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- PDB-1sid: MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE -

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Basic information

Entry
Database: PDB / ID: 1sid
TitleMURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE
ComponentsPOLYOMAVIRUS COAT PROTEIN VP1
KeywordsVIRUS / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMouse polyomavirus
MethodX-RAY DIFFRACTION / Resolution: 3.65 Å
AuthorsStehle, T. / Harrison, S.C.
Citation
Journal: Structure / Year: 1996
Title: Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments.
Authors: Stehle, T. / Harrison, S.C.
#1: Journal: To be Published
Title: The Structure of Simian Virus 40 Refined at 3.1 Angstroms Resolution
Authors: Stehle, T. / Gamblin, S.J. / Yan, Y. / Harrison, S.C.
#2: Journal: To be Published
Title: Structure Determination of Simian Virus 40 and Murine Polyomavirus by a Combination of 5-Fold and 30-Fold Electron Density Averaging
Authors: Yan, Y. / Stehle, T. / Liddington, R.C. / Zhao, H.C. / Harrison, S.C.
#3: Journal: Nature / Year: 1994
Title: Structure of Murine Polyomavirus Complexed with an Oligosaccharide Receptor Fragment
Authors: Stehle, T. / Yan, Y. / Benjamin, T.L. / Harrison, S.C.
History
DepositionDec 12, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _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_atom_id / _struct_conn.ptnr1_label_comp_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYOMAVIRUS COAT PROTEIN VP1
B: POLYOMAVIRUS COAT PROTEIN VP1
C: POLYOMAVIRUS COAT PROTEIN VP1
D: POLYOMAVIRUS COAT PROTEIN VP1
E: POLYOMAVIRUS COAT PROTEIN VP1
F: POLYOMAVIRUS COAT PROTEIN VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,23212
Polymers254,4316
Non-polymers3,8016
Water00
1
A: POLYOMAVIRUS COAT PROTEIN VP1
B: POLYOMAVIRUS COAT PROTEIN VP1
C: POLYOMAVIRUS COAT PROTEIN VP1
D: POLYOMAVIRUS COAT PROTEIN VP1
E: POLYOMAVIRUS COAT PROTEIN VP1
F: POLYOMAVIRUS COAT PROTEIN VP1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)15,493,918720
Polymers15,265,839360
Non-polymers228,079360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: POLYOMAVIRUS COAT PROTEIN VP1
B: POLYOMAVIRUS COAT PROTEIN VP1
C: POLYOMAVIRUS COAT PROTEIN VP1
D: POLYOMAVIRUS COAT PROTEIN VP1
E: POLYOMAVIRUS COAT PROTEIN VP1
F: POLYOMAVIRUS COAT PROTEIN VP1
hetero molecules
x 5


  • icosahedral pentamer
  • 1.29 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,291,16060
Polymers1,272,15330
Non-polymers19,00730
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: POLYOMAVIRUS COAT PROTEIN VP1
B: POLYOMAVIRUS COAT PROTEIN VP1
C: POLYOMAVIRUS COAT PROTEIN VP1
D: POLYOMAVIRUS COAT PROTEIN VP1
E: POLYOMAVIRUS COAT PROTEIN VP1
F: POLYOMAVIRUS COAT PROTEIN VP1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.55 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,549,39272
Polymers1,526,58436
Non-polymers22,80836
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: POLYOMAVIRUS COAT PROTEIN VP1
B: POLYOMAVIRUS COAT PROTEIN VP1
C: POLYOMAVIRUS COAT PROTEIN VP1
D: POLYOMAVIRUS COAT PROTEIN VP1
E: POLYOMAVIRUS COAT PROTEIN VP1
F: POLYOMAVIRUS COAT PROTEIN VP1
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 1.29 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,291,16060
Polymers1,272,15330
Non-polymers19,00730
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)570.000, 570.000, 570.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
DetailsSPACE GROUP I23, A=570 ANG. THERE ARE TWO VIRIONS PER UNIT CELL AND 30 VP1 MONOMERS IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. IN THIS STRUCTURE THERE ARE INVADING ARMS OF SYMMETRY-RELATED NEIGHBORING MONOMERS THAT INVADE THE REFERENCE PENTAMER. IN REFINEMENT, THE AUTHORS USED RESIDUES 337 TO THE C-TERMINUS FROM THE SYMMETRY-RELATED MONOMERS. IN THIS ENTRY, RESIDUES 337 TO THE C-TERMINUS ARE PRESENTED AS THE ACTUAL ARM OF THE MONOMER (THAT INVADES ANOTHER PENTAMER). BECAUSE THE REFINEMENT DID NOT USE A BOND BETWEEN RESIDUES 336 AND 337 (BECAUSE THEY BELONGED TO DIFFERENT CHAINS), THE GEOMETRY OF THAT BOND IS NOT ACCURATE. A STRICT PENTAMER SURROUNDED BY FIVE LOCAL PENTAMERS CONSTITUTES THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. APPLICATION OF THE FIRST FIVE MATRICES TO THE COORDINATE SET GENERATES THAT CRYSTALLOGRAPHIC ASYMMETRIC UNIT.

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Components

#1: Protein
POLYOMAVIRUS COAT PROTEIN VP1


Mass: 42405.109 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Mouse polyomavirus (strain p16 small-plaque)
Genus: Polyomavirus / Species: Murine polyomavirus / Strain: SMALL-PLAQUE P16 / References: UniProt: P49302
#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-8 mg/mlvirus1drop
210 mMHEPES1drop
30.25-0.3 Msodium sulfate1drop
42.5-5 %(v/v)glycerol1drop
50.55-0.6 Msodium sulfate1reservoir
610 mMHEPES1reservoir
75-10 %glycerol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.65→12 Å / Num. obs: 242373 / % possible obs: 73 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.65→12 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 --
Rwork0.236 --
obs0.236 242373 73 %
Refinement stepCycle: LAST / Resolution: 3.65→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16745 0 258 0 17003

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