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- PDB-7xca: Crystal structure of the porcine astrovirus capsid spike domain -

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Basic information

Entry
Database: PDB / ID: 7xca
TitleCrystal structure of the porcine astrovirus capsid spike domain
ComponentsCapsid protein spike domain
KeywordsVIRAL PROTEIN / porcine astrovirus / capsid / spike domain / VIRUS
Function / homologyTurkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / Capsid polyprotein VP90
Function and homology information
Biological speciesPorcine astrovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPan, L.X. / Zhang, W.C. / Yang, D.F. / Yang, L.Y. / Liu, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31860245 China
National Natural Science Foundation of China (NSFC)31960203 China
National Natural Science Foundation of China (NSFC)31760735 China
CitationJournal: To Be Published
Title: Crystal structure analysis of porcine astrovirus capsid spike and spike/neutralizing antibody complexes.
Authors: Pan, L.X. / Zhang, W.C. / Yang, D.F. / Yang, L.Y. / Liu, H.
History
DepositionMar 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Capsid protein spike domain
B: Capsid protein spike domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5694
Polymers59,5092
Non-polymers602
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-31 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.480, 105.170, 47.470
Angle α, β, γ (deg.)90.000, 111.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 24 - 232 / Label seq-ID: 24 - 232

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 24 through 232)AA
22chain 'B'BB

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Components

#1: Protein Capsid protein spike domain


Mass: 29754.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine astrovirus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: W5X1V8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.81 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 0.2M magnesium chloride, 25% PEG 3350, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→44.04 Å / Num. obs: 14608 / % possible obs: 99.57 % / Redundancy: 2 % / Biso Wilson estimate: 37.89 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.81
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 2840 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
REFMAC5.8.0267refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.04 Å / SU ML: 0.3142 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.8466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 1467 10.04 %
Rwork0.1781 13138 -
obs0.1836 14605 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 2 92 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413304
X-RAY DIFFRACTIONf_angle_d0.78224530
X-RAY DIFFRACTIONf_chiral_restr0.0497524
X-RAY DIFFRACTIONf_plane_restr0.0058576
X-RAY DIFFRACTIONf_dihedral_angle_d4.34581922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.28081410.23691290X-RAY DIFFRACTION99.86
2.59-2.690.32341490.23861301X-RAY DIFFRACTION99.38
2.69-2.820.3171460.2341330X-RAY DIFFRACTION99.8
2.82-2.960.29941470.22741310X-RAY DIFFRACTION99.39
2.96-3.150.26881460.21231290X-RAY DIFFRACTION99.31
3.15-3.390.23581500.20561331X-RAY DIFFRACTION100
3.39-3.730.20931410.16811305X-RAY DIFFRACTION99.52
3.73-4.270.22351470.15821329X-RAY DIFFRACTION100
4.27-5.380.19431490.13031310X-RAY DIFFRACTION99.39
5.38-44.040.1941510.15471342X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: -2.57711936111 Å / Origin y: 12.1779677173 Å / Origin z: 21.774985856 Å
111213212223313233
T0.227949280612 Å20.00249168382033 Å2-0.0180181744816 Å2-0.273896682518 Å20.0771477353481 Å2--0.20310667706 Å2
L1.28439156719 °2-0.394308073512 °2-0.463675030287 °2-3.65006845919 °20.983384923309 °2--0.960507038642 °2
S-0.11480959608 Å °-0.0901044916722 Å °0.0462233251295 Å °0.0732905261234 Å °0.237528121625 Å °-0.0792810181423 Å °0.0192486899177 Å °0.0630093047008 Å °-0.101710920738 Å °
Refinement TLS groupSelection details: all

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