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- PDB-4x14: JC Mad-1 polyomavirus VP1 in complex with GM1 oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 4x14
TitleJC Mad-1 polyomavirus VP1 in complex with GM1 oligosaccharide
ComponentsMajor capsid protein VP1
KeywordsVIRAL PROTEIN / beta-sandwich / jelly-roll / viral major capsid protein / glycan
Function / homology
Function and homology information


T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / 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
: / Major capsid protein VP1
Similarity search - Component
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStroh, L.J. / Stehle, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: J.Virol. / Year: 2015
Title: The Greater Affinity of JC Polyomavirus Capsid for alpha 2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity.
Authors: Stroh, L.J. / Maginnis, M.S. / Blaum, B.S. / Nelson, C.D. / Neu, U. / Gee, G.V. / O'Hara, B.A. / Motamedi, N. / DiMaio, D. / Atwood, W.J. / Stehle, T.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_conn_type / 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.name / _chem_comp.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_label_asym_id / _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 / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,80133
Polymers150,3795
Non-polymers4,42128
Water12,052669
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33870 Å2
ΔGint-37 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.450, 95.590, 129.670
Angle α, β, γ (deg.)90.00, 110.17, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSAA24 - 2887 - 271
21VALVALLYSLYSBB24 - 2887 - 271
12GLUGLUVALVALAA25 - 2878 - 270
22GLUGLUVALVALCC25 - 2878 - 270
13VALVALLYSLYSAA24 - 2887 - 271
23VALVALLYSLYSDD24 - 2887 - 271
14VALVALLYSLYSAA24 - 2887 - 271
24VALVALLYSLYSEE24 - 2887 - 271
15GLUGLULYSLYSBB25 - 2888 - 271
25GLUGLULYSLYSCC25 - 2888 - 271
16VALVALLYSLYSBB24 - 2887 - 271
26VALVALLYSLYSDD24 - 2887 - 271
17VALVALLYSLYSBB24 - 2887 - 271
27VALVALLYSLYSEE24 - 2887 - 271
18GLUGLUVALVALCC25 - 2878 - 270
28GLUGLUVALVALDD25 - 2878 - 270
19GLUGLULYSLYSCC25 - 2888 - 271
29GLUGLULYSLYSEE25 - 2888 - 271
110VALVALLYSLYSDD24 - 2887 - 271
210VALVALLYSLYSEE24 - 2887 - 271

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Major capsid protein VP1 / / Major structural protein VP1


Mass: 30075.861 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03089

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Sugars , 2 types, 3 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-1/a3-b2_a4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 694 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 75740 / % possible obs: 98.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 31 Å2 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 2 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXG

3nxg


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.564 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21119 3803 5 %RANDOM
Rwork0.18672 ---
obs0.18797 71937 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0.31 Å2
2--0.31 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9948 0 288 669 10905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910459
X-RAY DIFFRACTIONr_bond_other_d0.0040.029695
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9814212
X-RAY DIFFRACTIONr_angle_other_deg1.068322331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51751282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99224.22455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.085151639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1831559
X-RAY DIFFRACTIONr_chiral_restr0.0760.21637
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111673
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022350
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5481.2765140
X-RAY DIFFRACTIONr_mcbond_other0.5481.2765139
X-RAY DIFFRACTIONr_mcangle_it0.9511.916409
X-RAY DIFFRACTIONr_mcangle_other0.9511.916410
X-RAY DIFFRACTIONr_scbond_it0.8191.4995319
X-RAY DIFFRACTIONr_scbond_other0.8191.4995319
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3612.1897801
X-RAY DIFFRACTIONr_long_range_B_refined4.61111.23211528
X-RAY DIFFRACTIONr_long_range_B_other4.61111.23111528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A137080.06
12B137080.06
21A136400.06
22C136400.06
31A135320.08
32D135320.08
41A138050.05
42E138050.05
51B135610.06
52C135610.06
61B137120.06
62D137120.06
71B137360.06
72E137360.06
81C136410.07
82D136410.07
91C137420.05
92E137420.05
101D136580.08
102E136580.08
LS refinement shellResolution: 2.301→2.36 Å
Num. reflection% reflection
Rfree245 -
Rwork4852 -
obs-90.9 %
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)
11.4447-0.26091.44710.4468-0.15263.2784-0.09960.24830.0880.04930.034-0.1454-0.22070.27110.06550.1366-0.0328-0.02320.31510.07750.083460.222511.727218.6119
20.6387-0.37490.26970.82810.0730.8942-0.0390.19030.0525-0.0019-0.0205-0.0656-0.02570.16170.05950.0638-0.0456-0.01090.26820.05130.017458.02576.534619.6447
32.26970.48652.45940.45050.35214.1173-0.181-0.17070.26130.09990.0022-0.024-0.3837-0.120.17880.22550.0529-0.07380.1959-0.00250.121534.45929.68935.4242
41.0449-0.01270.10820.315-0.27571.5045-0.0785-0.00370.12220.0389-0.0228-0.0385-0.20220.04540.10140.12610.0068-0.0570.1550.04830.058639.137424.95228.7163
57.0715.12725.11054.23695.514510.11390.0947-0.3463-0.0050.1681-0.19310.00710.2897-0.18440.09840.24920.0791-0.06520.2432-0.01590.154622.2585.489764.0765
60.5779-0.06790.3241.1128-0.21350.7452-0.0395-0.0250.07270.05870.00740.019-0.0969-0.15260.03210.03360.0302-0.02450.24390.00110.033816.55759.983538.7473
70.1852-0.180.68082.97213.667911.5868-0.0247-0.0633-0.08070.07840.1374-0.03980.16640.3886-0.11280.168-0.0174-0.0040.24250.05290.152135.8749-25.031256.6568
81.0198-0.29410.06830.41570.01911.01560.0276-0.0475-0.0474-0.02610.02810.08570.1359-0.1277-0.05570.06-0.0361-0.04030.1865-0.0070.045722.7568-17.495435.4444
91.7703-0.26113.32280.6021-1.65769.23860.06990.197-0.05040.0402-0.0241-0.08230.19150.5502-0.04590.13690.09150.00580.2033-0.05430.106860.8758-19.572229.4255
100.92550.24760.36570.6231-0.09711.24730.06450.0761-0.0416-0.0404-0.04150.05010.15280.084-0.02310.06630.0398-0.0150.1915-0.03440.012647.8746-19.459423.5181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 68
2X-RAY DIFFRACTION2A69 - 288
3X-RAY DIFFRACTION3B24 - 62
4X-RAY DIFFRACTION4B63 - 288
5X-RAY DIFFRACTION5C25 - 42
6X-RAY DIFFRACTION6C43 - 288
7X-RAY DIFFRACTION7D24 - 42
8X-RAY DIFFRACTION8D43 - 288
9X-RAY DIFFRACTION9E24 - 54
10X-RAY DIFFRACTION10E55 - 288

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