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

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Basic information

Entry
Database: PDB / ID: 4hbo
TitleCrystal Structure of Rubella virus capsid protein (residues 127-277)
ComponentsCapsid proteinCapsid
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 / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / 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 / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / membrane / metal ion binding
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.241 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 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _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_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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


Theoretical massNumber of molelcules
Total (without water)74,9375
Polymers74,9375
Non-polymers00
Water0
1
A: Capsid protein

A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area3210 Å2
ΔGint-28 kcal/mol
Surface area9030 Å2
MethodPISA
2
B: Capsid protein

B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3180 Å2
ΔGint-23 kcal/mol
Surface area8560 Å2
MethodPISA
3
C: Capsid protein

C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4020 Å2
ΔGint-27 kcal/mol
Surface area9210 Å2
MethodPISA
4
D: Capsid protein

D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4210 Å2
ΔGint-34 kcal/mol
Surface area8540 Å2
MethodPISA
5
E: Capsid protein

E: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3970 Å2
ΔGint-32 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.790, 279.700, 76.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is a dimer. There are 5 monomers in the asymmetric unit (chain A, B, C, D and E), which form 5 biological units on application of a 2-fold along 'b' axis.

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Components

#1: Protein
Capsid protein / Capsid


Mass: 14987.403 Da / Num. of mol.: 5 / 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
Sequence detailsN-TERMINAL 20 AMINO ACIDS ASN PRO PHE GLN ALA ALA VAL ALA ARG GLY LEU ARG PRO PRO LEU HIS ASP PRO ...N-TERMINAL 20 AMINO ACIDS ASN PRO PHE GLN ALA ALA VAL ALA ARG GLY LEU ARG PRO PRO LEU HIS ASP PRO ASP THR WERE INCLUDED IN CRYSTALLIZATION SET UP BUT WERE DEGRADED DURING CRYSTALLIZATION

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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: 1.53 Å3/Da / Density % sol: 19.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 4000, 20% 2-propanol, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.241→50 Å / Num. obs: 7669 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.107 / Χ2: 1.351 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.25-3.3110.80.5223571.198192.7
3.31-3.3712.70.4323671.2381100
3.37-3.4312.70.3153661.1631100
3.43-3.5120.2853901.2461100
3.5-3.5812.60.2633571.257194.2
3.58-3.6612.60.2623811.373199.5
3.66-3.7512.60.183671.3091100
3.75-3.8512.10.2413921.327199.7
3.85-3.9712.70.1823601.27196.5
3.97-4.0912.60.1493721.3331100
4.09-4.2412.20.123811.341199.7
4.24-4.4112.40.0983891.349199
4.41-4.6112.70.0993751.3941100
4.61-4.8512.80.0983921.394199.5
4.85-5.1613.50.093801.3991100
5.16-5.5613.60.0923991.351100
5.56-6.1114.10.0853961.2551100
6.11-713.90.0943941.4121100
7-8.8113.60.0734141.5661100
8.81-5012.30.0614401.712199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å46.62 Å
Translation3.5 Å46.62 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HAR

4har


Resolution: 3.241→46.617 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5829 / SU ML: 0.44 / σ(F): 1.4 / Phase error: 44.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3679 1355 9.9 %Thin resolution shells
Rwork0.3398 ---
all0.3424 13688 --
obs0.3424 13688 96.69 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 338.52 Å2 / Biso mean: 96.507 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.241→46.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 0 0 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073250
X-RAY DIFFRACTIONf_angle_d1.1974418
X-RAY DIFFRACTIONf_chiral_restr0.084437
X-RAY DIFFRACTIONf_plane_restr0.008586
X-RAY DIFFRACTIONf_dihedral_angle_d16.3951144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2408-3.35660.41011450.39851171131693
3.3566-3.4910.35581410.32681278141999
3.491-3.64980.40281450.34591234137997
3.6498-3.84210.3841370.32571266140399
3.8421-4.08270.39051410.33631204134598
4.0827-4.39770.28471320.28971277140999
4.3977-4.83990.31521340.29051264139899
4.8399-5.53920.33721390.31711260139999
5.5392-6.97510.44251320.3741261139399
6.9751-46.62150.42711090.44991118122786
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)
11.77790.8809-0.14860.59510.19631.3591-0.047-0.6216-1.0584-0.07240.0406-0.77430.4745-0.15850.11821.0564-0.02970.16780.669-0.17042.1687-16.404823.233815.1755
22.716-0.79131.67784.4382-0.14643.9173-0.1033-0.65731.78680.5965-0.2131-0.596-0.3035-0.45460.11940.47830.05690.03520.6204-0.24881.2492-15.944432.8537-14.6615
34.7848-1.5601-0.56533.4818-1.19164.37690.1229-0.2285-0.16940.0776-0.1026-0.85060.25850.82930.27920.8673-0.0484-0.28130.5017-0.00790.98494.442460.8908-16.0054
45.58481.9811.28794.8428-0.09313.8995-0.37860.5576-0.50860.1738-0.1669-0.24760.2854-0.30680.52090.50360.18420.06050.5088-0.08480.42554.485150.286415.2703
56.0551-1.672-0.28544.79560.15353.4745-0.1341-0.4219-0.83990.8732-0.3762-0.70330.23270.4490.50890.3624-0.02880.07260.60490.12230.57114.63545.817-14.9094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 27:120))A27 - 120
2X-RAY DIFFRACTION2chain 'B' and ((resseq 27:120))B27 - 120
3X-RAY DIFFRACTION3chain 'C' and ((resseq 27:120))C27 - 120
4X-RAY DIFFRACTION4chain 'D' and ((resseq 27:120))D27 - 120
5X-RAY DIFFRACTION5chain 'E' and ((resseq 27:120))E27 - 120

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