PDB-6y66: Structure of Goose Hemorrhagic Polyomavirus VP1 in complex with 2...

ID or keywords:

Entry

Database: PDB / ID: 6y66

Title

Structure of Goose Hemorrhagic Polyomavirus VP1 in complex with 2-O-Methyl-5-N-acetyl-alpha-D-neuraminic acid

Components

Capsid protein VP1

Keywords

VIRAL PROTEIN / Major Capsid Protein / Polyomavirus

Function / homology

Function and homology information

T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function

Biological species

Goose hemorrhagic polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Stroh, L.J. / Rustmeier, N.H. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: 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

Deposition	Feb 26, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Aug 12, 2020	Group: 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 1.3	Jan 24, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6y66.cif.gz	585.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6y66_validation.pdf.gz	3.7 MB	Display	wwPDB validaton report
Full document	6y66_full_validation.pdf.gz	3.7 MB	Display
Data in XML	6y66_validation.xml.gz	120.7 KB	Display
Data in CIF	6y66_validation.cif.gz	173.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y6/6y66 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/6y66	HTTPS FTP

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Related structure data

Related structure data	6y5xC 6y5yC 6y5zC 6y60C 6y61C 6y63C 6y64C 6y65C 6y67C 6y6aC 6y9iC 4fmgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6y65-1 6y65-2 4por-1 4pot-2 4pos-1 4mbx-2 3bwq-d 4mby-2 4por-2 4poq-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#76 - Apr 2006 Hemagglutinin similarity (1) #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) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#76 - Apr 2006
Hemagglutinin
similarity (1)
#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)
#134 - Feb 2011
Integrin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (1)

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

317 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Capsid protein VP1

BBB: Capsid protein VP1

CCC: Capsid protein VP1

DDD: Capsid protein VP1

EEE: Capsid protein VP1

hetero molecules

defined by author&software
Evidence: gel filtration
159 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

FFF: Capsid protein VP1

GGG: Capsid protein VP1

HHH: Capsid protein VP1

III: Capsid protein VP1

JJJ: Capsid protein VP1

hetero molecules

defined by author&software
158 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.460, 90.540, 101.220
Angle α, β, γ (deg.)	94.232, 98.090, 107.867
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein

Capsid protein VP1

Mass: 31161.332 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Goose hemorrhagic polyomavirus / Gene: VP1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80FI3

#2: Sugar

ChemComp-MNA / 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID

Type: D-saccharide / Mass: 323.296 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₂H₂₁NO₉ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-IMD / IMIDAZOLE

Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₅N₂

#4: Chemical

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

Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 2665 / 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: 2.41 Å³/Da / Density % sol: 48.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Na formate, ammonium acetate, Na citrate tribasic, Na oxamate, Na K tartrate, MES, imidazole, PEG 8000, ethylene glycol

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 30, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.95→49.58 Å / Num. obs: 206886 / % possible obs: 97.71 % / Redundancy: 3.6 % / B_iso Wilson estimate: 18.43 Å² / CC_1/2: 0.993 / R_rim(I) all: 0.1468 / Net I/σ(I): 9.38
Reflection shell	Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 2.02 / Num. unique obs: 20425 / CC_1/2: 0.701 / R_rim(I) all: 0.7611

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg

Resolution: 1.95→49.577 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.942 / SU B: 3.429 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2008	2069	1 %
R_work	0.1652	-	-
all	0.166	-	-
obs	-	206888	97.724 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 17.311 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.879 Å²	-0.053 Å²	-1.35 Å²
2-	-	0.141 Å²	-1.315 Å²
3-	-	-	-0 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→49.577 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20026	0	333	2665	23024

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	20913
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	18926
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.662	28552
X-RAY DIFFRACTION	r_angle_other_deg	1.333	1.566	44066
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.652	5	2674
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.982	22.107	949
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.479	15	3128
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.975	15	122
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	2757
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	23592
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4130
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	3418
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	17786
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	10135
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	9267
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	2027
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.155	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.276	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.308	0.2	97
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.214	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.321	1.702	10687
X-RAY DIFFRACTION	r_mcbond_other	1.32	1.702	10686
X-RAY DIFFRACTION	r_mcangle_it	2.002	2.54	13361
X-RAY DIFFRACTION	r_mcangle_other	2.002	2.54	13362
X-RAY DIFFRACTION	r_scbond_it	1.773	1.881	10226
X-RAY DIFFRACTION	r_scbond_other	1.773	1.881	10227
X-RAY DIFFRACTION	r_scangle_it	2.67	2.746	15190
X-RAY DIFFRACTION	r_scangle_other	2.67	2.746	15191
X-RAY DIFFRACTION	r_lrange_it	4.643	21.247	23026
X-RAY DIFFRACTION	r_lrange_other	4.643	21.249	23027
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.04	0.05	8083
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.044	0.05	8039
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.042	0.05	8041
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.045	0.05	8096
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.03	0.05	8107
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.048	0.05	8017
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.044	0.05	8092
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.034	0.05	8004
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.04	0.05	8014
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.042	0.05	8033
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.047	0.05	8035
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.031	0.05	8097
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.037	0.05	8098
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.042	0.05	8023
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.047	0.05	8052
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.04	0.05	7995
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.045	0.05	8002
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.046	0.05	8008
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.042	0.05	8052
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.043	0.05	8034
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.051	0.05	8080
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.043	0.05	8028
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.044	0.05	8121
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.044	0.05	8078
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.053	0.05	8052
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.042	0.05	8064
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.05	0.05	7996
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.047	0.05	8047
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.038	0.05	7991
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.044	0.05	7982
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.042	0.05	8092
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.043	0.05	8039
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.047	0.05	8078
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.049	0.05	7997
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.049	0.05	7996
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.041	0.05	8017
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.043	0.05	8073
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.031	0.05	7997
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.036	0.05	8024
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.042	0.05	8009
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.041	0.05	8052
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.041	0.05	8097
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.036	0.05	8024
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.039	0.05	8030
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.039	0.05	8038

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
1.95-2	0.31	150	0.264	14899	0.265	15621	0.816	0.826	96.3383	0.264
2-2.055	0.247	148	0.232	14661	0.232	15311	0.875	0.884	96.7213	0.232
2.055-2.115	0.244	143	0.224	14184	0.224	14791	0.896	0.899	96.863	0.224
2.115-2.18	0.246	140	0.199	13842	0.2	14398	0.895	0.921	97.1107	0.199
2.18-2.251	0.204	136	0.18	13460	0.181	13975	0.935	0.943	97.288	0.18
2.251-2.33	0.2	132	0.17	13018	0.171	13489	0.943	0.951	97.4868	0.17
2.33-2.418	0.203	127	0.164	12565	0.164	13009	0.943	0.951	97.5632	0.164
2.418-2.516	0.223	123	0.165	12172	0.166	12582	0.932	0.95	97.719	0.165
2.516-2.628	0.206	117	0.151	11619	0.152	11994	0.95	0.961	97.8489	0.151
2.628-2.755	0.195	113	0.15	11175	0.151	11526	0.95	0.957	97.9351	0.15
2.755-2.904	0.223	107	0.152	10623	0.153	10937	0.937	0.955	98.1073	0.152
2.904-3.08	0.193	102	0.153	10055	0.154	10341	0.948	0.956	98.2207	0.153
3.08-3.291	0.19	95	0.145	9455	0.145	9694	0.954	0.967	98.5145	0.145
3.291-3.554	0.203	89	0.16	8817	0.161	9042	0.955	0.965	98.4959	0.16
3.554-3.891	0.168	83	0.153	8175	0.153	8362	0.966	0.969	98.7563	0.153
3.891-4.347	0.149	74	0.126	7364	0.126	7523	0.972	0.977	98.8701	0.126
4.347-5.013	0.141	66	0.123	6530	0.123	6665	0.982	0.983	98.9647	0.123
5.013-6.124	0.199	56	0.165	5474	0.166	5606	0.97	0.974	98.6443	0.165
6.124-8.595	0.214	43	0.173	4302	0.173	4366	0.967	0.968	99.519	0.173
8.595-49.577	0.197	25	0.186	2429	0.186	2463	0.966	0.962	99.6346	0.186

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