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- PDB-5tiq: The Structure of the Major Capsid protein of PBCV-1 -

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Basic information

Entry
Database: PDB / ID: 5tiq
TitleThe Structure of the Major Capsid protein of PBCV-1
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Major capsid protein Vp54 / Adenovirus Type 2 Hexon, domain 4 / Adenovirus Type 2 Hexon; domain 4 / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Major capsid protein
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.537 Å
AuthorsKlose, T. / De Castro, C. / Speciale, I. / Molinaro, A. / Van Etten, J.L. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of the chlorovirus PBCV-1 major capsid glycoprotein determined by combining crystallographic and carbohydrate molecular modeling approaches.
Authors: De Castro, C. / Klose, T. / Speciale, I. / Lanzetta, R. / Molinaro, A. / Van Etten, J.L. / Rossmann, M.G.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
SupersessionDec 20, 2017ID: 1J5Q
Revision 1.1Dec 20, 2017Group: Advisory / Database references
Category: citation / citation_author / pdbx_database_PDB_obs_spr
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Data collection
Category: chem_comp / pdbx_audit_support / pdbx_nonpoly_scheme
Item: _chem_comp.type / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.ndb_seq_num
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,55914
Polymers96,1372
Non-polymers9,42212
Water5,963331
1
A: Major capsid protein
hetero molecules

A: Major capsid protein
hetero molecules

A: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,85821
Polymers144,2053
Non-polymers13,65318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area30210 Å2
ΔGint-150 kcal/mol
Surface area47770 Å2
MethodPISA
2
B: Major capsid protein
hetero molecules

B: Major capsid protein
hetero molecules

B: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,81921
Polymers144,2053
Non-polymers14,61418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area26810 Å2
ΔGint-42 kcal/mol
Surface area48900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.763, 188.763, 188.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Major capsid protein / MCP / VP54


Mass: 48068.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: P30328

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Sugars , 3 types, 8 molecules

#2: Polysaccharide
6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose-(1-2)-beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose- ...6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose-(1-2)-beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)][alpha-D-galactopyranose-(1-2)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 1381.284 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhap[2Me,3Me]a1-2LRhapb1-4DXylpb1-4[DManpa1-3DRhapa1-3][DGalpa1-2]LFucpa1-3[DXylpb1-4]DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/8,9,8/[a2122h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5][a1122m-1a_1-5][a1122h-1a_1-5][a212h-1b_1-5][a2211m-1b_1-5][a2211m-1a_1-5_2*OC_3*OC]/1-2-3-4-5-6-7-8-6/a3-b1_a4-i1_b2-c1_b3-d1_b4-f1_d3-e1_f4-g1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Glcp]{[(3+1)][a-L-Fucp]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-Rhap]{[(3+1)][a-D-Manp]{}}[(4+1)][b-D-Xylp]{[(4+1)][b-L-Rhap]{[(2+1)][a-L-Rhap2Me3Me]{}}}}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[alpha-D-galactopyranose-(1-2)][beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[alpha-D-galactopyranose-(1-2)][beta-D-xylopyranose-(1-4)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 1060.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DRhapa1-3[DGalpa1-2][DXylpb1-4]LFucpa1-3[DXylpb1-4]DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,7,6/[a2122h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5][a1122m-1a_1-5][a1122h-1a_1-5][a212h-1b_1-5]/1-2-3-4-5-6-6/a3-b1_a4-g1_b2-c1_b3-d1_b4-f1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Glcp]{[(3+1)][a-L-Fucp]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-Rhap]{[(3+1)][a-D-Manp]{}}[(4+1)][b-D-Xylp]{}}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Glcp]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 335 molecules

#5: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Hg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.5-4.0 M sodium formate, 50 mM Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.0069 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2001
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0069 Å / Relative weight: 1
ReflectionResolution: 2.54→84.42 Å / Num. obs: 38400 / % possible obs: 99.4 % / Redundancy: 33 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.54→2.64 Å / Rmerge(I) obs: 0.33

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Processing

SoftwareName: PHENIX / Version: (1.12_2829: ???) / Classification: refinement
RefinementResolution: 2.537→43.305 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2805 3.93 %RANDOM
Rwork0.1788 ---
obs0.1806 38392 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.537→43.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 582 331 7633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037509
X-RAY DIFFRACTIONf_angle_d0.92510333
X-RAY DIFFRACTIONf_dihedral_angle_d11.1264386
X-RAY DIFFRACTIONf_chiral_restr0.541279
X-RAY DIFFRACTIONf_plane_restr0.0031229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5374-2.58120.3475980.23593333X-RAY DIFFRACTION95
2.5812-2.62810.31141260.24243392X-RAY DIFFRACTION97
2.6281-2.67870.28341160.23913404X-RAY DIFFRACTION98
2.6787-2.73330.31811300.22693434X-RAY DIFFRACTION99
2.7333-2.79280.21391590.21853414X-RAY DIFFRACTION99
2.7928-2.85770.26161260.2133441X-RAY DIFFRACTION99
2.8577-2.92920.24861500.22043440X-RAY DIFFRACTION100
2.9292-3.00830.28531500.22723419X-RAY DIFFRACTION100
3.0083-3.09680.22891430.22283435X-RAY DIFFRACTION100
3.0968-3.19680.24271640.19573418X-RAY DIFFRACTION100
3.1968-3.3110.23881410.18783456X-RAY DIFFRACTION100
3.311-3.44350.23791330.17733467X-RAY DIFFRACTION100
3.4435-3.60010.22241610.1683406X-RAY DIFFRACTION100
3.6001-3.78990.22791390.15943475X-RAY DIFFRACTION100
3.7899-4.02710.21641440.15253427X-RAY DIFFRACTION100
4.0271-4.33780.18111390.13913448X-RAY DIFFRACTION100
4.3378-4.77380.15511520.12853455X-RAY DIFFRACTION100
4.7738-5.46350.18811610.14223433X-RAY DIFFRACTION100
5.4635-6.87890.21211290.17153477X-RAY DIFFRACTION100
6.8789-43.31150.21961440.19213421X-RAY DIFFRACTION99
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)
10.83690.04-0.06150.65430.04490.55430.0101-0.1676-0.01630.2154-0.00660.00960.11940.0733-0.00020.3660.0160.00950.2658-0.00420.218239.267631.75956.6166
20.95210.26070.05191.0142-0.00920.9635-0.00950.2154-0.1458-0.07480.0164-0.05450.24160.1789-0.01280.27460.0558-0.01350.288-0.04870.181922.9938-2.08921.8633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 437)
2X-RAY DIFFRACTION2(chain 'B' and resid 13 through 437)

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