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- PDB-6y63: Structure of Sheep Polyomavirus VP1 in complex with 3'-Sialyllact... -

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Basic information

Entry
Database: PDB / ID: 6y63
TitleStructure of Sheep Polyomavirus VP1 in complex with 3'-Sialyllactosamine
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Polyomavirus
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Capsid protein VP1
Similarity search - Component
Biological speciesSheep polyomavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsStroh, L.J. / Rustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Mbio / Year: 2020
Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.
Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, T.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_conn_type
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.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,03649
Polymers324,66510
Non-polymers5,37139
Water41,5792308
1
AAA: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,88823
Polymers162,3335
Non-polymers2,55518
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29480 Å2
ΔGint-333 kcal/mol
Surface area42270 Å2
MethodPISA
2
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,14926
Polymers162,3335
Non-polymers2,81621
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30320 Å2
ΔGint-366 kcal/mol
Surface area42360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.286, 79.930, 145.884
Angle α, β, γ (deg.)90.000, 116.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 10 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJ

#1: Protein
Capsid protein VP1


Mass: 32466.500 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sheep polyomavirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3ZCF3

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Sugars , 2 types, 6 molecules

#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 2341 molecules

#3: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2308 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: KSCN, PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.651→48.81 Å / Num. obs: 322288 / % possible obs: 99.82 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rrim(I) all: 0.1012 / Net I/σ(I): 13.87
Reflection shellResolution: 1.651→1.71 Å / Mean I/σ(I) obs: 1.22 / Num. unique obs: 31681 / CC1/2: 0.471 / Rrim(I) all: 1.547

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg


Resolution: 1.651→48.807 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.469 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1999 7413 2.3 %
Rwork0.1689 --
all0.17 --
obs-322280 99.827 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.433 Å20 Å2-0.827 Å2
2--0.814 Å20 Å2
3---0.288 Å2
Refinement stepCycle: LAST / Resolution: 1.651→48.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19601 0 357 2308 22266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01320572
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718316
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.67128027
X-RAY DIFFRACTIONr_angle_other_deg1.3311.57842497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37552560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48222.4351039
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.774153082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.25315114
X-RAY DIFFRACTIONr_chiral_restr0.0690.22702
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024431
X-RAY DIFFRACTIONr_nbd_refined0.190.23564
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.217822
X-RAY DIFFRACTIONr_nbtor_refined0.1670.29901
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.29136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21860
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.227
X-RAY DIFFRACTIONr_nbd_other0.2170.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.252
X-RAY DIFFRACTIONr_mcbond_it1.4192.16310198
X-RAY DIFFRACTIONr_mcbond_other1.4182.16310197
X-RAY DIFFRACTIONr_mcangle_it2.1353.23412739
X-RAY DIFFRACTIONr_mcangle_other2.1353.23512740
X-RAY DIFFRACTIONr_scbond_it1.8822.3810374
X-RAY DIFFRACTIONr_scbond_other1.8812.3810375
X-RAY DIFFRACTIONr_scangle_it2.9183.515277
X-RAY DIFFRACTIONr_scangle_other2.9183.515278
X-RAY DIFFRACTIONr_lrange_it4.7426.48122807
X-RAY DIFFRACTIONr_lrange_other4.5225.89422240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.651-1.6930.3245370.319227900.319237680.6220.6298.14460.309
1.693-1.740.3025310.289225910.289231240.750.76899.99130.272
1.74-1.790.2785180.259219960.259225220.830.83899.96450.234
1.79-1.8450.255040.237213880.238218950.8720.86699.98630.209
1.845-1.9060.2414880.215207510.216212400.8910.999.99530.186
1.906-1.9720.2184720.202200210.202205000.9170.91899.96590.173
1.972-2.0470.1994560.185193700.185198280.9360.93899.98990.158
2.047-2.130.1994380.177186420.178190840.9360.94499.9790.152
2.13-2.2250.2164210.174178810.175183050.9350.94499.98360.148
2.225-2.3330.2134030.162171150.163175220.9380.95199.97720.137
2.333-2.4590.2063840.157162810.158166710.9460.95699.9640.133
2.459-2.6080.2093620.158154040.159157730.9410.95699.95560.135
2.608-2.7870.1763410.15144890.151148350.9580.96499.96630.13
2.787-3.010.1923180.151135140.152138350.9490.96399.97830.134
3.01-3.2960.1872930.156124300.157127280.9560.96299.96070.145
3.296-3.6830.1732660.151113060.152115790.9630.96699.93950.147
3.683-4.2480.1692350.13299860.133102380.9670.97599.8340.134
4.248-5.1930.1432000.12184690.12286770.980.98299.90780.127
5.193-7.3030.1991560.16166510.16268080.9640.9799.98530.165
7.303-48.8070.234900.19237920.19338890.9340.95199.820.208

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