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- PDB-7eqw: Crystal structure of capsid P domain of norovirus GI.3 DSV comple... -

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Basic information

Entry
Database: PDB / ID: 7eqw
TitleCrystal structure of capsid P domain of norovirus GI.3 DSV complexed with NA2 N-glycan
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / histo-blood group antigens / human norovirus / viral receptor
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Viral coat protein subunit / Capsid protein
Function and homology information
Biological speciesDesert Shield virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, Y.
CitationJournal: J.Virol. / Year: 2022
Title: Structural Insight into Terminal Galactose Recognition by Two Non-HBGA Binding GI.3 Noroviruses.
Authors: Wang, C. / Kang, H. / Tan, M. / Cong, J. / Su, D. / Li, X. / Chen, Y.
History
DepositionMay 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 5, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3453
Polymers70,8002
Non-polymers5451
Water8,503472
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Elution volumn at about 10ml on Superdex75
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-14 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.292, 100.808, 103.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Capsid protein


Mass: 35399.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desert Shield virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q66418
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2-3/a2-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15.5% (w/v) polyethylene glycol 3350, 0.2M Sodium tartrate dibasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 36381 / % possible obs: 99.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.052 / Rrim(I) all: 0.181 / Χ2: 1.216 / Net I/σ(I): 6.8 / Num. measured all: 379887
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.194.60.57116680.7720.2720.6380.52990.9
2.19-2.235.60.48717230.8220.2110.5340.59197.8
2.23-2.2770.46617720.8790.180.5020.66698.2
2.27-2.328.30.45118050.9130.1610.480.6599.7
2.32-2.379.30.44417970.930.150.4690.68699.5
2.37-2.4210.10.42518110.9410.1370.4470.719100
2.42-2.4810.80.40318140.9570.1260.4230.73699.9
2.48-2.55110.36517900.9590.1120.3820.837100
2.55-2.6211.20.32718180.9690.0990.3430.937100
2.62-2.7111.20.30218130.9710.0910.3161.051100
2.71-2.8111.40.27118170.9760.0810.2831.202100
2.81-2.9211.60.23118080.9830.0690.2421.432100
2.92-3.0511.70.22718540.9870.0670.2371.472100
3.05-3.2111.80.19718110.9840.0580.2051.766100
3.21-3.4111.90.17618300.9870.0520.1841.68100
3.41-3.6811.90.16618500.9850.0490.1741.625100
3.68-4.05120.15818560.9890.0470.1651.592100
4.05-4.6312.30.14518560.9890.0420.1511.46100
4.63-5.8312.40.13119010.9920.0380.1361.584100
5.83-5011.70.10419870.990.0320.1091.41799.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EQS

7eqs


Resolution: 2.15→32.64 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.093 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 1734 4.8 %RANDOM
Rwork0.1808 ---
obs0.1831 34588 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.72 Å2 / Biso mean: 33.49 Å2 / Biso min: 14.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.58 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 2.15→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 37 472 5108
Biso mean--72.79 38.9 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134775
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174178
X-RAY DIFFRACTIONr_angle_refined_deg1.31.6526527
X-RAY DIFFRACTIONr_angle_other_deg1.1671.5719760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.695597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24223.133233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49815687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9881520
X-RAY DIFFRACTIONr_chiral_restr0.0530.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02974
LS refinement shellResolution: 2.151→2.207 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 117 -
Rwork0.25 2320 -
all-2437 -
obs--90.56 %

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