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- PDB-4z4y: Crystal structure of GII.10 P domain in complex with 7.5mM B anti... -

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Basic information

Entry
Database: PDB / ID: 4z4y
TitleCrystal structure of GII.10 P domain in complex with 7.5mM B antigen (trisaccharide)
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / HBGA / norovirus / protruding domain
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus GII.10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsLeuthold, M.M. / Koromyslova, A.D. / Hansman, G.S.
CitationJournal: Virology / Year: 2015
Title: The sweet quartet: Binding of fucose to the norovirus capsid.
Authors: Koromyslova, A.D. / Leuthold, M.M. / Bowler, M.W. / Hansman, G.S.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
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 / diffrn_radiation_wavelength / 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 / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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
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: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,06012
Polymers69,0132
Non-polymers1,04710
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint26 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.123, 78.671, 69.775
Angle α, β, γ (deg.)90.000, 100.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 224 - 538 / Label seq-ID: 1 - 315

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Capsid protein / Capsid


Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: Protruding domain, UNP residues 224-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.10 / Plasmid: pMBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F4T5
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1a_1-5][a1221m-1a_1-5]/1-2-1/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium nitrate, bis-tris propane, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.984463 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984463 Å / Relative weight: 1
ReflectionResolution: 1.797→43.2 Å / Num. obs: 63976 / % possible obs: 99.08 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.04777 / Net I/σ(I): 18
Reflection shellResolution: 1.797→1.861 Å / Redundancy: 3.1 % / Mean I/σ(I) all: 6.12 / Mean I/σ(I) obs: 6.12 / Rejects: 0 / % possible all: 95.54

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU

3onu


Resolution: 1.797→43.2 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1834 3199 5 %
Rwork0.1455 60771 -
obs0.1474 63970 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.93 Å2 / Biso mean: 19.3708 Å2 / Biso min: 4.9 Å2
Refinement stepCycle: final / Resolution: 1.797→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 69 579 5414
Biso mean--21.83 27.64 -
Num. residues----622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015014
X-RAY DIFFRACTIONf_angle_d1.2436865
X-RAY DIFFRACTIONf_chiral_restr0.062775
X-RAY DIFFRACTIONf_plane_restr0.007903
X-RAY DIFFRACTIONf_dihedral_angle_d11.641786
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2782X-RAY DIFFRACTION6.047TORSIONAL
12B2782X-RAY DIFFRACTION6.047TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7968-1.82360.20581250.17392385251090
1.8236-1.85210.23151400.159926552795100
1.8521-1.88250.19181410.156126772818100
1.8825-1.9150.18991380.150126262764100
1.915-1.94980.19251390.1526392778100
1.9498-1.98730.16961390.146826472786100
1.9873-2.02790.18181410.142226612802100
2.0279-2.0720.19181380.14626382776100
2.072-2.12020.18371400.142226482788100
2.1202-2.17320.20751390.14532653279299
2.1732-2.23190.19881390.151426322771100
2.2319-2.29760.17911380.14712623276199
2.2976-2.37180.19031390.14452639277899
2.3718-2.45650.18671390.14952648278799
2.4565-2.55490.18841400.14626582798100
2.5549-2.67110.18151400.155626612801100
2.6711-2.81190.21761410.156326752816100
2.8119-2.98810.19121400.15126562796100
2.9881-3.21870.16681400.152226542794100
3.2187-3.54250.18941400.145526722812100
3.5425-4.05470.14341410.1372670281199
4.0547-5.10730.14551400.1192655279598
5.1073-43.21790.21911420.14722699284198
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)
10.7924-0.1870.00861.00120.30861.9144-0.02240.05660.0776-0.0363-0.0099-0.0025-0.16730.03760.01560.087-0.0154-0.00820.07310.01130.08349.17019.850411.177
20.86510.027-0.05381.0176-0.31071.274-0.03680.00390.08370.03750.05620.0615-0.1891-0.0997-0.00060.07950.01250.00150.06380.00210.08181.61399.868416.9655
32.02990.5256-0.18440.8854-0.04531.9893-0.10520.2901-0.1558-0.25910.0926-0.11240.08790.27670.01120.1701-0.01220.02980.1777-0.01260.102415.7663-2.0692-5.5927
41.72340.4570.17751.148-0.15730.92990.0881-0.0275-0.18580.0627-0.0257-0.06770.12250.0386-0.02680.0959-0.0014-0.01520.06370.01150.099417.4131-8.320623.1412
51.5138-0.31990.37220.8498-0.26720.89820.0313-0.1491-0.260.05940.03480.08470.1207-0.0822-0.04250.1051-0.0179-0.00390.08110.03830.12347.9237-11.433429.0178
61.8924-0.0403-0.31780.86580.26541.2590.08310.0742-0.0146-0.02020.0173-0.2895-0.07380.2387-0.06660.0891-0.01-0.0050.1231-0.00870.158833.75511.026123.4754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 327 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 328 through 455 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 456 through 538 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 224 through 318 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 319 through 426 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 427 through 538 )B0

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