PDB-7zin: JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromo...

ID or keywords:

Entry

Database: PDB / ID: 7zin

Title

JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aliphatic linker)

Components

Major capsid protein VP1

Keywords

VIRAL PROTEIN / Complex / Sialic acid / Capsid protein

Function / homology

Function and homology information

T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function

Biological species

JC polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.648 Å

Authors

Freytag, J. / Mueller, J.C. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: Biomacromolecules / Year: 2022
Title: Synthesis of Homo- and Heteromultivalent Fucosylated and Sialylated Oligosaccharide Conjugates via Preactivated N -Methyloxyamine Precision Macromolecules and Their Binding to Polyomavirus Capsid Proteins.
Authors: Konietzny, P.B. / Freytag, J. / Feldhof, M.I. / Muller, J.C. / Ohl, D. / Stehle, T. / Hartmann, L.

History

Deposition	Apr 8, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7zin.cif.gz	322.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7zin.ent.gz		Display	PDB format
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Validation report

Summary document	7zin_validation.pdf.gz	631.3 KB	Display	wwPDB validaton report
Full document	7zin_full_validation.pdf.gz	635.8 KB	Display
Data in XML	7zin_validation.xml.gz	27.3 KB	Display
Data in CIF	7zin_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zi/7zin ftp://data.pdbj.org/pub/pdb/validation_reports/zi/7zin	HTTPS FTP

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Related structure data

Related structure data	7zilC 7zimC 7zioC 7zipC 7ziqC 3nxdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (5)

Deposited unit

AAA: Major capsid protein VP1

BBB: Major capsid protein VP1

CCC: Major capsid protein VP1

DDD: Major capsid protein VP1

EEE: Major capsid protein VP1

hetero molecules

153 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	150.132, 96.692, 128.449
Angle α, β, γ (deg.)	90.000, 110.625, 90.000
Int Tables number	5
Space group name H-M	C121

#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 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03089

#2: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-lactose

Descriptor	Type	Program
DNeup5Aca2-6DGalpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 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_b6-c2	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

#3: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-lactose

#4: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1713 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 1.648→45 Å / Num. obs: 204346 / % possible obs: 98.8 % / Redundancy: 6.85 % / CC_1/2: 0.99 / R_rim(I) all: 0.15 / Net I/σ(I): 10.69
Reflection shell	Resolution: 1.65→1.75 Å / Mean I/σ(I) obs: 1.31 / Num. unique obs: 32369 / CC_1/2: 0.59 / R_rim(I) all: 1.41

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NXD

3nxd

Resolution: 1.648→44.855 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.959 / SU B: 2.171 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1914	4087	2 %
R_work	0.1664	200255	-
all	0.167	-	-
obs	-	204342	98.836 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 17.712 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.115 Å²	-0 Å²	-0.77 Å²
2-	-	1.408 Å²	-0 Å²
3-	-	-	-0.556 Å²

Refinement step

Cycle: LAST / Resolution: 1.648→44.855 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10110	0	128	1713	11951

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	10906
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.017	9681
X-RAY DIFFRACTION	r_angle_refined_deg	1.535	1.661	14912
X-RAY DIFFRACTION	r_angle_other_deg	1.44	1.581	22569
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.276	5	1410
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.329	22.824	556
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.583	15	1723
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.137	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1453
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	12491
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2257
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1841
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	9114
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	5230
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	4710
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.209	0.2	1314
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.117	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.184	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.2	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	1.352	1.656	5478
X-RAY DIFFRACTION	r_mcbond_other	1.351	1.655	5477
X-RAY DIFFRACTION	r_mcangle_it	2.143	2.47	6904
X-RAY DIFFRACTION	r_mcangle_other	2.143	2.47	6905
X-RAY DIFFRACTION	r_scbond_it	2.048	1.899	5428
X-RAY DIFFRACTION	r_scbond_other	2.048	1.9	5429
X-RAY DIFFRACTION	r_scangle_it	3.197	2.752	7993
X-RAY DIFFRACTION	r_scangle_other	3.197	2.753	7994
X-RAY DIFFRACTION	r_lrange_it	5.666	21.696	12353
X-RAY DIFFRACTION	r_lrange_other	5.245	20.491	11806

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.648-1.691	0.405	291	0.378	14299	0.378	15219	0.617	0.62	95.867	0.375
1.691-1.737	0.303	291	0.322	14255	0.322	14816	0.734	0.73	98.1777	0.312
1.737-1.787	0.308	285	0.267	13941	0.268	14489	0.83	0.841	98.1848	0.248
1.787-1.842	0.254	275	0.235	13478	0.235	13953	0.863	0.875	98.5666	0.21
1.842-1.903	0.256	269	0.214	13169	0.215	13651	0.873	0.891	98.4397	0.187
1.903-1.969	0.233	259	0.206	12680	0.207	13127	0.908	0.918	98.5678	0.177
1.969-2.043	0.19	251	0.169	12313	0.169	12681	0.943	0.946	99.0774	0.143
2.043-2.127	0.193	242	0.166	11880	0.167	12257	0.945	0.952	98.8986	0.141
2.127-2.221	0.169	233	0.149	11382	0.149	11709	0.954	0.962	99.1972	0.126
2.221-2.329	0.194	222	0.163	10922	0.164	11234	0.941	0.954	99.1989	0.136
2.329-2.455	0.179	212	0.135	10379	0.136	10649	0.959	0.968	99.4554	0.112
2.455-2.603	0.181	201	0.133	9847	0.134	10092	0.953	0.969	99.564	0.111
2.603-2.782	0.171	190	0.134	9303	0.134	9536	0.962	0.97	99.5491	0.114
2.782-3.004	0.166	176	0.142	8642	0.142	8832	0.962	0.966	99.8415	0.124
3.004-3.289	0.175	164	0.142	7993	0.142	8167	0.966	0.972	99.8776	0.129
3.289-3.675	0.169	147	0.146	7249	0.147	7402	0.966	0.97	99.9189	0.137
3.675-4.239	0.136	131	0.122	6414	0.122	6551	0.976	0.977	99.9084	0.117
4.239-5.18	0.157	111	0.128	5422	0.129	5540	0.975	0.982	99.8736	0.128
5.18-7.278	0.182	87	0.2	4240	0.199	4330	0.966	0.967	99.9307	0.192
7.278-44.855	0.21	50	0.2	2448	0.2	2504	0.95	0.959	99.7604	0.204

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