domain/homology
Structural polyprotein / Polyprotein
Similarity search - Component
Biological speciesRubella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.663 Å
AuthorsMangala Prasad, V. / Fokine, A. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Rubella virus capsid protein structure and its role in virus assembly and infection.
Authors: Mangala Prasad, V. / Willows, S.D. / Fokine, A. / Battisti, A.J. / Sun, S. / Plevka, P. / Hobman, T.C. / Rossmann, M.G.
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,54227
Polymers102,3066
Non-polymers4,23621
Water1,910106
1
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,89015
Polymers34,1022
Non-polymers2,78813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-8 kcal/mol
Surface area11900 Å2
MethodPISA
2
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5965
Polymers34,1022
Non-polymers4943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-24 kcal/mol
Surface area12360 Å2
MethodPISA
3
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0557
Polymers34,1022
Non-polymers9535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-22 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.760, 74.786, 96.075
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

21A-320-

HOH

DetailsThe biological unit is a dimer. There are 3 biological units in the asymmetric unit (chain A & B, chains C & D and chain E & F)

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Components

#1: Protein
Capsid protein


Mass: 17051.033 Da / Num. of mol.: 6 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubella virus / Strain: M33 / Gene: Capsid / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8QL55, UniProt: P08563*PLUS
#2: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.2M Sodium chloride, 1% Lauryldimethylamine-oxide, 0.05M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. all: 29218 / Num. obs: 29218 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.143 / Χ2: 5.254 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.66-2.713.70.42812451.843186.9
2.71-2.764.20.4613671.891192.2
2.76-2.814.60.49413751.784195.2
2.81-2.875.10.48314662.073198.4
2.87-2.935.50.38714602.13199.3
2.93-360.36814672.204199.9
3-3.076.50.34214762.41199.9
3.07-3.156.90.3314832.7441100
3.15-3.257.30.30214793.1611100
3.25-3.357.50.25414703.7611100
3.35-3.477.60.21814844.8931100
3.47-3.617.60.19914815.8121100
3.61-3.777.60.16214827.0231100
3.77-3.977.70.14314727.8591100
3.97-4.227.60.12814728.3871100
4.22-4.557.60.1115107.92199.9
4.55-57.60.09614777.636199.9
5-5.737.60.09814906.617199.9
5.73-7.217.60.08515065.6181100
7.21-507.40.0815569.5151100

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Phasing

PhasingMethod: SIRAS
Phasing MADD res high: 3.67 Å / D res low: 1000 Å / FOM : 0.31 / Reflection: 11016
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1U19.8270.8020.340.0880.464
2U600.3990.380.3650.655
3U42.7360.8060.0450.30.613
4U14.5340.3860.0410.0760.382
5U37.3710.5850.2590.1770.358
6U39.7390.5760.1690.3660.414
Phasing MAD shell
Resolution (Å)FOM Reflection
13.4-10000.36510
8.4-13.40.48904
6.54-8.40.441160
5.54-6.540.421374
4.89-5.540.31554
4.42-4.890.271681
4.07-4.420.221863
3.79-4.070.21970

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVEphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.663→47.623 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8142 / SU ML: 0.36 / σ(F): 1.35 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 2020 6.92 %THIN RESOLUTION SHELLS
Rwork0.185 ---
all0.1881 29202 --
obs0.1881 29202 97.53 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.727 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 163.28 Å2 / Biso mean: 53.0884 Å2 / Biso min: 14.53 Å2
Baniso -1Baniso -2Baniso -3
1-5.7034 Å2-0 Å2-3.7967 Å2
2--6.2744 Å2-0 Å2
3----11.9778 Å2
Refinement stepCycle: LAST / Resolution: 2.663→47.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 291 106 5109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085156
X-RAY DIFFRACTIONf_angle_d1.3376975
X-RAY DIFFRACTIONf_chiral_restr0.095647
X-RAY DIFFRACTIONf_plane_restr0.007890
X-RAY DIFFRACTIONf_dihedral_angle_d18.0551949
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6628-2.72940.36971010.2891461156275
2.7294-2.80320.39991010.27361880198193
2.8032-2.88570.31472020.26681868207098
2.8857-2.97880.24491010.244820432144100
2.9788-3.08520.31852020.228219022104100
3.0852-3.20880.31591010.213720372138100
3.2088-3.35480.25152020.20819432145100
3.3548-3.53160.24371010.193720142115100
3.5316-3.75270.20882020.181219422144100
3.7527-4.04240.18361010.151720272128100
4.0424-4.44890.19212020.144319532155100
4.4489-5.0920.19181010.133320312132100
5.092-6.41290.22291300.181220482178100
6.4129-47.63090.19831730.191820332206100
Refinement TLS params.Method: refined / Origin x: 33.2559 Å / Origin y: 15.0622 Å / Origin z: 70.6643 Å
111213212223313233
T0.399 Å20.021 Å20.0218 Å2-0.3375 Å20.0041 Å2--0.3084 Å2
L0.8127 °20.1183 °20.0069 °2-0.3755 °20.0518 °2--0.0504 °2
S-0.0406 Å °0.0352 Å °0 Å °-0.1048 Å °-0.0443 Å °-0.0439 Å °-0.0292 Å °-0.0204 Å °0.0816 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 122
2X-RAY DIFFRACTION1allB25 - 121
3X-RAY DIFFRACTION1allC25 - 124
4X-RAY DIFFRACTION1allD24 - 122
5X-RAY DIFFRACTION1allE26 - 121
6X-RAY DIFFRACTION1allF25 - 123
7X-RAY DIFFRACTION1allB - A1 - 202
8X-RAY DIFFRACTION1allA1 - 205
9X-RAY DIFFRACTION1allD - F1 - 202
10X-RAY DIFFRACTION1allD - F1 - 202
11X-RAY DIFFRACTION1allE - D1 - 203
12X-RAY DIFFRACTION1allB1 - 205
13X-RAY DIFFRACTION1allB - A1 - 207
14X-RAY DIFFRACTION1allF1 - 321

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