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

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Basic information

Entry
Database: PDB / ID: 5tip
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
beta-D-glucopyranose / : / Major capsid protein
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKlose, T. / De Castro, C. / Speciale, I. / Molinaro, A. / Van Etten, J.L. / Rossmann, M.G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
National Science Foundation (NSF, United States)EPS-1004049 United States
Stanley Medical Research Institute11R-003 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P20-RR15635 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
SupersessionOct 18, 2017ID: 1M3Y
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
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 1.4Nov 27, 2019Group: Author supporting evidence / Data collection / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_nonpoly_scheme
Item: _chem_comp.type / _entity.src_method ..._chem_comp.type / _entity.src_method / _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_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_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_atom_id_2 / _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
C: Major capsid protein
D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,69824
Polymers192,2744
Non-polymers16,42520
Water20,8791159
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)157,25718
Polymers144,2053
Non-polymers13,05115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area34560 Å2
ΔGint-4 kcal/mol
Surface area46300 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)156,24718
Polymers144,2053
Non-polymers12,04215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area33870 Å2
ΔGint-13 kcal/mol
Surface area45420 Å2
MethodPISA
3
C: Major capsid protein
hetero molecules

C: Major capsid protein
hetero molecules

C: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,85718
Polymers144,2053
Non-polymers11,65215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area33880 Å2
ΔGint-12 kcal/mol
Surface area45060 Å2
MethodPISA
4
D: Major capsid protein
hetero molecules

D: Major capsid protein
hetero molecules

D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,73418
Polymers144,2053
Non-polymers12,52915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area34590 Å2
ΔGint-10 kcal/mol
Surface area45830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.792, 188.792, 188.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Major capsid protein / MCP / VP54


Mass: 48068.430 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: P30328

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Sugars , 6 types, 16 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.: 5
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.: 3
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
#5: Polysaccharide beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-galactopyranose-(1-2)][alpha-D- ...beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-galactopyranose-(1-2)][alpha-D-rhamnopyranose-(1-3)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 1044.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapb1-4DXylpb1-4[DGalpa1-2][DRhapa1-3]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][a212h-1b_1-5][a2211m-1b_1-5]/1-2-3-4-5-6-5/a3-b1_a4-g1_b2-c1_b3-d1_b4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Glcp]{[(3+1)][a-L-Fucp]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-Rhap]{}[(4+1)][b-D-Xylp]{[(4+1)][b-L-Rhap]{}}}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[beta-L-rhamnopyranose-(1-4)-beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)][alpha-D-galactopyranose-(1-2)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 1207.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DRhapa1-3[LRhapb1-4DXylpb1-4][DGalpa1-2]LFucpa1-3[DXylpb1-4]DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/7,8,7/[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]/1-2-3-4-5-6-7-6/a3-b1_a4-h1_b2-c1_b3-d1_b4-f1_d3-e1_f4-g1WURCSPDB2Glycan 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]{}}}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#8: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 1163 molecules

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


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1159 / 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: 57.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.4~4.0 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-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2002
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.696
11L, -K, H20.304
ReflectionResolution: 2→100 Å / Num. obs: 148902 / % possible obs: 99 % / Redundancy: 40 % / Rmerge(I) obs: 0.132
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.532 / % possible all: 98.8

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Processing

SoftwareName: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement
RefinementResolution: 2→84.43 Å / Cross valid method: THROUGHOUT / σ(F): 5.6 / Phase error: 25.34 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4236 3.04 %RANDOM
Rwork0.1761 ---
obs0.1831 139146 92.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→84.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13580 0 1049 1159 15788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415039
X-RAY DIFFRACTIONf_angle_d0.86820675
X-RAY DIFFRACTIONf_dihedral_angle_d11.825626
X-RAY DIFFRACTIONf_chiral_restr0.4842530
X-RAY DIFFRACTIONf_plane_restr0.0032480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.03450.27881890.28466340X-RAY DIFFRACTION85
2.0345-2.07140.26482010.26356505X-RAY DIFFRACTION87
2.0714-2.11120.30642070.26126457X-RAY DIFFRACTION87
2.1112-2.15420.27131860.24916648X-RAY DIFFRACTION88
2.1542-2.2010.30351790.24476516X-RAY DIFFRACTION88
2.201-2.25210.27262180.23956690X-RAY DIFFRACTION90
2.2521-2.30830.25081970.23356768X-RAY DIFFRACTION90
2.3083-2.37050.2411980.22796776X-RAY DIFFRACTION91
2.3705-2.44010.25452070.23316800X-RAY DIFFRACTION91
2.4401-2.51860.26362190.22336908X-RAY DIFFRACTION92
2.5186-2.60840.2382200.22066927X-RAY DIFFRACTION93
2.6084-2.71240.27532230.21437023X-RAY DIFFRACTION94
2.7124-2.83540.21832270.20557126X-RAY DIFFRACTION95
2.8354-2.98420.21292440.18947156X-RAY DIFFRACTION96
2.9842-3.17010.19592150.17987203X-RAY DIFFRACTION96
3.1701-3.41310.20922200.16357274X-RAY DIFFRACTION96
3.4131-3.75350.1582390.14347235X-RAY DIFFRACTION96
3.7535-4.28950.13762010.12967121X-RAY DIFFRACTION94
4.2895-5.37760.16841570.12636433X-RAY DIFFRACTION84
5.3776-17.38040.20081480.17755090X-RAY DIFFRACTION66

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