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- PDB-5lfe: Protruding domain of GII.4 human norovirus isolate 8-14 in comple... -

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Basic information

Entry
Database: PDB / ID: 5lfe
TitleProtruding domain of GII.4 human norovirus isolate 8-14 in complex with HBGA type B (triglycan)
ComponentsVP1
KeywordsVIRAL PROTEIN / Viral capsid protein / Protruding domain / Norovirus / HBGA / Histo-blood group antigen
Function / homology
Function and homology information


virion component => GO:0044423 / host cell cytoplasm / cytoplasm
Similarity search - Function
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 Hu/GII.4/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: To be published
Title: Four decades of structural evolution of GII.4 norovirus
Authors: Singh, B.K. / Hansman, G.S.
History
DepositionJul 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
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 / 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: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8833
Polymers68,3942
Non-polymers4881
Water5,999333
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-5 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 55.420, 87.100
Angle α, β, γ (deg.)90.000, 99.380, 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 / End auth comp-ID: MET / End label comp-ID: MET

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROchain AAA222 - 5301 - 309
2LYSLYSchain BBB225 - 5304 - 309

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Components

#1: Protein VP1


Mass: 34197.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M4QNL3
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG6000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.965 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.27→46.58 Å / Num. obs: 26503 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.121 / Net I/σ(I): 7.32
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.27-2.330.7041.860.798183.8
2.33-2.390.4283.020.863198.7
2.39-2.460.3613.510.878198.5
2.46-2.530.3283.880.902198.8
2.53-2.620.2784.460.93197.2
2.62-2.710.2544.760.955194.5
2.71-2.810.2015.720.962198.6
2.81-2.930.1716.530.963198.8
2.93-3.060.1387.580.977199.2
3.06-3.210.1078.80.987199.5
3.21-3.380.1119.40.983195.7
3.38-3.580.1259.130.985183.3
3.58-3.830.0812.620.988161.7
3.83-4.140.07913.010.988176.2
4.14-4.530.0613.880.996199.8
4.53-5.070.05813.520.995199.7
5.07-5.850.05812.190.996199.9
5.85-7.170.05812.020.9951100
7.17-10.140.04814.130.9981100
10.140.03915.170.999199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.36 Å46.57 Å
Translation7.36 Å46.57 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOS

4oos


Resolution: 2.3→46.575 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.96
RfactorNum. reflection% reflection
Rfree0.2765 1269 4.98 %
Rwork0.2325 --
obs0.2347 25458 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.26 Å2 / Biso mean: 37.8752 Å2 / Biso min: 0.48 Å2
Refinement stepCycle: final / Resolution: 2.3→46.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 33 333 5131
Biso mean--35.99 28.76 -
Num. residues----615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044943
X-RAY DIFFRACTIONf_angle_d0.8816764
X-RAY DIFFRACTIONf_chiral_restr0.034741
X-RAY DIFFRACTIONf_plane_restr0.005894
X-RAY DIFFRACTIONf_dihedral_angle_d13.7291797
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3574X-RAY DIFFRACTION10.443TORSIONAL
12B3574X-RAY DIFFRACTION10.443TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.39210.34621440.28252751289598
2.3921-2.5010.31451470.25182787293499
2.501-2.63280.30531450.25252772291797
2.6328-2.79770.30431440.24272710285496
2.7977-3.01370.33161480.24212814296299
3.0137-3.31690.27841470.23052793294099
3.3169-3.79670.30041060.28512105221174
3.7967-4.78270.25791320.20372519265188
4.7827-46.58440.1731560.166429383094100
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)
1-0.15440.03660.16721.6833-0.60370.3813-0.0392-0.07940.22330.22170.06550.0631-0.2421-0.15480.03130.43180.0229-0.00730.3027-0.01080.237454.8025-20.8482116.3302
20.8255-0.06230.16310.2245-0.03682.1098-0.18790.0119-0.37480.0983-0.34790.13520.5391-0.32440.01430.2310.0137-0.04650.3245-0.0540.339547.47444.257100.4347
30.24080.28120.06530.4326-0.78222.2513-0.0165-0.12570.00240.12320.04280.116-0.2967-0.045-0.0330.40550.04380.05370.21510.00920.281249.4352-2.078102.0573
41.02720.25660.99820.7215-0.12456.0322-0.19090.074-0.34960.1938-0.12060.36470.4783-0.3576-0.04080.2830.0551-0.02210.2837-0.02690.25254.29071.1583117.0319
50.00320.011-0.00181.1123-0.8342-0.00440.0511-0.0910.050.0606-0.0490.1174-0.059-0.1068-0.01570.2878-0.02140.00940.2984-0.00430.191453.7812-20.5252122.4365
60.52780.3497-0.44420.8785-0.47091.0819-0.0017-0.5398-0.41490.2098-0.2499-0.1005-0.049-0.04470.04940.3799-0.0205-0.00650.2957-0.00240.251355.4904-34.4141127.914
70.04930.7117-0.23541.7790.35690.7974-0.0723-0.00940.0482-0.05430.1369-0.0353-0.0530.05-0.0470.28520.012600.22690.01820.243169.2385-19.925398.8458
81.0305-0.8-0.63581.66231.62592.62520.0351-0.04340.1067-0.07060.1949-0.29210.02950.0229-0.2120.3823-0.04-0.0330.27290.0090.258874.2928-1.9736113.1727
91.2893-2.2406-0.19913.84060.18113.01660.09290.03040.2869-0.2267-0.1625-0.2805-0.1303-0.38120.08490.2753-0.0011-0.06950.2861-0.01550.351976.6042.8908112.07
10-0.50370.18730.48050.16030.39830.56090.0019-0.038-0.01550.0417-0.0083-0.0834-0.07860.04910.01270.30050.00820.00110.2619-0.00160.236772.9858-12.125996.0404
110.9114-0.74230.56532.1652-0.63481.98680.0656-0.0443-0.1227-0.3192-0.11820.19880.4488-0.2602-0.05560.5824-0.0339-0.03650.2123-0.04620.43563.7712-34.443291.5944
121.6497-0.6106-0.55650.7336-0.10091.12070.0170.0365-0.2263-0.00960.0629-0.08640.1817-0.1204-0.04720.43030.0223-0.02390.2237-0.03080.269866.3321-25.947286.6064
131.4392-1.353-0.61891.9722-1.00612.9146-0.15410.3707-0.3542-0.3129-0.04530.1608-0.1932-0.0940.03760.34930.0096-0.03820.1234-0.0840.399168.5324-35.204388.1406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 285 )A222 - 285
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 303 )A286 - 303
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 380 )A304 - 380
4X-RAY DIFFRACTION4chain 'A' and (resid 381 through 398 )A381 - 398
5X-RAY DIFFRACTION5chain 'A' and (resid 399 through 513 )A399 - 513
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 530 )A514 - 530
7X-RAY DIFFRACTION7chain 'B' and (resid 225 through 285 )B225 - 285
8X-RAY DIFFRACTION8chain 'B' and (resid 286 through 352 )B286 - 352
9X-RAY DIFFRACTION9chain 'B' and (resid 353 through 380 )B353 - 380
10X-RAY DIFFRACTION10chain 'B' and (resid 381 through 464 )B381 - 464
11X-RAY DIFFRACTION11chain 'B' and (resid 465 through 484 )B465 - 484
12X-RAY DIFFRACTION12chain 'B' and (resid 485 through 513 )B485 - 513
13X-RAY DIFFRACTION13chain 'B' and (resid 514 through 530 )B514 - 530

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